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Altoukhi SM, Zamkah MM, Alharbi RA, Alghamdi SK, Aldawsari LS, Tarabulsi M, Rizk H, Sandokji Y. Understanding the effects of COVID-19 on patients with diabetic nephropathy: a systematic review. Ann Med Surg (Lond) 2024; 86:3478-3486. [PMID: 38846830 PMCID: PMC11152851 DOI: 10.1097/ms9.0000000000002053] [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: 12/27/2023] [Accepted: 03/30/2024] [Indexed: 06/09/2024] Open
Abstract
Background Diabetic nephropathy is one of the consequences of diabetes mellitus that causes a continuous decline in the eGFR. After the COVID-19 pandemic, studies have shown that patients with diabetic nephropathy who had contracted COVID-19 have higher rates of morbidity and disease progression. The aim of this study was to systematically review the literature to determine and understand the effects and complications of SARS-CoV-2 on patients with diabetic nephropathy. Materials and methods The authors' research protocol encompassed the study selection process, search strategy, inclusion/exclusion criteria, and a data extraction plan. A systematic review was conducted by a team of five reviewers, with an additional reviewer assigned to address any discrepancies. To ensure comprehensive coverage, the authors employed multiple search engines including PubMed, ResearchGate, ScienceDirect, SDL, Ovid, and Google Scholar. Results A total of 14 articles meeting the inclusion criteria revealed that COVID-19 directly affects the kidneys by utilizing ACE2 receptors for cell entry, which is significant because ACE2 receptors are widely expressed in the kidney. Conclusion COVID-19 affects kidney health, especially in individuals with diabetic nephropathy. The mechanisms include direct viral infection and immune-mediated injury. Early recognition and management are vital for improving the outcomes.
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Affiliation(s)
| | | | | | | | | | | | - Hisham Rizk
- General Surgery, Faculty of Medicine, University of Jeddah, Jeddah, Saudi Arabia
| | - Yousif Sandokji
- General Surgery, Faculty of Medicine, University of Jeddah, Jeddah, Saudi Arabia
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2
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Legouis D, Rinaldi A, Malpetti D, Arnoux G, Verissimo T, Faivre A, Mangili F, Rinaldi A, Ruinelli L, Pugin J, Moll S, Clivio L, Bolis M, de Seigneux S, Azzimonti L, Cippà PE. A transfer learning framework to elucidate the clinical relevance of altered proximal tubule cell states in kidney disease. iScience 2024; 27:109271. [PMID: 38487013 PMCID: PMC10937833 DOI: 10.1016/j.isci.2024.109271] [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: 06/16/2023] [Revised: 10/26/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024] Open
Abstract
The application of single-cell technologies in clinical nephrology remains elusive. We generated an atlas of transcriptionally defined cell types and cell states of human kidney disease by integrating single-cell signatures reported in the literature with newly generated signatures obtained from 5 patients with acute kidney injury. We used this information to develop kidney-specific cell-level information ExtractoR (K-CLIER), a transfer learning approach specifically tailored to evaluate the role of cell types/states on bulk RNAseq data. We validated the K-CLIER as a reliable computational framework to obtain a dimensionality reduction and to link clinical data with single-cell signatures. By applying K-CLIER on cohorts of patients with different kidney diseases, we identified the most relevant cell types associated with fibrosis and disease progression. This analysis highlighted the central role of altered proximal tubule cells in chronic kidney disease. Our study introduces a new strategy to exploit the power of single-cell technologies toward clinical applications.
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Affiliation(s)
- David Legouis
- Division of Intensive Care, Department of Acute Medicine, University Hospital of Geneva, 1205 Geneva, Switzerland
- Laboratory of Nephrology, Department of Medicine and Cell Physiology, University Hospital and University of Geneva, 1205 Geneva, Switzerland
| | - Anna Rinaldi
- Laboratories for Translational Research, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Division of Nephrology, Department of Medicine, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
| | - Daniele Malpetti
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), USI/SUPSI, Lugano, Switzerland
| | - Gregoire Arnoux
- Laboratory of Nephrology, Department of Medicine and Cell Physiology, University Hospital and University of Geneva, 1205 Geneva, Switzerland
| | - Thomas Verissimo
- Laboratory of Nephrology, Department of Medicine and Cell Physiology, University Hospital and University of Geneva, 1205 Geneva, Switzerland
| | - Anna Faivre
- Laboratory of Nephrology, Department of Medicine and Cell Physiology, University Hospital and University of Geneva, 1205 Geneva, Switzerland
- Division of Nephrology, Department of Medicine, University Hospital of Geneva, 1205 Geneva, Switzerland
| | - Francesca Mangili
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), USI/SUPSI, Lugano, Switzerland
| | - Andrea Rinaldi
- Institute of Oncological Research, 6500 Bellinzona, Switzerland
| | | | - Jerome Pugin
- Division of Intensive Care, Department of Acute Medicine, University Hospital of Geneva, 1205 Geneva, Switzerland
| | - Solange Moll
- Division of Pathology, Department of Diagnostic, University Hospital of Geneva, 1205 Geneva, Switzerland
| | - Luca Clivio
- Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
| | - Marco Bolis
- Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
- Laboratory of Computational Oncology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Sophie de Seigneux
- Laboratory of Nephrology, Department of Medicine and Cell Physiology, University Hospital and University of Geneva, 1205 Geneva, Switzerland
- Division of Nephrology, Department of Medicine, University Hospital of Geneva, 1205 Geneva, Switzerland
| | - Laura Azzimonti
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), USI/SUPSI, Lugano, Switzerland
| | - Pietro E. Cippà
- Laboratories for Translational Research, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Division of Nephrology, Department of Medicine, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland
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3
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Ghag R, Kaushal M, Nwanne G, Knoten A, Kiryluk K, Rosenberg A, Menez S, Bagnasco SM, Sperati CJ, Atta MG, Gaut JP, Williams JC, El-Achkar TM, Arend LJ, Parikh CR, Jain S. Single Nucleus RNA Sequencing of Remnant Kidney Biopsies and Urine Cell RNA Sequencing Reveal Cell Specific Markers of Covid-19 Acute Kidney Injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566497. [PMID: 37986991 PMCID: PMC10659401 DOI: 10.1101/2023.11.10.566497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Acute kidney injury (AKI) in COVID-19 patients is associated with high mortality and morbidity. Critically ill COVID-19 patients are at twice the risk of in-hospital mortality compared to non-COVID AKI patients. We know little about the cell-specific mechanism in the kidney that contributes to worse clinical outcomes in these patients. New generation single cell technologies have the potential to provide insights into physiological states and molecular mechanisms in COVID-AKI. One of the key limitations is that these patients are severely ill posing significant risks in procuring additional biopsy tissue. We recently generated single nucleus RNA-sequencing data using COVID-AKI patient biopsy tissue as part of the human kidney atlas. Here we describe this approach in detail and report deeper comparative analysis of snRNAseq of 4 COVID-AKI, 4 reference, and 6 non-COVID-AKI biopsies. We also generated and analyzed urine transcriptomics data to find overlapping COVID-AKI-enriched genes and their corresponding cell types in the kidney from snRNA-seq data. We identified all major and minor cell types and states by using by using less than a few cubic millimeters of leftover tissue after pathological workup in our approach. Differential expression analysis of COVID-AKI biopsies showed pathways enriched in viral response, WNT signaling, kidney development, and cytokines in several nephron epithelial cells. COVID-AKI profiles showed a much higher proportion of altered TAL cells than non-COVID AKI and the reference samples. In addition to kidney injury and fibrosis markers indicating robust remodeling we found that, 17 genes overlap between urine cell COVID-AKI transcriptome and the snRNA-seq data from COVID-AKI biopsies. A key feature was that several of the distal nephron and collecting system cell types express these markers. Some of these markers have been previously observed in COVID-19 studies suggesting a common mechanism of injury and potentially the kidney as one of the sources of soluble factors with a potential role in disease progression. Translational Statement The manuscript describes innovation, application and discovery that impact clinical care in kidney disease. First, the approach to maximize use of remnant frozen clinical biopsies to inform on clinically relevant molecular features can augment existing pathological workflow for any frozen tissue without much change in the protocol. Second, this approach is transformational in medical crises such as pandemics where mechanistic insights are needed to evaluate organ injury, targets for drug therapy and diagnostic and prognostic markers. Third, the cell type specific and soluble markers identified and validated can be used for diagnoses or prognoses in AKI due to different etiologies and in multiorgan injury.
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4
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Jain R, Mathew D. Mechanisms influencing the high prevalence of COVID-19 in diabetics: A systematic review. MEDICAL RESEARCH ARCHIVES 2023; 11:4540. [PMID: 38933091 PMCID: PMC11198970 DOI: 10.18103/mra.v11i10.4540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Diabetics have an increased risk of contracting COVID-19 infection and tend to have more severe symptoms. This systematic review explores the potential mechanisms influencing the high prevalence of COVID-19 infections in individuals with diabetes. It reviews the emerging evidence about the interactions between viral and diabetic pathways, particularly how diabetes physiology could contribute to higher viral reception, viral entry and pathogenicity, and the severity of disease symptoms. Finally, it examines the challenges we face in studying these mechanisms and offers new strategies that might assist our fight against current and future pandemics.
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Affiliation(s)
- Roshni Jain
- Cell and Molecular Biology Program, University of Nevada, Reno, NV 89557
- Department of Biology, University of Nevada, Reno, NV 89557
| | - Dennis Mathew
- Cell and Molecular Biology Program, University of Nevada, Reno, NV 89557
- Department of Biology, University of Nevada, Reno, NV 89557
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5
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Sen T, Ju W, Nair V, Ladd P, Menon R, Otto EA, Pyle L, Vigers T, Nelson RG, Arnott C, Neal B, Hansen MK, Kretzler M, Bjornstad P, Heerspink HJL. Sodium glucose co-transporter 2 inhibition increases epidermal growth factor expression and improves outcomes in patients with type 2 diabetes. Kidney Int 2023; 104:828-839. [PMID: 37543256 DOI: 10.1016/j.kint.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 06/30/2023] [Accepted: 07/21/2023] [Indexed: 08/07/2023]
Abstract
Underlying molecular mechanisms of the kidney protective effects of sodium glucose co-transporter 2 (SGLT2) inhibitors are not fully elucidated. Therefore, we studied the association between urinary epidermal growth factor (uEGF), a mitogenic factor involved in kidney repair, and kidney outcomes in patients with type 2 diabetes (T2D). The underlying molecular mechanisms of the SGLT2 inhibitor canagliflozin on EGF using single-cell RNA sequencing from kidney tissue were examined. Urinary EGF-to-creatinine ratio (uEGF/Cr) was measured in 3521 CANagliflozin cardioVascular Assessment Study (CANVAS) participants at baseline and week 52. Associations of uEGF/Cr with kidney outcome were assessed using multivariable-adjusted Cox regression models. Single-cell RNA sequencing was performed using protocol kidney biopsy tissue from ten young patients with T2D on SGLT2i, six patients with T2D on standard care only, and six healthy controls (HCs). In CANVAS, each doubling in baseline uEGF/Cr was associated with a 12% (95% confidence interval 1-22) decreased risk of kidney outcome. uEGF/Cr decreased after 52 weeks with placebo and remained stable with canagliflozin (between-group difference +7.3% (2.0-12.8). In young persons with T2D, EGF mRNA was primarily expressed in the thick ascending loop of Henle. Expression in biopsies from T2D without SGLT2i was significantly lower compared to HCs, whereas treatment with SGLT2i increased EGF levels closer to the healthy state. In young persons with T2D without SGLT2i, endothelin-1 emerged as a key regulator of the EGF co-expression network. SGLT2i treatment was associated with a shift towards normal EGF expression. Thus, decreased uEGF represents increased risk of kidney disease progression in patients with T2D. Canagliflozin increased kidney tissue expression of EGF and was associated with a downstream signaling cascade linked to tubular repair and reversal of tubular injury.
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Affiliation(s)
- Taha Sen
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Wenjun Ju
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Viji Nair
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Patricia Ladd
- Department of Radiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Rajasree Menon
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Edgar A Otto
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Laura Pyle
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA; Section of Endocrinology, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Tim Vigers
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA; Section of Endocrinology, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, USA
| | - Clare Arnott
- The George Institute for Global Health, University New South Wales (UNSW), Sydney, New South Wales, Australia; Department of Cardiology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Bruce Neal
- The George Institute for Global Health, University New South Wales (UNSW), Sydney, New South Wales, Australia
| | - Michael K Hansen
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
| | - Petter Bjornstad
- Section of Endocrinology, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA; Division of Renal Diseases and Hypertension, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA.
| | - Hiddo J L Heerspink
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands; The George Institute for Global Health, University New South Wales (UNSW), Sydney, New South Wales, Australia.
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6
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Zhang X, Ahn S, Qiu P, Datta S. Identification of shared biological features in four different lung cell lines infected with SARS-CoV-2 virus through RNA-seq analysis. Front Genet 2023; 14:1235927. [PMID: 37662846 PMCID: PMC10468990 DOI: 10.3389/fgene.2023.1235927] [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: 06/06/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has resulted in millions of confirmed cases and deaths worldwide. Understanding the biological mechanisms of SARS-CoV-2 infection is crucial for the development of effective therapies. This study conducts differential expression (DE) analysis, pathway analysis, and differential network (DN) analysis on RNA-seq data of four lung cell lines, NHBE, A549, A549.ACE2, and Calu3, to identify their common and unique biological features in response to SARS-CoV-2 infection. DE analysis shows that cell line A549.ACE2 has the highest number of DE genes, while cell line NHBE has the lowest. Among the DE genes identified for the four cell lines, 12 genes are overlapped, associated with various health conditions. The most significant signaling pathways varied among the four cell lines. Only one pathway, "cytokine-cytokine receptor interaction", is found to be significant among all four cell lines and is related to inflammation and immune response. The DN analysis reveals considerable variation in the differential connectivity of the most significant pathway shared among the four lung cell lines. These findings help to elucidate the mechanisms of SARS-CoV-2 infection and potential therapeutic targets.
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Affiliation(s)
- Xiaoxi Zhang
- Department of Biostatistics, University of Florida, Gainesville, FL, United States
| | - Seungjun Ahn
- Department of Biostatistics, University of Florida, Gainesville, FL, United States
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Peihua Qiu
- Department of Biostatistics, University of Florida, Gainesville, FL, United States
| | - Somnath Datta
- Department of Biostatistics, University of Florida, Gainesville, FL, United States
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7
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Bhatraju PK, Stanaway IB, Palmer MR, Menon R, Schaub JA, Menez S, Srivastava A, Wilson FP, Kiryluk K, Palevsky PM, Naik AS, Sakr SS, Jarvik GP, Parikh CR, Ware LB, Ikizler TA, Siew ED, Chinchilli VM, Coca SG, Garg AX, Go AS, Kaufman JS, Kimmel PL, Himmelfarb J, Wurfel MM. Genome-wide Association Study for AKI. KIDNEY360 2023; 4:870-880. [PMID: 37273234 PMCID: PMC10371295 DOI: 10.34067/kid.0000000000000175] [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: 11/17/2022] [Accepted: 04/03/2023] [Indexed: 06/06/2023]
Abstract
Key Points Two genetic variants in the DISP1-TLR5 gene locus were associated with risk of AKI. DISP1 and TLR5 were differentially regulated in kidney biopsy tissue from patients with AKI compared with no AKI. Background Although common genetic risks for CKD are well established, genetic factors influencing risk for AKI in hospitalized patients are poorly understood. Methods We conducted a genome-wide association study in 1369 participants in the Assessment, Serial Evaluation, and Subsequent Sequelae of AKI Study; a multiethnic population of hospitalized participants with and without AKI matched on demographics, comorbidities, and kidney function before hospitalization. We then completed functional annotation of top-performing variants for AKI using single-cell RNA sequencing data from kidney biopsies in 12 patients with AKI and 18 healthy living donors from the Kidney Precision Medicine Project. Results No genome-wide significant associations with AKI risk were found in Assessment, Serial Evaluation, and Subsequent Sequelae of AKI (P < 5×10 −8 ). The top two variants with the strongest association with AKI mapped to the dispatched resistance-nodulation-division (RND) transporter family member 1 (DISP1) gene and toll-like receptor 5 (TLR5) gene locus, rs17538288 (odds ratio, 1.55; 95% confidence interval, 1.32 to 182; P = 9.47×10 −8 ) and rs7546189 (odds ratio, 1.53; 95% confidence interval, 1.30 to 1.81; P = 4.60×10 −7 ). In comparison with kidney tissue from healthy living donors, kidney biopsies in patients with AKI showed differential DISP1 expression in proximal tubular epithelial cells (adjusted P = 3.9× 10−2) and thick ascending limb of the loop of Henle (adjusted P = 8.7× 10−3) and differential TLR5 gene expression in thick ascending limb of the loop of Henle (adjusted P = 4.9× 10−30). Conclusions AKI is a heterogeneous clinical syndrome with various underlying risk factors, etiologies, and pathophysiology that may limit the identification of genetic variants. Although no variants reached genome-wide significance, we report two variants in the intergenic region between DISP1 and TLR5 , suggesting this region as a novel risk for AKI susceptibility.
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Affiliation(s)
- Pavan K Bhatraju
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
| | - Ian B Stanaway
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
| | - Melody R Palmer
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Rajasree Menon
- Division of Nephrology, Department of Medicine, Michigan Medicine, Ann Arbor, Michigan
| | - Jennifer A Schaub
- Division of Nephrology, Department of Medicine, Michigan Medicine, Ann Arbor, Michigan
| | - Steven Menez
- Division of Nephrology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Anand Srivastava
- Department of Medicine, Division of Nephrology and Hypertension, Northwestern University School of Medicine, Chicago, Illinois
| | - F Perry Wilson
- Program of Applied Translational Research, Yale School of Medicine, New Haven, Connecticut
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York City, New York
| | - Paul M Palevsky
- Kidney Medicine Section, VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Abhijit S Naik
- Division of Nephrology, University of Michigan, Ann Arbor, Michigan
| | - Sana S Sakr
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Chirag R Parikh
- Division of Nephrology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lorraine B Ware
- Division of Allergy, Pulmonary and Critical Care, Vanderbilt University Medical Center, Nashville, Tennessee
| | - T Alp Ikizler
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Edward D Siew
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Vernon M Chinchilli
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Steve G Coca
- Section of Nephrology, Department of Internal Medicine, Mount Sinai School of Medicine, New York, New York
| | - Amit X Garg
- Division of Nephrology, Department of Medicine, Western University, London, Ontario, Canada
| | - Alan S Go
- Division of Nephrology, Department of Medicine, University of California, San Francisco, California
- Division of Research, Kaiser Permanente Northern California, Oakland, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California
| | - James S Kaufman
- Division of Nephrology, New York University School of Medicine, New York, New York
- Division of Nephrology, VA New York Harbor Healthcare System, New York, New York
| | - Paul L Kimmel
- Division of Renal Diseases and Hypertension, Department of Medicine, George Washington University Medical Center, Washington, DC
| | - Jonathan Himmelfarb
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
| | - Mark M Wurfel
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
- Kidney Research Institute, Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
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8
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Pan J, Gao Y, Han H, Pan T, Guo J, Li S, Xu J, Li Y. Multi-omics characterization of RNA binding proteins reveals disease comorbidities and potential drugs in COVID-19. Comput Biol Med 2023; 155:106651. [PMID: 36805221 PMCID: PMC9916187 DOI: 10.1016/j.compbiomed.2023.106651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
The COVID-19 has led to a devastating global health crisis, which emphasizes the urgent need to deepen our understanding of the molecular mechanism and identifying potential antiviral drugs. Here, we comprehensively analyzed the transcriptomic and proteomic profiles of 178 COVID-19 patients, ranging from asymptomatic to critically ill. Our analyses found that the RNA binding proteins (RBPs) were likely to be perturbed in infection. Interactome analysis revealed that RBPs interact with virus proteins and the viral interacting RBPs were likely to locate in central regions of human protein-protein interaction network. Functional enrichment analysis revealed that the viral interacting RBPs were likely to be enriched in RNA transport, apoptosis and viral genome replication-related pathways. Based on network proximity analyses of 299 human complex-disease genes and COVID-19-related RBPs in the human interactome, we revealed the significant associations between complex diseases and COVID-19. Network analysis also implicated potential antiviral drugs for treatment of COVID-19. In summary, our integrative characterization of COVID-19 patients may thus help providing evidence regarding pathophysiology and potential therapeutic strategies for COVID-19.
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Affiliation(s)
- Jiwei Pan
- NHC Key Laboratory of Tropical Disease Control, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Yueying Gao
- NHC Key Laboratory of Tropical Disease Control, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Huirui Han
- NHC Key Laboratory of Tropical Disease Control, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Tao Pan
- NHC Key Laboratory of Tropical Disease Control, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Jing Guo
- NHC Key Laboratory of Tropical Disease Control, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Si Li
- NHC Key Laboratory of Tropical Disease Control, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Yongsheng Li
- NHC Key Laboratory of Tropical Disease Control, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China.
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9
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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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10
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Hadjadj S, Saulnier P, Ruan Y, Zhu X, Pekmezaris R, Marre M, Halimi JM, Wargny M, Rea R, Gourdy P, Cariou B, Myers AK, Khunti K. Associations of microvascular complications with all-cause death in patients with diabetes and COVID-19: The CORONADO, ABCD COVID-19 UK national audit and AMERICADO study groups. Diabetes Obes Metab 2023; 25:78-88. [PMID: 36053971 PMCID: PMC9538242 DOI: 10.1111/dom.14845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/04/2022] [Accepted: 08/15/2022] [Indexed: 12/14/2022]
Abstract
AIM To provide a detailled analysis of the microvascular burden in patients with diabetes hopitalized for COVD-19. MATERIALS AND METHODS We analysed data from the French CORONADO initiative and the UK Association of British Clinical Diabetologists (ABCD) COVID-19 audit, two nationwide multicentre studies, and the AMERICADO, a multicentre study conducted in New York area. We assessed the association between risk of all-cause death during hospital stay and the following microvascular complications in patients with diabetes hospitalized for COVID-19: diabetic retinopathy and/or diabetic kidney disease and/or history of diabetic foot ulcer. RESULTS Among 2951 CORONADO, 3387 ABCD COVID-19 audit and 9327 AMERICADO participants, microvascular diabetic complications status was ascertained for 1314 (44.5%), 1809 (53.4%) and 7367 (79.0%) patients, respectively: 1010, 1059 and 1800, respectively, had ≥1 severe microvascular complication(s) and 304, 750 and 5567, respectively, were free of any complications. The patients with isolated diabetic kidney disease had an increased risk of all-cause death during hospital stay: odds ratio [OR] 2.53 (95% confidence interval [CI] 1.66-3.83), OR 1.24 (95% CI 1.00-1.56) and OR 1.66 (95% CI 1.40-1.95) in the CORONADO, the ABCD COVID-19 national audit and the AMERICADO studies, respectively. After adjustment for age, sex, hypertension and cardiovascular disease (CVD), compared to those without microvascular complications, patients with microvascular complications had an increased risk of all-cause death during hospital stay in the CORONADO, the ABCD COVID-19 diabetes national audit and the AMERICADO studies: adjusted OR (adj OR) 2.57 (95% CI 1.69-3.92), adj OR 1.22 (95% CI 1.00-1.52) and adj OR 1.33 (95% CI 1.15-1.53), respectively. In meta-analysis of the three studies, compared to patients free of complications, those with microvascular complications had an unadjusted OR for all-cause death during hospital stay of 2.05 (95% CI 1.42-2.97), which decreased to 1.62 (95% CI 1.19-2.119) after adjustment for age and sex, and to 1.50 (1.12-2.02) after hypertension and CVD were further added to the model. CONCLUSION Microvascular burden is associated with an increased risk of death in patients hospitalized for COVID-19.
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Affiliation(s)
- Samy Hadjadj
- Nantes UniversitéCHU Nantes, CNRS, Inserm, l'Institut du ThoraxNantesFrance
| | - Pierre‐Jean Saulnier
- Centre d'Investigation Clinique CIC 1402Université de Poitiers, Inserm, CHU de PoitiersPoitiersFrance
| | - Yue Ruan
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUK
- Oxford NIHR Biomedical Research CentreOxfordUK
| | - Xu Zhu
- Institute of Health System ScienceFeinstein Institutes for Medical ResearchManhassetNew York
| | - Renee Pekmezaris
- Institute of Health System ScienceFeinstein Institutes for Medical ResearchManhassetNew York
| | - Michel Marre
- Clinique Ambroise Paré Neuilly‐sur‐Seine, Centre de Recherches des CordeliersUniversité Paris DiderotParisFrance
| | - Jean Michel Halimi
- CHU de Tours, Service Néphrologie, Dialyse et Transplantation, Tours, France & EA4245Tours UniversityToursFrance
| | - Matthieu Wargny
- Nantes UniversitéCHU Nantes, CNRS, Inserm, l'Institut du ThoraxNantesFrance
- Nantes Université, CHU Nantes, Pôle Hospitalo‐Universitaire 11: Santé Publique, Clinique des données, INSERMNantesFrance
| | - Rustam Rea
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUK
- Oxford NIHR Biomedical Research CentreOxfordUK
| | - Pierre Gourdy
- CHU de Toulouse & UMR1297/I2MCUniversité de ToulouseToulouseFrance
| | - Bertrand Cariou
- Nantes UniversitéCHU Nantes, CNRS, Inserm, l'Institut du ThoraxNantesFrance
| | - Alyson K. Myers
- Department of Medicine, Division of EndocrinologyNorthwell HealthManhassetNew York
| | - Kamlesh Khunti
- University Hospitals of Leicester NHS TrustDiabetes Research Centre, Leicester General HospitalLeicesterUK
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11
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Denicolò S, Nair V, Leierer J, Rudnicki M, Kretzler M, Mayer G, Ju W, Perco P. Assessment of Fibrinogen-like 2 (FGL2) in Human Chronic Kidney Disease through Transcriptomics Data Analysis. Biomolecules 2022; 13:89. [PMID: 36671474 PMCID: PMC9855364 DOI: 10.3390/biom13010089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 01/03/2023] Open
Abstract
Fibrinogen-like 2 (FGL2) was recently found to be associated with fibrosis in a mouse model of kidney damage and was proposed as a potential therapeutic target in chronic kidney disease (CKD). We assessed the association of renal FGL2 mRNA expression with the disease outcome in two independent CKD cohorts (NEPTUNE and Innsbruck CKD cohort) using Kaplan Meier survival analysis. The regulation of FGL2 in kidney biopsies of CKD patients as compared to healthy controls was further assessed in 13 human CKD transcriptomics datasets. The FGL2 protein expression in human renal tissue sections was determined via immunohistochemistry. The regulators of FGL2 mRNA expression in renal tissue were identified in the co-expression and upstream regulator analysis of FGL2-positive renal cells via the use of single-cell RNA sequencing data from the kidney precision medicine project (KPMP). Higher renal FGL2 mRNA expression was positively associated with kidney fibrosis and negatively associated with eGFR. Renal FGL2 mRNA expression was upregulated in CKD as compared with healthy controls and associated with CKD progression in the Innsbruck CKD cohort (p-value = 0.0036) and NEPTUNE cohort (p-value = 0.0048). The highest abundance of FGL2 protein in renal tissue was detected in the thick ascending limb of the loop of Henle and macula densa, proximal tubular cells, as well as in glomerular endothelial cells. The upstream regulator analysis identified TNF, IL1B, IFNG, NFKB1, and SP1 as factors potentially inducing FGL2-co-expressed genes, whereas factors counterbalancing FGL2-co-expressed genes included GLI1, HNF1B, or PPARGC1A. In conclusion, renal FGL2 mRNA expression is elevated in human CKD, and higher FGL2 levels are associated with fibrosis and worse outcomes.
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Affiliation(s)
- Sara Denicolò
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Viji Nair
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Johannes Leierer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Michael Rudnicki
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gert Mayer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Wenjun Ju
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paul Perco
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, 6020 Innsbruck, Austria
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12
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Liu J, Nair V, Zhao YY, Chang DY, Limonte C, Bansal N, Fermin D, Eichinger F, Tanner EC, Bellovich KA, Steigerwalt S, Bhat Z, Hawkins JJ, Subramanian L, Rosas SE, Sedor JR, Vasquez MA, Waikar SS, Bitzer M, Pennathur S, Brosius FC, De Boer I, Chen M, Kretzler M, Ju W. Multi-Scalar Data Integration Links Glomerular Angiopoietin-Tie Signaling Pathway Activation With Progression of Diabetic Kidney Disease. Diabetes 2022; 71:2664-2676. [PMID: 36331122 PMCID: PMC9750948 DOI: 10.2337/db22-0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/17/2022] [Indexed: 11/06/2022]
Abstract
Diabetic kidney disease (DKD) is the leading cause of end-stage kidney disease (ESKD). Prognostic biomarkers reflective of underlying molecular mechanisms are critically needed for effective management of DKD. A three-marker panel was derived from a proteomics analysis of plasma samples by an unbiased machine learning approach from participants (N = 58) in the Clinical Phenotyping and Resource Biobank study. In combination with standard clinical parameters, this panel improved prediction of the composite outcome of ESKD or a 40% decline in glomerular filtration rate. The panel was validated in an independent group (N = 68), who also had kidney transcriptomic profiles. One marker, plasma angiopoietin 2 (ANGPT2), was significantly associated with outcomes in cohorts from the Cardiovascular Health Study (N = 3,183) and the Chinese Cohort Study of Chronic Kidney Disease (N = 210). Glomerular transcriptional angiopoietin/Tie (ANG-TIE) pathway scores, derived from the expression of 154 ANG-TIE signaling mediators, correlated positively with plasma ANGPT2 levels and kidney outcomes. Higher receptor expression in glomeruli and higher ANG-TIE pathway scores in endothelial cells corroborated potential functional effects in the kidney from elevated plasma ANGPT2 levels. Our work suggests that ANGPT2 is a promising prognostic endothelial biomarker with likely functional impact on glomerular pathogenesis in DKD.
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Affiliation(s)
- Jiahao Liu
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Viji Nair
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Yi-yang Zhao
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China
| | - Dong-yuan Chang
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China
| | | | - Nisha Bansal
- Division of Nephrology, University of Washington, Seattle, WA
| | - Damian Fermin
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Felix Eichinger
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Emily C. Tanner
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | | | - Susan Steigerwalt
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Zeenat Bhat
- Department of Nephrology and Hypertension, Department of Medicine, Wayne State University, Detroit, MI
| | - Jennifer J. Hawkins
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Lalita Subramanian
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Sylvia E. Rosas
- Kidney and Hypertension Unit, Joslin Diabetes Center and Harvard Medical School, Boston, MA
| | - John R. Sedor
- Department of Medicine, Cleveland Clinic, Cleveland, OH
| | - Miguel A. Vasquez
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX
| | - Sushrut S. Waikar
- Section of Nephrology, Department of Medicine, Boston University School of Medicine and Boston Medical Center, Brookline, MA
| | - Markus Bitzer
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Subramaniam Pennathur
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Frank C. Brosius
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Division of Nephrology, Department of Medicine, University of Arizona, Tucson, AZ
| | - Ian De Boer
- Division of Nephrology, University of Washington, Seattle, WA
| | - Min Chen
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Wenjun Ju
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
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13
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Stefansson VTN, Nair V, Melsom T, Looker HC, Mariani LH, Fermin D, Eichinger F, Menon R, Subramanian L, Ladd P, Harned R, Harder JL, Hodgin JB, Bjornstad P, Nelson PJ, Eriksen BO, Nelson RG, Kretzler M. Molecular programs associated with glomerular hyperfiltration in early diabetic kidney disease. Kidney Int 2022; 102:1345-1358. [PMID: 36055599 PMCID: PMC10161735 DOI: 10.1016/j.kint.2022.07.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 07/14/2022] [Accepted: 07/27/2022] [Indexed: 01/12/2023]
Abstract
Hyperfiltration is a state of high glomerular filtration rate (GFR) observed in early diabetes that damages glomeruli, resulting in an iterative process of increasing filtration load on fewer and fewer remaining functional glomeruli. To delineate underlying cellular mechanisms of damage associated with hyperfiltration, transcriptional profiles of kidney biopsies from Pima Indians with type 2 diabetes with or without early-stage diabetic kidney disease were grouped into two hyperfiltration categories based on annual iothalamate GFR measurements. Twenty-six participants with a peak GFR measurement within two years of biopsy were categorized as the hyperfiltration group, and 26 in whom biopsy preceded peak GFR by over two years were considered pre-hyperfiltration. The hyperfiltration group had higher hemoglobin A1c, higher urine albumin-to-creatinine ratio, increased glomerular basement membrane width and lower podocyte density compared to the pre-hyperfiltration group. A glomerular 1240-gene transcriptional signature identified in the hyperfiltration group was enriched for endothelial stress response signaling genes, including endothelin-1, tec-kinase and transforming growth factor-β1 pathways, with the majority of the transcripts mapped to endothelial and inflammatory cell clusters in kidney single cell transcriptional data. Thus, our analysis reveals molecular pathomechanisms associated with hyperfiltration in early diabetic kidney disease involving putative ligand-receptor pairs with downstream intracellular targets linked to cellular crosstalk between endothelial and mesangial cells.
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Affiliation(s)
- Vidar T N Stefansson
- Metabolic and Renal Research Group, UiT The Arctic University of Norway, Tromsø, Norway; Section of Nephrology, University Hospital of North Norway, Tromsø, Norway
| | - Viji Nair
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA; Medical Clinic and Policlinic IV, Nephrology Center, Department of Internal Medicine, University of Munich, Munich, Germany
| | - Toralf Melsom
- Metabolic and Renal Research Group, UiT The Arctic University of Norway, Tromsø, Norway; Section of Nephrology, University Hospital of North Norway, Tromsø, Norway
| | - Helen C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, USA
| | - Laura H Mariani
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Damian Fermin
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Felix Eichinger
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Lalita Subramanian
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Patricia Ladd
- Department of Radiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Roger Harned
- Department of Radiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jennifer L Harder
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jeffrey B Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Petter Bjornstad
- Department of Pediatrics, Section of Endocrinology, University of Colorado School of Medicine, Aurora, Colorado, USA; Department of Medicine, Division of Renal Diseases and Hypertension, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Peter J Nelson
- Medical Clinic and Policlinic IV, Nephrology Center, Department of Internal Medicine, University of Munich, Munich, Germany
| | - Bjørn O Eriksen
- Metabolic and Renal Research Group, UiT The Arctic University of Norway, Tromsø, Norway; Section of Nephrology, University Hospital of North Norway, Tromsø, Norway
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona, USA
| | - Matthias Kretzler
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
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14
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Gerges D, Hevesi Z, Schmidt SH, Kapps S, Pajenda S, Geist B, Schmidt A, Wagner L, Winnicki W. Tubular epithelial progenitors are excreted in urine during recovery from severe acute kidney injury and are able to expand and differentiate in vitro. PeerJ 2022; 10:e14110. [PMID: 36285332 PMCID: PMC9588302 DOI: 10.7717/peerj.14110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/02/2022] [Indexed: 01/21/2023] Open
Abstract
Background Acute kidney injury (AKI) is a serious condition associated with chronic kidney disease, dialysis requirement and a high risk of death. However, there are specialized repair mechanisms for the nephron, and migrated committed progenitor cells are the key players. Previous work has described a positive association between renal recovery and the excretion of tubular progenitor cells in the urine of kidney transplant recipients. The aim of this work was to describe such structures in non-transplanted AKI patients and to focus on their differentiation. Methods Morning urine was obtained from four patients with AKI stage 3 and need for RRT on a consecutive basis. Urine sediment gene expression was performed to assess which part of the tubular or glomerular segment was affected by injury, along with measurement of neprilysin. Urine output and sediment morphology were monitored, viable hyperplastic tubular epithelial clusters were isolated and characterized by antibody or cultured in vitro. These cells were monitored by phase contrast microscopy, gene, and protein expression over 9 days by qPCR and confocal immunofluorescence. Furthermore, UMOD secretion into the supernatant was quantitatively measured. Results Urinary neprilysin decreased rapidly with increasing urinary volume in ischemic, toxic, nephritic, and infection-associated AKI, whereas the decrease in sCr required at least 2 weeks. While urine output increased, dead cells were present in the sediment along with debris followed by hyperplastic agglomerates. Monitoring of urine sediment for tubular cell-specific gene transcript levels NPHS2 (podocyte), AQP1 and AQP6 (proximal tubule), and SLC12A1 (distal tubule) by qPCR revealed different components depending on the cause of AKI. Confocal immunofluorescence staining confirmed the presence of intact nephron-specific epithelial cells, some of which appeared in clusters expressing AQP1 and PAX8 and were 53% positive for the stem cell marker PROM1. Isolated tubule epithelial progenitor cells were grown in vitro, expanded, and reached confluence within 5-7 days, while the expression of AQP1 and UMOD increased, whereas PROM1 and Ki67 decreased. This was accompanied by a change in cell morphology from a disproportionately high nuclear/cytoplasmic ratio at day 2-7 with mitotic figures. In contrast, an apoptotic morphology of approximately 30% was found at day 9 with the appearance of multinucleated cells that were associable with different regions of the nephron tubule by marker proteins. At the same time, UMOD was detected in the culture supernatant. Conclusion During renal recovery, a high replicatory potential of tubular epithelial progenitor cells is found in urine. In vitro expansion and gene expression show differentiation into tubular cells with marker proteins specific for different nephron regions.
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Affiliation(s)
- Daniela Gerges
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - Zsofia Hevesi
- Center for Brain Research, Medical University Vienna, Vienna, Austria
| | - Sophie H. Schmidt
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - Sebastian Kapps
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - Sahra Pajenda
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - Barbara Geist
- Department of Biochemical Imaging and Image-guided Therapy, Division of Nuclear Medicine, Medical University Vienna, Vienna, Austria
| | - Alice Schmidt
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - Ludwig Wagner
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - Wolfgang Winnicki
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
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15
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Yang Y, Zou S, Xu G. An update on the interaction between COVID-19, vaccines, and diabetic kidney disease. Front Immunol 2022; 13:999534. [DOI: 10.3389/fimmu.2022.999534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/03/2022] [Indexed: 01/08/2023] Open
Abstract
Up to now, coronavirus disease 2019 (COVID-19) is still affecting worldwide due to its highly infectious nature anrapid spread. Diabetic kidney disease (DKD) is an independent risk factor for severe COVID-19 outcomes, and they have a certain correlation in some aspects. Particularly, the activated renin–angiotensin–aldosterone system, chronic inflammation, endothelial dysfunction, and hypercoagulation state play an important role in the underlying mechanism linking COVID-19 to DKD. The dipeptidyl peptidase-4 inhibitor is considered a potential therapy for COVID-19 and has similarly shown organ protection in DKD. In addition, neuropilin-1 as an alternative pathway for angiotensin-converting enzyme 2 also contributes to severe acute respiratory syndrome coronavirus 2 entering the host cells, and its decreased expression can affect podocyte migration and adhesion. Here, we review the pathogenesis and current evidence of the interaction of DKD and COVID-19, as well as focus on elevated blood glucose following vaccination and its possible mechanism. Grasping the pathophysiology of DKD patients with COVID-19 is of great clinical significance for the formulation of therapeutic strategies.
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16
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Bitzer M, Ju W, Subramanian L, Troost JP, Tychewicz J, Steck B, Wiggins RC, Gipson DS, Gadegbeku CA, Brosius FC, Kretzler M, Pennathur S. The Michigan O'Brien Kidney Research Center: transforming translational kidney research through systems biology. Am J Physiol Renal Physiol 2022; 323:F401-F410. [PMID: 35924446 PMCID: PMC9485002 DOI: 10.1152/ajprenal.00091.2022] [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: 04/08/2022] [Revised: 07/19/2022] [Accepted: 07/28/2022] [Indexed: 11/22/2022] Open
Abstract
Research on kidney diseases is being transformed by the rapid expansion and innovations in omics technologies. The analysis, integration, and interpretation of big data, however, have been an impediment to the growing interest in applying these technologies to understand kidney function and failure. Targeting this urgent need, the University of Michigan O'Brien Kidney Translational Core Center (MKTC) and its Administrative Core established the Applied Systems Biology Core. The Core provides need-based support for the global kidney community centered on enabling incorporation of systems biology approaches by creating web-based, user-friendly analytic and visualization tools, like Nephroseq and Nephrocell, guiding with experimental design, and processing, analysis, and integration of large data sets. The enrichment core supports systems biology education and dissemination through workshops, seminars, and individualized training sessions. Meanwhile, the Pilot and Feasibility Program of the MKTC provides pilot funding to both early-career and established investigators new to the field, to integrate a systems biology approach into their research projects. The relevance and value of the portfolio of training and services offered by MKTC are reflected in the expanding community of young investigators, collaborators, and users accessing resources and engaging in systems biology-based kidney research, thereby motivating MKTC to persevere in its mission to serve the kidney research community by enabling access to state-of-the-art data sets, tools, technologies, expertise, and learning opportunities for transformative basic, translational, and clinical studies that will usher in solutions to improve the lives of people impacted by kidney disease.
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Affiliation(s)
- Markus Bitzer
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Wenjun Ju
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Lalita Subramanian
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jonathan P Troost
- Division of Pediatric Nephrology, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - Joseph Tychewicz
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Becky Steck
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Roger C Wiggins
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Debbie S Gipson
- Division of Pediatric Nephrology, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - Crystal A Gadegbeku
- Department of Kidney Medicine, Glickman Urological and Kidney Institute, Cleveland Clinic Health System, Cleveland, Ohio
| | - Frank C Brosius
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
- Division of Nephrology, The University of Arizona College of Medicine Tucson, Tucson, Arizona
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Subramaniam Pennathur
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
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17
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Pulido Perez P, Póndigo de los Angeles JA, Perez Peralta A, Ramirez Mojica E, Torres Rasgado E, Hernandez-Hernandez ME, Romero JR. Reduction in Serum Magnesium Levels and Renal Function Are Associated with Increased Mortality in Obese COVID-19 Patients. Nutrients 2022; 14:nu14194054. [PMID: 36235704 PMCID: PMC9571102 DOI: 10.3390/nu14194054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 12/02/2022] Open
Abstract
Several studies provide evidence that obesity is a significant risk factor for adverse outcomes in coronavirus disease 2019 (COVID-19). Altered renal function and disturbances in magnesium levels have been reported to play important pathophysiological roles in COVID-19. However, the relationship between obesity, renal function, circulating magnesium levels, and mortality in patients with COVID-19 remains unclear. In this retrospective cohort study, we characterized 390 hospitalized patients with COVID-19 that were categorized according to their body mass index (BMI). Patients were clinically characterized and biochemical parameters, renal function, and electrolyte markers measured upon admission. We found that in patients who died, BMI was associated with reduced estimated glomerular filtration rate (eGFR, Rho: −0.251, p = 0.001) and serum magnesium levels (Rho: −0.308, p < 0.0001). Multiple linear regression analyses showed that death was significantly associated with obesity (p = 0.001). The Cox model for obese patients showed that magnesium levels were associated with increased risk of death (hazard ratio: 0.213, 95% confidence interval: 0.077 to 0.586, p = 0.003). Thus, reduced renal function and lower magnesium levels were associated with increased mortality in obese COVID-19 patients. These results suggest that assessment of kidney function, including magnesium levels, may assist in developing effective treatment strategies to reduce mortality among obese COVID-19 patients.
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Affiliation(s)
- Patricia Pulido Perez
- Faculty of Medicine, Autonomous University of Puebla, 13 Sur 2901 Col. Volcanes, Puebla 72420, Mexico
| | | | - Alonso Perez Peralta
- Internal Medicine Department, University Hospital of Puebla, Mexico. Av 27 Poniente, Los Volcanes, Puebla 72410, Mexico
| | - Eloisa Ramirez Mojica
- Internal Medicine Department, University Hospital of Puebla, Mexico. Av 27 Poniente, Los Volcanes, Puebla 72410, Mexico
| | - Enrique Torres Rasgado
- Faculty of Medicine, Autonomous University of Puebla, 13 Sur 2901 Col. Volcanes, Puebla 72420, Mexico
- Correspondence: ; Tel.: +52-(222)-229-5500; Fax: +52-(222)-240-5032
| | - Maria Elena Hernandez-Hernandez
- Faculty of Medicine, Autonomous University of Puebla, 13 Sur 2901 Col. Volcanes, Puebla 72420, Mexico
- Doctorate in Biological Science, Autonomous University of Tlaxcala, La Loma Xicohtencatl, Tlaxcala 90070, Mexico
| | - Jose R. Romero
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
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18
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Maremonti F, Locke S, Tonnus W, Beer K, Brucker A, Gonzalez NZ, Latk M, Belavgeni A, Hoppenz P, Hugo C, Linkermann A. COVID-19 and Diabetic Nephropathy. Horm Metab Res 2022; 54:510-513. [PMID: 35388439 DOI: 10.1055/a-1819-4822] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Diabetic nephropathy is the most common condition that requires a chronic renal replacement therapy, such as hemodialysis, peritoneal dialysis, kidney transplantation, or simultaneous kidney-pancreas transplantation. Chronic kidney disease progression, that is the loss of nephrons, which causes the continuous decline of the eGFR, underlies the pathogenesis of diabetic nephropathy. During the COVID-19 pandemic, it became clear that diabetic nephropathy is amongst the independent risk factors that predicts unfavourable outcome upon SARS-CoV2 infection. While we still lack conclusive mechanistic insights into how nephrons are rapidly lost upon SARS-CoV2 infection and why patients with diabetic nephropathy are more susceptible to severe outcomes upon SARS-CoV2 infection, here, we discuss several aspects of the interface of COVID-19 with diabetic nephropathy. We identify the shortage of reliable rodent models of diabetic nephropathy, limited treatment options for human diabetic nephropathy and the lack of knowledge about virus-induced signalling pathways of regulated necrosis, such as necroptosis, as key factors that explain our failure to understand this system. Finally, we focus on immunosuppressed patients and discuss vaccination efficacy in these and diabetic patients. We conclude that more basic science and mechanistic understanding will be required both in diabetic nephropathy as well as in host immune responses to the SARS-CoV2 virus if novel therapeutic strategies are desired.
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Affiliation(s)
| | - Sophie Locke
- Nephrology, Dresden University Hospital, Dresden, Germany
| | - Wulf Tonnus
- Nephrology, Dresden University Hospital, Dresden, Germany
| | - Kristina Beer
- Nephrology, Dresden University Hospital, Dresden, Germany
| | - Anne Brucker
- Nephrology, Dresden University Hospital, Dresden, Germany
| | | | - Marcus Latk
- Nephrology, Dresden University Hospital, Dresden, Germany
| | | | - Paul Hoppenz
- Nephrology, Dresden University Hospital, Dresden, Germany
| | - Christian Hugo
- Nephrology, Dresden University Hospital, Dresden, Germany
| | - Andreas Linkermann
- Nephrology, Dresden University Hospital, Dresden, Germany
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
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19
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Potential Similarities in Sex Difference in Key Genes and Their Expression, Network, EQTL and Pathways between COVID-19 and Chronic Kidney Disease Based on Mouse Model. J Pers Med 2022; 12:jpm12071190. [PMID: 35887687 PMCID: PMC9323909 DOI: 10.3390/jpm12071190] [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: 04/18/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022] Open
Abstract
COVID-19 and chronic kidney disease (CKD) share similarity in sex bias and key genes in the disease pathway of sex difference. We investigated the sex difference of molecular pathways of four key players of these two diseases using an existing large set of whole genome expression profiles from the kidneys of female and male mouse models. Our data show that there is little to no correlation at the whole genome expression level between female and male mice among these four genes. There are considerable sex differences among genes in upstream regulation, Ace2 complex interaction, and downstream pathways. Snap25 and Plcb4 may play important roles in the regulation of the expression level of Adam17, Tmprss2, and Cd146 in females. In males, Adh4 is a candidate gene for the regulation of Adam17, while Asl, Auts2, and Rabger1 are candidates for Tmprss2. Within the Ace2 complex, Cd146 directly influences the expression level of Adam17 and Ace2 in the female, while in the male Adam potentially has a stronger influence on Ace2 than that of Tmprss2. Among the top 100 most related genes, only one or two genes from four key genes and 11 from the control B-Actin were found to be the same between sexes. Among the top 10 sets of genes in the downstream pathway of Ace2, only two sets are the same between the sexes. We concluded that these known key genes and novel genes in CKD may play significant roles in the sex difference in the CKD and COVID-19 disease pathways.
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20
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Batista Simões JL, Sobierai LD, Pereira SM, Rodrigues Dos Santos MV, Bagatini MD. Therapeutic potential of P2X7 purinergic receptor modulation in the main organs affected by the COVID-19 cytokine storm. Curr Pharm Des 2022; 28:1798-1814. [PMID: 35838210 DOI: 10.2174/1381612828666220713115906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/31/2022] [Indexed: 01/08/2023]
Abstract
Defined by the World Health Organization as a global public health pandemic, coronavirus 2019 (COVID-19) has a global impact and the death of thousands of people. The "severe acute respiratory syndrome coronavirus 2" virus (SARS-CoV-2) is the etiologic agent of this disease, which uses the angiotensin-converting enzyme receptor 2 (ACE2) to infect the body, so any organ that expresses the gene ACE2 is a possible target for the new coronavirus. In addition, in severe cases of COVID-19, a cytokine storm occurs, which triggers widespread systemic inflammation due to the uncontrolled release of proinflammatory cytokines. In this perspective, the modulation of purinergic receptors are highlighted in the literature as a possible therapy, considering its application in other viral infections and systemic inflammation. Therefore, the objective of this review is to gather information on the modulation of the P2X7 receptor in the main organs directly affected by the virus and by the cytokine storm: heart, brain, lung, liver and kidneys. Thus, demonstrating possible therapies for reducing inflammation, as well as reducing the level of morbidity and mortality of COVID-19.
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21
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Exfoliated Kidney Cells from Urine for Early Diagnosis and Prognostication of CKD: The Way of the Future? Int J Mol Sci 2022; 23:ijms23147610. [PMID: 35886957 PMCID: PMC9324667 DOI: 10.3390/ijms23147610] [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: 05/30/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/17/2022] Open
Abstract
Chronic kidney disease (CKD) is a global health issue, affecting more than 10% of the worldwide population. The current approach for formal diagnosis and prognostication of CKD typically relies on non-invasive serum and urine biomarkers such as serum creatinine and albuminuria. However, histological evidence of tubulointerstitial fibrosis is the 'gold standard' marker of the likelihood of disease progression. The development of novel biomedical technologies to evaluate exfoliated kidney cells from urine for non-invasive diagnosis and prognostication of CKD presents opportunities to avoid kidney biopsy for the purpose of prognostication. Efforts to apply these technologies more widely in clinical practice are encouraged, given their potential as a cost-effective approach, and no risk of post-biopsy complications such as bleeding, pain and hospitalization. The identification of biomarkers in exfoliated kidney cells from urine via western blotting, enzyme-linked immunosorbent assay (ELISA), immunofluorescence techniques, measurement of cell and protein-specific messenger ribonucleic acid (mRNA)/micro-RNA and other techniques have been reported. Recent innovations such as multispectral autofluorescence imaging and single-cell RNA sequencing (scRNA-seq) have brought additional dimensions to the clinical application of exfoliated kidney cells from urine. In this review, we discuss the current evidence regarding the utility of exfoliated proximal tubule cells (PTC), podocytes, mesangial cells, extracellular vesicles and stem/progenitor cells as surrogate markers for the early diagnosis and prognostication of CKD. Future directions for development within this research area are also identified.
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22
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Robeva R, Petrova D, Elenkova A, Tankova T, Zacharieva S. C-peptide levels and glycemic indices in COVID-19 patients. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2090858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Ralitsa Robeva
- Department of Endocrinology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Daniela Petrova
- Department of Endocrinology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Atanaska Elenkova
- Department of Endocrinology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Tsvetalina Tankova
- Department of Endocrinology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Sabina Zacharieva
- Department of Endocrinology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
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23
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A diabetic milieu increases ACE2 expression and cellular susceptibility to SARS-CoV-2 infections in human kidney organoids and patient cells. Cell Metab 2022; 34:857-873.e9. [PMID: 35561674 PMCID: PMC9097013 DOI: 10.1016/j.cmet.2022.04.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/02/2022] [Accepted: 04/19/2022] [Indexed: 12/14/2022]
Abstract
It is not well understood why diabetic individuals are more prone to develop severe COVID-19. To this, we here established a human kidney organoid model promoting early hallmarks of diabetic kidney disease development. Upon SARS-CoV-2 infection, diabetic-like kidney organoids exhibited higher viral loads compared with their control counterparts. Genetic deletion of the angiotensin-converting enzyme 2 (ACE2) in kidney organoids under control or diabetic-like conditions prevented viral detection. Moreover, cells isolated from kidney biopsies from diabetic patients exhibited altered mitochondrial respiration and enhanced glycolysis, resulting in higher SARS-CoV-2 infections compared with non-diabetic cells. Conversely, the exposure of patient cells to dichloroacetate (DCA), an inhibitor of aerobic glycolysis, resulted in reduced SARS-CoV-2 infections. Our results provide insights into the identification of diabetic-induced metabolic programming in the kidney as a critical event increasing SARS-CoV-2 infection susceptibility, opening the door to the identification of new interventions in COVID-19 pathogenesis targeting energy metabolism.
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24
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Limonte CP, Valo E, Drel V, Natarajan L, Darshi M, Forsblom C, Henderson CM, Hoofnagle AN, Ju W, Kretzler M, Montemayor D, Nair V, Nelson RG, O’Toole JF, Toto RD, Rosas SE, Ruzinski J, Sandholm N, Schmidt IM, Vaisar T, Waikar SS, Zhang J, Rossing P, Ahluwalia TS, Groop PH, Pennathur S, Snell-Bergeon JK, Costacou T, Orchard TJ, Sharma K, de Boer IH. Urinary Proteomics Identifies Cathepsin D as a Biomarker of Rapid eGFR Decline in Type 1 Diabetes. Diabetes Care 2022; 45:1416-1427. [PMID: 35377940 PMCID: PMC9210873 DOI: 10.2337/dc21-2204] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/04/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Understanding mechanisms underlying rapid estimated glomerular filtration rate (eGFR) decline is important to predict and treat kidney disease in type 1 diabetes (T1D). RESEARCH DESIGN AND METHODS We performed a case-control study nested within four T1D cohorts to identify urinary proteins associated with rapid eGFR decline. Case and control subjects were categorized based on eGFR decline ≥3 and <1 mL/min/1.73 m2/year, respectively. We used targeted liquid chromatography-tandem mass spectrometry to measure 38 peptides from 20 proteins implicated in diabetic kidney disease. Significant proteins were investigated in complementary human cohorts and in mouse proximal tubular epithelial cell cultures. RESULTS The cohort study included 1,270 participants followed a median 8 years. In the discovery set, only cathepsin D peptide and protein were significant on full adjustment for clinical and laboratory variables. In the validation set, associations of cathepsin D with eGFR decline were replicated in minimally adjusted models but lost significance with adjustment for albuminuria. In a meta-analysis with combination of discovery and validation sets, the odds ratio for the association of cathepsin D with rapid eGFR decline was 1.29 per SD (95% CI 1.07-1.55). In complementary human cohorts, urine cathepsin D was associated with tubulointerstitial injury and tubulointerstitial cathepsin D expression was associated with increased cortical interstitial fractional volume. In mouse proximal tubular epithelial cell cultures, advanced glycation end product-BSA increased cathepsin D activity and inflammatory and tubular injury markers, which were further increased with cathepsin D siRNA. CONCLUSIONS Urine cathepsin D is associated with rapid eGFR decline in T1D and reflects kidney tubulointerstitial injury.
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Affiliation(s)
- Christine P. Limonte
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA
- Kidney Research Institute, University of Washington, Seattle, WA
| | - Erkka Valo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Viktor Drel
- Division of Nephrology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Loki Natarajan
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health and Moores Cancer Center at UC San Diego Health, La Jolla, CA
| | - Manjula Darshi
- Division of Nephrology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Clark M. Henderson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Andrew N. Hoofnagle
- Kidney Research Institute, University of Washington, Seattle, WA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
- Division of Metabolism, Endocrinology, and Nutrition, UW Medicine Diabetes Institute, University of Washington, Seattle, WA
| | - Wenjun Ju
- Division of Nephrology, University of Michigan, Ann Arbor, MI
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Matthias Kretzler
- Division of Nephrology, University of Michigan, Ann Arbor, MI
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Daniel Montemayor
- Division of Nephrology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Viji Nair
- Division of Nephrology, University of Michigan, Ann Arbor, MI
| | - Robert G. Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ
| | - John F. O’Toole
- Department of Nephrology and Hypertension, Cleveland Clinic, Cleveland, OH
| | - Robert D. Toto
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX
| | | | - John Ruzinski
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA
- Kidney Research Institute, University of Washington, Seattle, WA
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Insa M. Schmidt
- Section of Nephrology, Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA
| | - Tomas Vaisar
- Division of Metabolism, Endocrinology, and Nutrition, UW Medicine Diabetes Institute, University of Washington, Seattle, WA
| | - Sushrut S. Waikar
- Section of Nephrology, Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA
| | - Jing Zhang
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health and Moores Cancer Center at UC San Diego Health, La Jolla, CA
| | - Peter Rossing
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tarunveer S. Ahluwalia
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Subramaniam Pennathur
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI
| | - Janet K. Snell-Bergeon
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO
| | | | | | - Kumar Sharma
- Division of Nephrology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Ian H. de Boer
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA
- Kidney Research Institute, University of Washington, Seattle, WA
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25
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Impact of COVID-19 on Kidney of Diabetic Patients. Medicina (B Aires) 2022; 58:medicina58050644. [PMID: 35630061 PMCID: PMC9143731 DOI: 10.3390/medicina58050644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/01/2022] [Accepted: 05/05/2022] [Indexed: 12/02/2022] Open
Abstract
Given the current state of COVID-19, it is crucial to reveal its evolving relationship with and effect on different body organ systems and their diseases. The severity and outcome of COVID-19 have a very complex relationship, especially to the vital organs including the kidney, either in their state of health or disease. Additionally, it is well known that diabetes affects the kidney, leading to diabetic nephropathy. The kidney is also affected by different pathological and immunopathological reactions with COVID-19 infection, leading to acute kidney injury. Therefore, this review intended to extract the recent advances, updates, and discoveries about the effects of COVID-19 on diabetic patients and the relationship between COVID-19 invasion and the diabetic kidney and to discuss the current state of knowledge that has not yet been proved or disproved, leading to numerous controversial issues in looking for the effect of COVID-19 associated with diabetes mellitus on the human kidney.
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26
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Menon R, Otto EA, Berthier CC, Nair V, Farkash EA, Hodgin JB, Yang Y, Luo J, Woodside KJ, Zamani H, Norman SP, Wiggins RC, Kretzler M, Naik AS. Glomerular endothelial cell-podocyte stresses and crosstalk in structurally normal kidney transplants. Kidney Int 2022; 101:779-792. [PMID: 34952098 PMCID: PMC9067613 DOI: 10.1016/j.kint.2021.11.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 10/14/2021] [Accepted: 11/15/2021] [Indexed: 12/18/2022]
Abstract
Increased podocyte detachment begins immediately after kidney transplantation and is associated with long-term allograft failure. We hypothesized that cell-specific transcriptional changes in podocytes and glomerular endothelial cells after transplantation would offer mechanistic insights into the podocyte detachment process. To test this, we evaluated cell-specific transcriptional profiles of glomerular endothelial cells and podocytes from 14 patients of their first-year surveillance biopsies with normal histology from low immune risk recipients with no post-transplant complications and compared these to biopsies of 20 healthy living donor controls. Glomerular endothelial cells from these surveillance biopsies were enriched for genes related to fluid shear stress, angiogenesis, and interferon signaling. In podocytes, pathways were enriched for genes in response to growth factor signaling and actin cytoskeletal reorganization but also showed evidence of podocyte stress as indicated by reduced nephrin (adhesion protein) gene expression. In parallel, transcripts coding for proteins required to maintain podocyte adherence to the underlying glomerular basement membrane were downregulated, including the major glomerular podocyte integrin α3 and the actin cytoskeleton-related gene synaptopodin. The reduction in integrin α3 protein expression in surveillance biopsies was confirmed by immunoperoxidase staining. The combined growth and stress response of patient allografts post-transplantation paralleled similar changes in a rodent model of nephrectomy-induced glomerular hypertrophic stress that progress to develop proteinuria and glomerulosclerosis with shortened kidney life span. Thus, even among patients with apparently healthy allografts with no detectable histologic abnormality including alloimmune injury, transcriptomic changes reflecting cell stresses are already set in motion that could drive hypertrophy-associated glomerular disease progression.
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Affiliation(s)
- Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
| | - Edgar A Otto
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Celine C Berthier
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Viji Nair
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Evan A Farkash
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jeffrey B Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yingbao Yang
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jinghui Luo
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kenneth J Woodside
- Division of Transplant Surgery, Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Haniyeh Zamani
- School of Arts and Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Silas P Norman
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Roger C Wiggins
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Abhijit S Naik
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
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27
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Sherman EJ, Mirabelli C, Tang VT, Khan TG, Leix K, Kennedy AA, Graham SE, Willer CJ, Tai AW, Sexton JZ, Wobus CE, Emmer BT. Identification of cell type specific ACE2 modifiers by CRISPR screening. PLoS Pathog 2022; 18:e1010377. [PMID: 35231079 PMCID: PMC8929698 DOI: 10.1371/journal.ppat.1010377] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 03/17/2022] [Accepted: 02/15/2022] [Indexed: 12/26/2022] Open
Abstract
SARS-CoV-2 infection is initiated by binding of the viral spike protein to its receptor, ACE2, on the surface of host cells. ACE2 expression is heterogeneous both in vivo and in immortalized cell lines, but the molecular pathways that govern ACE2 expression remain unclear. We now report high-throughput CRISPR screens for functional modifiers of ACE2 surface abundance. In liver-derived HuH7 cells, we identified 35 genes whose disruption was associated with a change in the surface abundance of ACE2. Enriched among these ACE2 regulators were established transcription factors, epigenetic regulators, and functional networks. We further characterized individual HuH7 cell lines with disruption of SMAD4, EP300, PIAS1, or BAMBI and found these genes to regulate ACE2 at the mRNA level and to influence cellular susceptibility to SARS-CoV-2 infection. Orthogonal screening of lung-derived Calu-3 cells revealed a distinct set of ACE2 modifiers comprised of ACE2, KDM6A, MOGS, GPAA1, and UGP2. Collectively, our findings clarify the host factors involved in SARS-CoV-2 entry, highlight the cell type specificity of ACE2 regulatory networks, and suggest potential targets for therapeutic development. The amount of ACE2 on the surface of human cells is an important determinant of SARS-CoV-2 infection, but the molecular pathways that regulate ACE2 remain poorly understood. Identification of these pathways may clarify host factors involved in COVID-19 outcomes and offer targets for therapeutic development. ACE2-targeted therapies may furthermore be less susceptible than viral spike-targeted therapies to evasion by SARS-CoV-2 variants. To systematically identify regulators of human ACE2, we therefore performed high-throughput CRISPR screening for modifiers of ACE2 surface abundance in HuH7 liver-derived and Calu-3 lung-derived cell lines. Unexpectedly, aside from ACE2 itself, we identified distinct sets of ACE2 modifiers in either cell line. For a subset of ACE2 regulators, we validated their functional effect on ACE2, confirmed their relevance to SARS-CoV-2 infection, and clarified their level of regulation. Our findings demonstrate the important influence of cell type on investigations of SARS-CoV-2 infection and nominate candidate pathways for ACE2-targeted therapeutic development.
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Affiliation(s)
- Emily J. Sherman
- Department of Internal Medicine, Division of Hospital Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Carmen Mirabelli
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Vi T. Tang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States of America
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Taslima G. Khan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Chemical Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kyle Leix
- Department of Internal Medicine, Division of Hospital Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrew A. Kennedy
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sarah E. Graham
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Cristen J. Willer
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrew W. Tai
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, United States of America
- VA Ann Arbor Healthcare System, Ann Arbor, Michigan, United States of America
| | - Jonathan Z. Sexton
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Brian T. Emmer
- Department of Internal Medicine, Division of Hospital Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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28
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Kohli A, Sauerhering L, Fehling SK, Klann K, Geiger H, Becker S, Koch B, Baer PC, Strecker T, Münch C. Proteomic landscape of SARS-CoV-2– and MERS-CoV–infected primary human renal epithelial cells. Life Sci Alliance 2022; 5:5/5/e202201371. [PMID: 35110370 PMCID: PMC8814637 DOI: 10.26508/lsa.202201371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 12/24/2022] Open
Abstract
Translatome and proteome analyses of human proximal and distal tubular cells during coronavirus infection reveal distinctive host cell response patterns important for viral replication and renal pathology. Acute kidney injury is associated with mortality in COVID-19 patients. However, host cell changes underlying infection of renal cells with SARS-CoV-2 remain unknown and prevent understanding of the molecular mechanisms that may contribute to renal pathology. Here, we carried out quantitative translatome and whole-cell proteomics analyses of primary renal proximal and distal tubular epithelial cells derived from human donors infected with SARS-CoV-2 or MERS-CoV to disseminate virus and cell type–specific changes over time. Our findings revealed shared pathways modified upon infection with both viruses, as well as SARS-CoV-2-specific host cell modulation driving key changes in innate immune activation and cellular protein quality control. Notably, MERS-CoV infection–induced specific changes in mitochondrial biology that were not observed in response to SARS-CoV-2 infection. Furthermore, we identified extensive modulation in pathways associated with kidney failure that changed in a virus- and cell type–specific manner. In summary, we provide an overview of the effects of SARS-CoV-2 or MERS-CoV infection on primary renal epithelial cells revealing key pathways that may be essential for viral replication.
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Affiliation(s)
- Aneesha Kohli
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Lucie Sauerhering
- Institute of Virology, Philipps University Marburg, Marburg, Germany
- German Center for Infection Research (DZIF), Partner Sites Gieβen-Marburg-Langen, Marburg, Germany
| | - Sarah K Fehling
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Kevin Klann
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Helmut Geiger
- Division of Nephrology, Department of Internal Medicine III, University Hospital, Goethe-University, Frankfurt am Main, Germany
| | - Stephan Becker
- Institute of Virology, Philipps University Marburg, Marburg, Germany
- German Center for Infection Research (DZIF), Partner Sites Gieβen-Marburg-Langen, Marburg, Germany
| | - Benjamin Koch
- Division of Nephrology, Department of Internal Medicine III, University Hospital, Goethe-University, Frankfurt am Main, Germany
| | - Patrick C Baer
- Division of Nephrology, Department of Internal Medicine III, University Hospital, Goethe-University, Frankfurt am Main, Germany
| | - Thomas Strecker
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Frankfurt am Main, Germany
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29
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Dugbartey GJ, Alornyo KK, Ohene BO, Boima V, Antwi S, Sener A. Renal consequences of the novel coronavirus disease 2019 (COVID-19) and hydrogen sulfide as a potential therapy. Nitric Oxide 2022; 120:16-25. [PMID: 35032641 PMCID: PMC8755416 DOI: 10.1016/j.niox.2022.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 12/14/2022]
Abstract
The novel coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, is a global pandemic which is primarily considered a respiratory illness. However, emerging reports show that the virus exhibits both pulmonary and extra-pulmonary manifestations in humans, with the kidney as a major extra-pulmonary target due to its abundant expression of angiotensin-converting enzyme 2 and transmembrane protease serine 2, which facilitate entry of the virus into cells. Acute kidney injury has become prevalent in COVID-19 patients without prior any history of kidney dysfunction. In addition, the virus also worsens kidney conditions and increases mortality of COVID-19 patients with pre-existing chronic kidney disease, renal cancer, diabetic nephropathy, end-stage kidney disease as well as dialysis and kidney transplant patients. In the search for antiviral agents for the treatment of COVID-19, hydrogen sulfide (H2S), the third established member of gasotransmitter family, is emerging as a potential candidate, possessing important therapeutic properties including antiviral, anti-inflammatory, anti-thrombotic and antioxidant properties. A recent clinical study revealed higher serum H2S levels in survivors of COVID-19 pneumonia with reduced interleukin-6 levels compared to fatal cases. In this review, we summarize the global impact of COVID-19 on kidney conditions and discuss the emerging role of H2S as a potential COVID-19 therapy.
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Affiliation(s)
- George J Dugbartey
- Department of Pharmacology and Toxicology, School of Pharmacy, College of Health Sciences, University of Ghana, Legon, Accra, Ghana.
| | - Karl K Alornyo
- Department of Pharmacology and Toxicology, School of Pharmacy, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Bright O Ohene
- Department of Pharmacology and Toxicology, School of Pharmacy, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Vincent Boima
- Department of Medicine and Therapeutics, University of Ghana Medical School, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Sampson Antwi
- Department of Child Health, School of Medical Sciences, Kwame Nkrumah University of Science and Technology and Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Alp Sener
- Department of Surgery, Division of Urology, London Health Sciences Center, Western University, London, Ontario, Canada; Matthew Mailing Center for Translational Transplant Studies, London Health Sciences Center, Western University, London, Ontario, Canada; Multi-organ Transplant Program, London Health Sciences Center, Ontario, Canada; Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
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30
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Does Oxidative Stress Management Help Alleviation of COVID-19 Symptoms in Patients Experiencing Diabetes? Nutrients 2022; 14:nu14020321. [PMID: 35057501 PMCID: PMC8780958 DOI: 10.3390/nu14020321] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome (SARS)-CoV-2 virus causes novel coronavirus disease 2019 (COVID-19) with other comorbidities such as diabetes. Diabetes is the most common cause of diabetic nephropathy, which is attributed to hyperglycemia. COVID-19 produces severe complications in people with diabetes mellitus. This article explains how SARS-CoV-2 causes more significant kidney damage in diabetic patients. Importantly, COVID-19 and diabetes share inflammatory pathways of disease progression. SARS-CoV-2 binding with ACE-2 causes depletion of ACE-2 (angiotensin-converting enzyme 2) from blood vessels, and subsequently, angiotensin-II interacts with angiotensin receptor-1 from vascular membranes that produce NADPH (nicotinamide adenine dinucleotide hydrogen phosphate) oxidase, oxidative stress, and constriction of blood vessels. Since diabetes and COVID-19 can create oxidative stress, we hypothesize that COVID-19 with comorbidities such as diabetes can synergistically increase oxidative stress leading to end-stage renal failure and death. Antioxidants may therefore prevent renal damage-induced death by inhibiting oxidative damage and thus can help protect people from COVID-19 related comorbidities. A few clinical trials indicated how effective the antioxidant therapy is against improving COVID-19 symptoms, based on a limited number of patients who experienced COVID-19. In this review, we tried to understand how effective antioxidants (such as vitamin D and flavonoids) can act as food supplements or therapeutics against COVID-19 with diabetes as comorbidity based on recently available clinical, preclinical, or in silico studies.
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31
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Martinez Valenzuela L, Oliveras L, Gomà M, Quiros E, Antón-Pámpols P, Gómez-Preciado F, Fulladosa X, Cruzado JM, Torras J, Draibe J. Th1 Cytokines Signature in 2 Cases of IgA Nephropathy Flare after mRNA-Based SARS-CoV-2 Vaccine: Exploring the Pathophysiology. Nephron Clin Pract 2022; 146:564-572. [PMID: 35640535 PMCID: PMC9393770 DOI: 10.1159/000524619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/08/2022] [Indexed: 12/13/2022] Open
Abstract
mRNA-based vaccines have dramatically shifted the course of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. IgA nephropathy (IgAN) flare is the most reported renal adverse effect after the administration of these vaccines. Unraveling the mechanistic pathways leading to these flares is necessary to confirm a causal association. Herein, we report 2 cases of IgAN flare after SARS-CoV-2 vaccination in patients previously diagnosed with IgAN. We describe and compare the clinical and analytical features of the disease at the time of the diagnostic with the post-vaccine flare. In addition, we obtained serum and urine of these patients at the moment of the flare and determined the levels of IL-2, TNF-α, and IFNγ using a multiplex bead-based assay. As diseased controls, we included n = 13 patients diagnosed with IgAN who had available serum and urine samples at the moment of the diagnostic stored in our biobank. We also included 6 healthy controls. Compared to the first episode, postvaccination flares were more severe in terms of peak serum creatinine, albuminuria, and urinary erythrocyte count. The histological lesions found at the biopsy performed during the post-vaccine flare were similar to those found at the diagnostic. One of the patients who suffered a post-vaccine flare showed increased serum IL-2 and TNFα compared to the IgAN-diseased controls and the healthy controls. In conclusion, although several cases of post-vaccine IgAN flares have been reported, there are no mechanistic studies on the occurrence of these flares. We here suggest that hyperactivation of the Th1 pathway may be involved, but larger studies with more refined methods for numerical and functional Th1 lymphocytes evaluation are required.
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Affiliation(s)
- Laura Martinez Valenzuela
- Nephrology Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Laia Oliveras
- Nephrology Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Montserrat Gomà
- Department of Pathology, Bellvitge University Hospital, Hospitalet de Llobregat, Barcelona, Spain
| | - Eugenia Quiros
- Department of Pathology, Bellvitge University Hospital, Hospitalet de Llobregat, Barcelona, Spain
| | - Paula Antón-Pámpols
- Nephrology Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Francisco Gómez-Preciado
- Nephrology Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Fulladosa
- Nephrology Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Josep Maria Cruzado
- Nephrology Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Juan Torras
- Nephrology Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Juliana Draibe
- Nephrology Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
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32
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Foe and friend in the COVID-19-associated acute kidney injury: an insight on intrarenal renin-angiotensin system. Acta Biochim Biophys Sin (Shanghai) 2021; 54:1-11. [PMID: 35130610 PMCID: PMC9828085 DOI: 10.3724/abbs.2021002] [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] [Indexed: 01/08/2023] Open
Abstract
Since the first reported case in December of 2019, the coronavirus disease 2019 (COVID-19) has became an international public health emergency. So far, there are more than 228,206,384 confirmed cases including 4,687,066 deaths. Kidney with high expression of angiotensin-converting enzyme 2 (ACE2) is one of the extrapulmonary target organs affected in patients with COVID-19. Acute kidney injury (AKI) is one of the independent risk factors for the death of COVID-19 patients. The imbalance between ACE2-Ang(1-7)-MasR and ACE-Ang II-AT1R axis in the kidney may contribute to COVID-19-associated AKI. Although series of research have shown the inconsistent effects of multiple common RAS inhibitors on ACE2 expression and enzyme activity, most of the retrospective cohort studies indicated the safety and protective effects of ACEI/ARB in COVID-19 patients. This review article highlights the current knowledge on the possible involvement of intrarenal RAS in COVID-19-associated AKI with a primary focus on the opposing effects of ACE2-Ang(1-7)-MasR and ACE-Ang II-AT1R signaling in the kidney. Human recombinant soluble ACE2 or ACE2 variants with preserved ACE2-enzymatic activity may be the best options to improve COVID-19-associated AKI.
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33
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Helms L, Marchiano S, Stanaway IB, Hsiang TY, Juliar BA, Saini S, Zhao YT, Khanna A, Menon R, Alakwaa F, Mikacenic C, Morrell ED, Wurfel MM, Kretzler M, Harder JL, Murry CE, Himmelfarb J, Ruohola-Baker H, Bhatraju PK, Gale M, Freedman BS. Cross-validation of SARS-CoV-2 responses in kidney organoids and clinical populations. JCI Insight 2021; 6:e154882. [PMID: 34767537 PMCID: PMC8783682 DOI: 10.1172/jci.insight.154882] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/10/2021] [Indexed: 11/17/2022] Open
Abstract
Kidneys are critical target organs of COVID-19, but susceptibility and responses to infection remain poorly understood. Here, we combine SARS-CoV-2 variants with genome-edited kidney organoids and clinical data to investigate tropism, mechanism, and therapeutics. SARS-CoV-2 specifically infects organoid proximal tubules among diverse cell types. Infections produce replicating virus, apoptosis, and disrupted cell morphology, features of which are revealed in the context of polycystic kidney disease. Cross-validation of gene expression patterns in organoids reflects proteomic signatures of COVID-19 in the urine of critically ill patients indicating interferon pathway upregulation. SARS-CoV-2 viral variants alpha, beta, gamma, kappa, and delta exhibit comparable levels of infection in organoids. Infection is ameliorated in ACE2-/- organoids and blocked via treatment with de novo-designed spike binder peptides. Collectively, these studies clarify the impact of kidney infection in COVID-19 as reflected in organoids and clinical populations, enabling assessment of viral fitness and emerging therapies.
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Affiliation(s)
- Louisa Helms
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
| | - Silvia Marchiano
- Department of Medicine
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Division of Cardiology
- Center for Cardiovascular Biology
| | - Ian B. Stanaway
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
| | - Tien-Ying Hsiang
- Center for Innate Immunity and Immune Disease, Department of Immunology
| | - Benjamin A. Juliar
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
- Institute for Stem Cell and Regenerative Medicine
| | - Shally Saini
- Institute for Stem Cell and Regenerative Medicine
- Department of Biochemistry; and
| | - Yan Ting Zhao
- Institute for Stem Cell and Regenerative Medicine
- Department of Biochemistry; and
- Department of Oral Health Sciences, School of Dentistry, University of Washington School of Medicine, Seattle, Washington, USA
| | - Akshita Khanna
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Center for Cardiovascular Biology
| | - Rajasree Menon
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Fadhl Alakwaa
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Carmen Mikacenic
- Department of Medicine
- Translational Research, Benaroya Research Institute, Seattle, Washington, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Eric D. Morrell
- Department of Medicine
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Mark M. Wurfel
- Department of Medicine
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jennifer L. Harder
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Charles E. Murry
- Department of Medicine
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Division of Cardiology
- Center for Cardiovascular Biology
- Sana Biotechnology, Seattle, Washington, USA
| | | | - Hannele Ruohola-Baker
- Institute for Stem Cell and Regenerative Medicine
- Department of Biochemistry; and
- Department of Oral Health Sciences, School of Dentistry, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Pavan K. Bhatraju
- Department of Medicine
- Kidney Research Institute
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology
| | - Benjamin S. Freedman
- Department of Medicine
- Division of Nephrology
- Kidney Research Institute
- Institute for Stem Cell and Regenerative Medicine
- Department of Laboratory Medicine and Pathology
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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34
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Figueroa-Pizano MD, Campa-Mada AC, Carvajal-Millan E, Martinez-Robinson KG, Chu AR. The underlying mechanisms for severe COVID-19 progression in people with diabetes mellitus: a critical review. AIMS Public Health 2021; 8:720-742. [PMID: 34786431 PMCID: PMC8568590 DOI: 10.3934/publichealth.2021057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/20/2021] [Indexed: 01/08/2023] Open
Abstract
Diabetes mellitus (DM) has a high incidence of comorbidities among patients with severe coronavirus disease 2019 (COVID-19). The elevated prevalence of DM in the world population makes it a significant risk factor because diabetic individuals appear to be prone to clinical complications and have increased mortality rates. Here, we review the possible underlying mechanisms involved in DM that led to worse outcomes in COVID-19. The impacts of hyperglycemia side effects, secondary comorbidities, weakened innate and adaptive immunity, chronic inflammation, and poor nutritional status, commonly present in DM, are discussed. The role of the SARS-CoV-2 receptor and its polymorphic variations on higher binding affinity to facilitate viral uptake in people with DM were also considered. Clinical differences between individuals with type 1 DM and type 2 DM affected by COVID-19 and the potential diabetogenic effect of SARS-CoV-2 infection were addressed.
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Affiliation(s)
- María D Figueroa-Pizano
- Research Center for Food and Development, CIAD, AC, Carretera Gustavo Enrique Astiazarán Rosas No. 46, C.P. 83304, Hermosillo, Sonora, México
| | - Alma C Campa-Mada
- Research Center for Food and Development, CIAD, AC, Carretera Gustavo Enrique Astiazarán Rosas No. 46, C.P. 83304, Hermosillo, Sonora, México
| | - Elizabeth Carvajal-Millan
- Research Center for Food and Development, CIAD, AC, Carretera Gustavo Enrique Astiazarán Rosas No. 46, C.P. 83304, Hermosillo, Sonora, México
| | - Karla G Martinez-Robinson
- Research Center for Food and Development, CIAD, AC, Carretera Gustavo Enrique Astiazarán Rosas No. 46, C.P. 83304, Hermosillo, Sonora, México
| | - Agustin Rascon Chu
- Research Center for Food and Development, CIAD, AC, Carretera Gustavo Enrique Astiazarán Rosas No. 46, C.P. 83304, Hermosillo, Sonora, México
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35
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Yi TW, Laing C, Kretzler M, Nkulikiyinka R, Legrand M, Jardine M, Rossignol P, Smyth B. Digital health and artificial intelligence in kidney research: a report from the 2020 Kidney Disease Clinical Trialists (KDCT) meeting. Nephrol Dial Transplant 2021; 37:620-627. [PMID: 34791422 DOI: 10.1093/ndt/gfab320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Indexed: 11/14/2022] Open
Abstract
The exponential growth in digital technology coupled with the global COVID-19 pandemic is driving a profound change in the delivery of medical care and research conduct. The growing availability of electronic monitoring, electronic health records, smartphones and other devices, and access to ever greater computational power, provides new opportunities, but also new challenges. Artificial intelligence (AI) exemplifies the potential of this digital revolution, which also includes other tools such as mobile health (mHealth) services and wearables. Despite digital technology becoming commonplace, its use in medicine and medical research is still in its infancy, with many clinicians and researchers having limited experience with such tools in their usual practice. This paper, derived from the 'Digital Health and Artificial Intelligence' session of the Kidney Disease Clinical Trialists virtual workshop held in September 2020, aims to illustrate the breadth of applications to which digital tools and AI can be applied in clinical medicine and research. It highlights several innovative projects incorporating digital technology that range from streamlining medical care of those with acute kidney injury to the use of AI to navigate the vast genomic and proteomic data gathered in kidney disease. Important considerations relating to any new digital health project are presented, with a view to encouraging the further evolution and refinement of these new tools in a manner that fosters collaboration and the generation of robust evidence.
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Affiliation(s)
- Tae Won Yi
- The George Institute for Global Health, University of New South Wales, Sydney, New South Wales, Australia.,Department of Medicine, Clinician Investigator Program, University of British Columbia, Vancouver, Canada.,NHMRC Clinical Trials Centre, University of Sydney, Camperdown, Australia
| | - Chris Laing
- University College London Centre for Nephrology, Royal Free Hospital, London, United Kingdom.,Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Matthieu Legrand
- Department of Anesthesia and Perioperative Care, Division of Critical Care Medicine, University of California, San Francisco, CA, USA
| | - Meg Jardine
- NHMRC Clinical Trials Centre, University of Sydney, Camperdown, Australia.,Department of Renal Medicine, Concord Repatriation and General Hospital, Concord, New South Wales, Australia
| | - Patrick Rossignol
- Université de Lorraine, INSERM Centre d'Investigation Clinique Plurithématique 1433, Centre Hospitalier Régional Universitaire de Nancy, INSERM U1116, French Clinical Research Infrastructure Network Investigation Network Initiative-Cardiovascular and Renal Clinical Trialists, Nancy, France
| | - Brendan Smyth
- NHMRC Clinical Trials Centre, University of Sydney, Camperdown, Australia.,Department of Renal Medicine, St George Hospital, Kogarah, New South Wales, Australia
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36
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Cheung MD, Erman EN, Liu S, Erdmann NB, Ghajar-Rahimi G, Moore KH, Edberg JC, George JF, Agarwal A. Single-Cell RNA Sequencing of Urinary Cells Reveals Distinct Cellular Diversity in COVID-19-Associated AKI. KIDNEY360 2021; 3:28-36. [PMID: 35368565 PMCID: PMC8967619 DOI: 10.34067/kid.0005522021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/03/2021] [Indexed: 01/10/2023]
Abstract
Background AKI is a common sequela of infection with SARS-CoV-2 and contributes to the severity and mortality from COVID-19. Here, we tested the hypothesis that kidney alterations induced by COVID-19-associated AKI could be detected in cells collected from urine. Methods We performed single-cell RNA sequencing (scRNAseq) on cells recovered from the urine of eight hospitalized patients with COVID-19 with (n=5) or without AKI (n=3) as well as four patients with non-COVID-19 AKI (n=4) to assess differences in cellular composition and gene expression during AKI. Results Analysis of 30,076 cells revealed a diverse array of cell types, most of which were kidney, urothelial, and immune cells. Pathway analysis of tubular cells from patients with AKI showed enrichment of transcripts associated with damage-related pathways compared with those without AKI. ACE2 and TMPRSS2 expression was highest in urothelial cells among cell types recovered. Notably, in one patient, we detected SARS-CoV-2 viral RNA in urothelial cells. These same cells were enriched for transcripts associated with antiviral and anti-inflammatory pathways. Conclusions We successfully performed scRNAseq on urinary sediment from hospitalized patients with COVID-19 to noninvasively study cellular alterations associated with AKI and established a dataset that includes both injured and uninjured kidney cells. Additionally, we provide preliminary evidence of direct infection of urinary bladder cells by SARS-CoV-2. The urinary sediment contains a wealth of information and is a useful resource for studying the pathophysiology and cellular alterations that occur in kidney diseases.
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Affiliation(s)
- Matthew D. Cheung
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama,Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama,Division of Cardiothoracic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Elise N. Erman
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama,Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama,Division of Cardiothoracic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Shanrun Liu
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Nathaniel B. Erdmann
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Gelare Ghajar-Rahimi
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama,Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama,Division of Cardiothoracic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kyle H. Moore
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama,Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama,Division of Cardiothoracic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jeffrey C. Edberg
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - James F. George
- Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama,Division of Cardiothoracic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama
| | - Anupam Agarwal
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama,Department of Medicine, Nephrology Research and Training Center, University of Alabama at Birmingham, Birmingham, Alabama
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Zhou Z, Kuang H, Ma Y, Zhang L. Application of extracorporeal therapies in critically ill COVID-19 patients. J Zhejiang Univ Sci B 2021; 22:701-717. [PMID: 34514751 PMCID: PMC8435342 DOI: 10.1631/jzus.b2100344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is a major public health event caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 has spread widely all over the world. A high proportion of patients become severely or critically ill, and suffer high mortality due to respiratory failure and multiple organ dysfunction. Therefore, providing timely and effective treatment for critically ill patients is essential to reduce overall mortality. Convalescent plasma therapy and pharmacological treatments, such as aerosol inhalation of interferon-α (IFN-α), corticosteroids, and tocilizumab, have all been applied in clinical practice; however, their effects remain controversial. Recent studies have shown that extracorporeal therapies might have a potential role in treating critically ill COVID-19 patients. In this review, we examine the application of continuous renal replacement therapy (CRRT), therapeutic plasma exchange (TPE), hemoadsorption (HA), extracorporeal membrane oxygenation (ECMO), and extracorporeal carbon dioxide removal (ECCO2R) in critically ill COVID-19 patients to provide support for the further diagnosis and treatment of COVID-19.
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Affiliation(s)
- Zhifeng Zhou
- Department of Nephrology, Kidney Research Institute, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Huang Kuang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing 100034, China
| | - Yuexian Ma
- Department of Nephrology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China
| | - Ling Zhang
- Department of Nephrology, Kidney Research Institute, West China Hospital, Sichuan University, Chengdu 610041, China.
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38
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Hou YC, Lu KC, Kuo KL. The Efficacy of COVID-19 Vaccines in Chronic Kidney Disease and Kidney Transplantation Patients: A Narrative Review. Vaccines (Basel) 2021; 9:885. [PMID: 34452010 PMCID: PMC8402591 DOI: 10.3390/vaccines9080885] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/06/2021] [Accepted: 08/08/2021] [Indexed: 12/13/2022] Open
Abstract
The SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic has posed a huge threat to global health because of its rapid spread and various mutant variants. Critical illness occurs in the elderly and vulnerable individuals, such as those with chronic kidney disease. The severity of SARS-CoV-2 infection is associated with the severity of chronic kidney disease (CKD)and even kidney transplantation (KT) because of the chronic use of immunosuppressive agents. To develop adaptive immunity against SARS-CoV-2, vaccination against the spike protein is important. Current phase III trials of vaccines against SARS-CoV-2 have not focused on a specific group of individuals, such as patients with CKD or those undergoing dialysis or kidney transplantation. Chronic use of immunosuppressive agents might disturb the immune response to the SARS-CoV-2 spike protein. On the basis of limited evidence, the immune compromised status of CKD patients might decrease neutralizing antibody development after a single dose of a specific vaccine. Boosting dosage more than the protocol might increase the titer of the neutralizing antibody in CKD patients. Further evidence is needed to understand the factors disturbing the immunogenicity of the SARS-CoV-2 vaccine, and CKD patients should receive the recommended dose of the SARS-CoV-2 vaccine due to their relatively immune compromised status.
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Affiliation(s)
- Yi-Chou Hou
- Division of Nephrology, Department of Medicine, Cardinal-Tien Hospital, New Taipei City 231, Taiwan;
- School of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan
| | - Kuo-Cheng Lu
- Division of Nephrology, Department of Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 231, Taiwan;
- School of Medicine, Buddhist Tzu Chi University, Hualien 970, Taiwan
| | - Ko-Lin Kuo
- Division of Nephrology, Department of Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 231, Taiwan;
- School of Medicine, Buddhist Tzu Chi University, Hualien 970, Taiwan
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39
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ACE2 protein expression within isogenic cell lines is heterogeneous and associated with distinct transcriptomes. Sci Rep 2021; 11:15900. [PMID: 34354120 PMCID: PMC8342525 DOI: 10.1038/s41598-021-95308-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/16/2021] [Indexed: 12/23/2022] Open
Abstract
The membrane protein angiotensin-converting enzyme 2 (ACE2) is a physiologic regulator of the renin-angiotensin system and the cellular receptor for the SARS-CoV-2 virus. Prior studies of ACE2 expression have primarily focused on mRNA abundance, with investigation at the protein level limited by uncertain specificity of commercial ACE2 antibodies. Here, we report our development of a sensitive and specific flow cytometry-based assay for cellular ACE2 protein abundance. Application of this approach to multiple cell lines revealed an unexpected degree of cellular heterogeneity, with detectable ACE2 protein in only a subset of cells in each isogenic population. This heterogeneity was mediated at the mRNA level by transcripts predominantly initiated from the ACE2 proximal promoter. ACE2 expression was heritable but not fixed over multiple generations of daughter cells, with gradual drift toward the original heterogeneous background. RNA-seq profiling identified distinct transcriptomes of ACE2-expressing relative cells to non-expressing cells, with enrichment in functionally related genes and transcription factor target sets. Our findings provide a validated approach for the specific detection of ACE2 protein at the surface of single cells, support an epigenetic mechanism of ACE2 gene regulation, and identify specific pathways associated with ACE2 expression in HuH7 cells.
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40
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Nelson RG, Knowler WC, Kretzler M, Lemley KV, Looker HC, Mauer M, Mitch WE, Najafian B, Bennett PH. Pima Indian Contributions to Our Understanding of Diabetic Kidney Disease. Diabetes 2021; 70:1603-1616. [PMID: 34285119 PMCID: PMC8385607 DOI: 10.2337/dbi20-0043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/23/2021] [Indexed: 11/13/2022]
Abstract
Prospective studies in informative populations are crucial to increasing our knowledge of disease. In this perspective, we describe a half century of studies in an American Indian population that transformed our understanding of kidney disease in type 2 diabetes, now recognized as the leading cause of kidney failure worldwide. Serial examinations conducted for many years that included the collection of data and samples across multiple domains captured an unprecedented volume of clinical, physiologic, morphometric, genomic, and transcriptomic data. This work permitted us to extensively characterize the course and determinants of diabetic kidney disease, its pathophysiologic underpinnings, and important secular trends of urgent concern to populations worldwide, including the emergence of youth-onset type 2 diabetes and its effect on development of diabetic kidney disease in midlife. By combining these data using the tools of integrative biology, we are developing new mechanistic insights into the development and progression of diabetic kidney disease in type 2 diabetes. These insights have already contributed to the identification and successful therapeutic targeting of a novel pathway in DKD. We anticipate that this work will continue to expand our understanding of this complex disease and influence its management in the coming years.
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Affiliation(s)
- Robert G Nelson
- National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ
| | - William C Knowler
- National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Kevin V Lemley
- Department of Pediatrics, University of Southern California Keck School of Medicine, Children's Hospital Los Angeles, Los Angeles, CA
| | - Helen C Looker
- National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ
| | - Michael Mauer
- Department of Pediatrics and Medicine, University of Minnesota, Minneapolis, MN
| | - William E Mitch
- Division of Nephrology, Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Behzad Najafian
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA
| | - Peter H Bennett
- National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ
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Deleersnijder D, Callemeyn J, Arijs I, Naesens M, Van Craenenbroeck AH, Lambrechts D, Sprangers B. Current Methodological Challenges of Single-Cell and Single-Nucleus RNA-Sequencing in Glomerular Diseases. J Am Soc Nephrol 2021; 32:1838-1852. [PMID: 34140401 PMCID: PMC8455274 DOI: 10.1681/asn.2021020157] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) allow transcriptomic profiling of thousands of cells from a renal biopsy specimen at a single-cell resolution. Both methods are promising tools to unravel the underlying pathophysiology of glomerular diseases. This review provides an overview of the technical challenges that should be addressed when designing single-cell transcriptomics experiments that focus on glomerulopathies. The isolation of glomerular cells from core needle biopsy specimens for single-cell transcriptomics remains difficult and depends upon five major factors. First, core needle biopsies generate little tissue material, and several samples are required to identify glomerular cells. Second, both fresh and frozen tissue samples may yield glomerular cells, although every experimental pipeline has different (dis)advantages. Third, enrichment for glomerular cells in human tissue before single-cell analysis is challenging because no effective standardized pipelines are available. Fourth, the current warm cell-dissociation protocols may damage glomerular cells and induce transcriptional artifacts, which can be minimized by using cold dissociation techniques at the cost of less efficient cell dissociation. Finally, snRNA-seq methods may be superior to scRNA-seq in isolating glomerular cells; however, the efficacy of snRNA-seq on core needle biopsy specimens remains to be proven. The field of single-cell omics is rapidly evolving, and the integration of these techniques in multiomics assays will undoubtedly create new insights in the complex pathophysiology of glomerular diseases.
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Affiliation(s)
- Dries Deleersnijder
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology, Rega Institute, KU Leuven, Leuven, Belgium,Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
| | - Jasper Callemeyn
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium,Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Ingrid Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium,Vlaams Instituut voor Biotechnologie Center for Cancer Biology, Leuven, Belgium
| | - Maarten Naesens
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium,Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Amaryllis H. Van Craenenbroeck
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium,Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium,Vlaams Instituut voor Biotechnologie Center for Cancer Biology, Leuven, Belgium
| | - Ben Sprangers
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology, Rega Institute, KU Leuven, Leuven, Belgium,Division of Nephrology, University Hospitals Leuven, Leuven, Belgium,Correspondence: Prof. Ben Sprangers, Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology (Rega Institute), KU Leuven, Herestraat 49, Leuven 3000, Belgium.
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42
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Srivastava SP, Srivastava R, Chand S, Goodwin JE. Coronavirus Disease (COVID)-19 and Diabetic Kidney Disease. Pharmaceuticals (Basel) 2021; 14:751. [PMID: 34451848 PMCID: PMC8398861 DOI: 10.3390/ph14080751] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/17/2021] [Accepted: 07/26/2021] [Indexed: 01/08/2023] Open
Abstract
The present review describes COVID-19 severity in diabetes and diabetic kidney disease. We discuss the crucial effect of COVID-19-associated cytokine storm and linked injuries and associated severe mesenchymal activation in tubular epithelial cells, endothelial cells, and macrophages that influence neighboring cell homeostasis, resulting in severe proteinuria and organ fibrosis in diabetes. Altered microRNA expression disrupts cellular homeostasis and the renin-angiotensin-system, targets reno-protective signaling proteins, such as angiotensin-converting enzyme 2 (ACE2) and MAS1 receptor (MAS), and facilitates viral entry and replication in kidney cells. COVID-19-associated endotheliopathy that interacts with other cell types, such as neutrophils, platelets, and macrophages, is one factor that accelerates prethrombotic reactions and thrombus formation, resulting in organ failures in diabetes. Apart from targeting vital signaling through ACE2 and MAS, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are also associated with higher profibrotic dipeptidyl transferase-4 (DPP-4)-mediated mechanisms and suppression of AMP-activated protein kinase (AMPK) activation in kidney cells. Lowered DPP-4 levels and restoration of AMPK levels are organ-protective, suggesting a pathogenic role of DPP-4 and a protective role of AMPK in diabetic COVID-19 patients. In addition to standard care provided to COVID-19 patients, we urgently need novel drug therapies that support the stability and function of both organs and cell types in diabetes.
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Affiliation(s)
- Swayam Prakash Srivastava
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Rohit Srivastava
- Laboratory of Medical Transcriptomics, Department of Endocrinology, Nephrology Services, Hadassah Hebrew-University Medical Center, Jerusalem 91905, Israel;
| | - Subhash Chand
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Julie E. Goodwin
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06511, USA
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43
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Mourad D, Azar NS, Azar ST. Diabetic Nephropathy and COVID-19: The Potential Role of Immune Actors. Int J Mol Sci 2021; 22:ijms22157762. [PMID: 34360529 PMCID: PMC8346171 DOI: 10.3390/ijms22157762] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/19/2021] [Accepted: 07/01/2021] [Indexed: 12/17/2022] Open
Abstract
Nowadays, type II diabetes mellitus, more specifically ensuing diabetic nephropathy, and severe COVID-19 disease are known to be closely associated. The exact mechanisms behind this association are less known. An implication for the angiotensin-converting enzyme 2 remains controversial. Some researchers have started looking into other potential actors, such as neuropilin-1, mitochondrial glutathione, vitamin D, and DPP4. In particular, neuropilin-1 seems to play an important role in the underlying mechanism linking COVID-19 and diabetic nephropathy. We suggest, based on the findings in this review, that its up-regulation in the diabetic kidney facilitates viral entry in this tissue, and that the engagement of both processes leads to a depletion of neuropilin-1, which was demonstrated to be strongly associated with the pathogenesis of DN. More studies are needed to confirm this hypothesis, and research should be directed towards elucidating the potential roles of all these suggested actors and eventually discovering new therapeutic strategies that could reduce the burden of COVID-19 in patients with diabetic nephropathy.
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Affiliation(s)
- Diane Mourad
- Department of Internal Medicine, Endocrinology Division, Faculty of Medicine and Medical Center, American University of Beirut, Beirut 11-0236, Lebanon;
| | - Nadim S. Azar
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine and Medical Center, American University of Beirut, Beirut 11-0236, Lebanon;
| | - Sami T. Azar
- Department of Internal Medicine, Endocrinology Division, Faculty of Medicine and Medical Center, American University of Beirut, Beirut 11-0236, Lebanon;
- Endocrinology, Diabetes and Metabolism Division, American University of Beirut Medical Center, Beirut 11-0236, Lebanon
- Correspondence: ; Tel.: +961-323-4250
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44
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Morgan S, Malatras A, Duguez S, Duddy W. Optimized Molecular Interaction Networks for the Study of Skeletal Muscle. J Neuromuscul Dis 2021; 8:S223-S239. [PMID: 34308911 DOI: 10.3233/jnd-210680] [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: 11/15/2022]
Abstract
BACKGROUND Molecular interaction networks (MINs) aim to capture the complex relationships between interacting molecules within a biological system. MINs can be constructed from existing knowledge of molecular functional associations, such as protein-protein binding interactions (PPI) or gene co-expression, and these different sources may be combined into a single MIN. A given MIN may be more or less optimal in its representation of the important functional relationships of molecules in a tissue. OBJECTIVE The aim of this study was to establish whether a combined MIN derived from different types of functional association could better capture muscle-relevant biology compared to its constituent single-source MINs. METHODS MINs were constructed from functional association databases for both protein-binding and gene co-expression. The networks were then compared based on the capture of muscle-relevant genes and gene ontology (GO) terms, tested in two different ways using established biological network clustering algorithms. The top performing MINs were combined to test whether an optimal MIN for skeletal muscle could be constructed. RESULTS The STRING PPI network was the best performing single-source MIN among those tested. Combining STRING with interactions from either the MyoMiner or CoXPRESSdb gene co-expression sources resulted in a combined network with improved performance relative to its constituent networks. CONCLUSION MINs constructed from multiple types of functional association can better represent the functional relationships of molecules in a given tissue. Such networks may be used to improve the analysis and interpretation of functional genomics data in the study of skeletal muscle and neuromuscular diseases. Networks and clusters described by this study, including the combinations of STRING with MyoMiner or with CoXPRESSdb, are available for download from https://www.sys-myo.com/myominer/download.php.
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Affiliation(s)
- Stephen Morgan
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, Northern Ireland, UK
| | - Apostolos Malatras
- Department of Biological Sciences, Molecular Medicine Research Center, University of Cyprus, University Avenue, Nicosia, Cyprus
| | - Stephanie Duguez
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, Northern Ireland, UK
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, Northern Ireland, UK
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45
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Deleersnijder D, Van Craenenbroeck AH, Sprangers B. Deconvolution of Focal Segmental Glomerulosclerosis Pathophysiology Using Transcriptomics Techniques. GLOMERULAR DISEASES 2021; 1:265-276. [PMID: 36751384 PMCID: PMC9677714 DOI: 10.1159/000518404] [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: 04/23/2021] [Accepted: 07/08/2021] [Indexed: 11/19/2022]
Abstract
Background Focal segmental glomerulosclerosis is a histopathological pattern of renal injury and comprises a heterogeneous group of clinical conditions with different pathophysiology, clinical course, prognosis, and treatment. Nevertheless, subtype differentiation in clinical practice often remains challenging, and we currently lack reliable diagnostic, prognostic, and therapeutic biomarkers. The advent of new transcriptomics techniques in kidney research poses great potential in the identification of gene expression biomarkers that can be applied in clinical practice. Summary Transcriptomics techniques have been completely revolutionized in the last 2 decades, with the evolution from low-throughput reverse-transcription polymerase chain reaction and in situ hybridization techniques to microarrays and next-generation sequencing techniques, including RNA-sequencing and single-cell transcriptomics. The integration of human gene expression profiles with functional in vitro and in vivo experiments provides a deeper mechanistic insight into the candidate genes, which enable the development of novel-targeted therapies. The correlation of gene expression profiles with clinical outcomes of large patient cohorts allows for the development of clinically applicable biomarkers that can aid in diagnosis and predict prognosis and therapy response. Finally, the integration of transcriptomics with other "omics" modalities creates a holistic view on disease pathophysiology. Key Messages New transcriptomics techniques allow high-throughput gene expression profiling of patients with focal segmental glomerulosclerosis (FSGS). The integration with clinical outcomes and fundamental mechanistic studies enables the discovery of new clinically useful biomarkers that will finally improve the clinical outcome of patients with FSGS.
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Affiliation(s)
- Dries Deleersnijder
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology, Rega Institute, KU Leuven, Leuven, Belgium,Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
| | - Amaryllis H. Van Craenenbroeck
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium,Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Ben Sprangers
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology, Rega Institute, KU Leuven, Leuven, Belgium,Division of Nephrology, University Hospitals Leuven, Leuven, Belgium,*Ben Sprangers,
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46
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Lin H, Ma X, Xiao F, Su H, Shi Y, Liu Y, Song L, Zhang Z, Zhang C, Peng H. Identification of a special cell type as a determinant of the kidney tropism of SARS-CoV-2. FEBS J 2021; 288:5163-5178. [PMID: 34228902 PMCID: PMC8420455 DOI: 10.1111/febs.16114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/09/2021] [Accepted: 07/06/2021] [Indexed: 12/01/2022]
Abstract
The kidney tropism of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has been well‐validated clinically and often leads to various forms of renal damage in coronavirus disease‐2019 (COVID‐19) patients. However, the underlying mechanisms and diagnostic approaches remain to be determined. We interrogated the expression of virus‐related host factors in single‐cell RNA sequencing (scRNA‐seq) datasets of normal human kidneys and kidneys with pre‐existing diseases and validated the results with urinary proteomics of COVID‐19 patients and healthy individuals. We also assessed the effects of genetic variants on kidney susceptibility using expression quantitative trait loci (eQTLs) databases. We identified a subtype of tubular cells, which we named PT‐3 cells, as being vulnerable to SARS‐CoV‐2 infections in the kidneys. PT‐3 cells were enriched in viral entry factors and replication and assembly machinery but lacked antiviral restriction factors. Immunohistochemistry confirmed positive staining of PT‐3 cell marker SCL36A2 on kidney sections from COVID‐19 patients. Urinary proteomic analyses of COVID‐19 patients revealed that markers of PT‐3 cells were significantly increased, along with elevated viral receptor angiotensin‐converting enzyme 2. We further found that the proportion of PT‐3 cells increased in diabetic nephropathy but decreased in kidney allografts and lupus nephropathy, suggesting that kidney susceptibility varied among these diseases. We finally identified several eQTLs that regulate the expression of host factors in kidney cells. PT‐3 cells may represent a key determinant for the kidney tropism of SARS‐CoV‐2, and detection of PT‐3 cells may be used to assess the risk of renal infection during COVID‐19.
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Affiliation(s)
- Hongchun Lin
- Nephrology Division, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xinxin Ma
- Nephrology Division, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Fang Xiao
- Department of Cadres Medical Care and Geriatrics, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hua Su
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaling Shi
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yuntao Liu
- Department of Emergency, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, China.,Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, China
| | - Lan Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeOmics, China
| | - Zhongde Zhang
- Department of Emergency, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, China.,Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, China
| | - Chun Zhang
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Peng
- Nephrology Division, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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Sherman EJ, Mirabelli C, Tang VT, Khan TG, Kennedy AA, Graham SE, Willer CJ, Tai AW, Sexton JZ, Wobus CE, Emmer BT. Identification of ACE2 modifiers by CRISPR screening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.06.10.447768. [PMID: 34127970 PMCID: PMC8202422 DOI: 10.1101/2021.06.10.447768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
SARS-CoV-2 infection is initiated by binding of the viral spike protein to its receptor, ACE2, on the surface of host cells. ACE2 expression is heterogeneous both in vivo and in immortalized cell lines, but the molecular pathways that govern ACE2 expression remain unclear. We now report high-throughput CRISPR screens for functional modifiers of ACE2 surface abundance. We identified 35 genes whose disruption was associated with a change in the surface abundance of ACE2 in HuH7 cells. Enriched among these ACE2 regulators were established transcription factors, epigenetic regulators, and functional networks. We further characterized individual cell lines with disruption of SMAD4, EP300, PIAS1 , or BAMBI and found these genes to regulate ACE2 at the mRNA level and to influence cellular susceptibility to SARS-CoV-2 infection. Collectively, our findings clarify the host factors involved in SARS-CoV-2 entry and suggest potential targets for therapeutic development.
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48
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Menez S, Ju W, Menon R, Moledina DG, Thiessen Philbrook H, McArthur E, Jia Y, Obeid W, Mansour SG, Koyner JL, Shlipak MG, Coca SG, Garg AX, Bomback AS, Kellum JA, Kretzler M, Parikh CR. Urinary EGF and MCP-1 and risk of CKD after cardiac surgery. JCI Insight 2021; 6:147464. [PMID: 33974569 PMCID: PMC8262289 DOI: 10.1172/jci.insight.147464] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/05/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Assessment of chronic kidney disease (CKD) risk after acute kidney injury (AKI) is based on limited markers primarily reflecting glomerular function. We evaluated markers of cell integrity (EGF) and inflammation (monocyte chemoattractant protein-1, MCP-1) for predicting long-term kidney outcomes after cardiac surgery. METHODS We measured EGF and MCP-1 in postoperative urine samples from 865 adults who underwent cardiac surgery at 2 sites in Canada and the United States and assessed EGF and MCP-1’s associations with the composite outcome of CKD incidence or progression. We used single-cell RNA-Seq (scRNA-Seq) of AKI patient biopsies to perform transcriptomic analysis of programs corregulated with the associated genes. RESULTS Over a median (IQR) follow-up of 5.8 (4.2–7.1) years, 266 (30.8%) patients developed the composite CKD outcome. Postoperatively, higher levels of urinary EGF were protective and higher levels of MCP-1 were associated with the composite CKD outcome (adjusted HR 0.83, 95% CI 0.73–0.95 and 1.10, 95% CI 1.00–1.21, respectively). Intrarenal scRNA-Seq transcriptomes in patients with AKI-defined cell populations revealed concordant changes in EGF and MCP-1 levels and underlying molecular processes associated with loss of EGF expression and gain of CCL2 (encoding MCP-1) expression. CONCLUSION Urinary EGF and MCP-1 were each independently associated with CKD after cardiac surgery. These markers may serve as noninvasive indicators of tubular damage, supported by tissue transcriptomes, and provide an opportunity for novel interventions in cardiac surgery. TRIAL REGISTRATION ClinicalTrials.gov NCT00774137. FUNDING The NIH funded the TRIBE-AKI Consortium and Kidney Precision Medicine Project. Yale O’Brien Kidney Center, American Heart Association, Patterson Trust Fund, Dr. Adam Linton Chair in Kidney Health Analytics, Canadian Institutes of Health Research, ICES, Ontario Ministry of Health and Long-Term Care, Academic Medical Organization of Southwestern Ontario, Schulich School of Medicine & Dentistry, Western University, Lawson Health Research Institute, Chan Zuckerberg Initiative Human Cell Atlas Kidney Seed Network.
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Affiliation(s)
- Steven Menez
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Wenjun Ju
- Division of Nephrology, Department of Medicine, and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Rajasree Menon
- Division of Nephrology, Department of Medicine, and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Dennis G Moledina
- Section of Nephrology and.,Clinical and Translational Research Accelerator, Department of Internal Medicine, Yale University 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
| | | | - Yaqi Jia
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Wassim Obeid
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sherry G Mansour
- Section of Nephrology and.,Clinical and Translational Research Accelerator, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jay L Koyner
- Section of Nephrology, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Michael G Shlipak
- Kidney Health Research Collaborative and Division of General Internal Medicine, San Francisco Veterans Affairs Medical Center, University of California San Francisco, San Francisco, California, USA
| | - Steven G Coca
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Amit X Garg
- ICES, Ontario, Canada.,Division of Nephrology, Department of Medicine, and.,Department of Epidemiology and Biostatistics, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Andrew S Bomback
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - John A Kellum
- The Center for Critical Care Nephrology, Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Matthias Kretzler
- Division of Nephrology, Department of Medicine, and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Chirag R Parikh
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Du HX, Zhu JQ, Chen J, Zhou HF, Yang JH, Wan HT. Revealing the therapeutic targets and molecular mechanisms of emodin-treated coronavirus disease 2019 via a systematic study of network pharmacology. Aging (Albany NY) 2021; 13:14571-14589. [PMID: 34088885 PMCID: PMC8221358 DOI: 10.18632/aging.203098] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/13/2021] [Indexed: 04/30/2023]
Abstract
Emodin has shown pharmacological effects in the treatment of infection with severe acute respiratory syndrome coronavirus-2, which leads to coronavirus disease 2019 (COVID-19). Thus, we speculated that emodin may possess anti-COVID-19 activity. In this study, using bioinformatics databases, we screened and harvested the candidate genes or targets of emodin and COVID-19 prior to the determination of pharmacological targets and molecular mechanisms of emodin against COVID-19. We discovered core targets for the treatment of COVID-19, including mitogen-activated protein kinase 1 (MAPK1), tumor protein (TP53), tumor necrosis factor (TNF), caspase-3 (CASP3), epidermal growth factor receptor (EGFR), vascular endothelial growth factor A (VEGFA), interleukin 1B (IL1B), mitogen-activated protein kinase 14 (MAPK14), prostaglandin-endoperoxide synthase 2 (PTGS2), B-cell lymphoma-2-like protein 1 (BCL2L1), interleukin-8 (CXCL8), myeloid cell leukemia-1 (MCL1), and colony stimulating factor 2 (CSF2). The GO analysis of emodin against COVID-19 mainly included cytokine-mediated signaling pathway, response to lipopolysaccharide, response to molecule of bacterial origin, developmental process involved in reproduction, and reproductive structure development. The KEGG results exhibited that the molecular pathways mainly included IL-17 signaling pathway, AGE-RAGE signaling pathway in diabetic complications, TNF signaling pathway, pertussis, proteoglycans in cancer, pathways in cancer, MAPK signaling pathway, NOD-like receptor signaling pathway, NF-kappa B signaling pathway, etc. Also, molecular docking results revealed the docking capability between emodin and COVID-19 and the potential pharmacological activity of emodin against COVID-19. Taken together, these findings uncovered the targets and pharmacological mechanisms of emodin for treating COVID-19 and suggested that the vital targets might be used as biomarkers against COVID-19.
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Affiliation(s)
- Hai-Xia Du
- College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Jia-Qi Zhu
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Jing Chen
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Hui-Fen Zhou
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Jie-Hong Yang
- College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Hai-Tong Wan
- College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
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50
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Wei Y, Jiang Z. The evolution and future of diabetic kidney disease research: a bibliometric analysis. BMC Nephrol 2021; 22:158. [PMID: 33926393 PMCID: PMC8084262 DOI: 10.1186/s12882-021-02369-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/20/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Diabetic kidney disease (DKD) is one of the most important complications of diabetic mellitus. It is essential for nephrologists to understand the evolution and development trends of DKD. METHODS Based on the total cited numbers in the Web of Science Core Collection, which was searched through September 28th, 2020, we performed a bibliometric analysis of the top 100 most cited full-length original articles on the subject of DKD. The timespans, authors, contributions, subcategories, and topics of those 100 articles were analysed. In addition, the evolution of topics in DKD research was investigated. RESULTS There were 23,968 items under the subject of DKD in the Web of Science Core Collection. The top 100 cited articles, published from 1999 to 2017, were cited 38,855 times in total. Researchers from the USA contributed the most publications. The number of articles included in 'Experimental studies (EG)', 'Clinical studies (CS)', 'Epidemiological studies (ES)', and 'Pathological and pathophysiological studies (PP)' were 65, 26, 7, and 2, respectively. Among the 15 topics, the most popular topic is the renin-angiotensin-aldosterone system (RAAS), occurring in 26 articles, including 6 of the top 10 most cited articles. The evolution of topics reveals that the role of RAAS inhibitor is a continuous hotspot, and sodium-glucose cotransporter 2 (SGLT-2) inhibitor and glucagon-like peptide 1 (GLP-1) agonist are two renoprotective agents which represent novel therapeutic methods in DKD. In addition, the 26 clinical studies among the top 100 most cited articles were highlighted, as they help guide clinical practice to better serve patients. CONCLUSIONS This bibliometric analysis of the top 100 most cited articles revealed important studies, popular topics, and trends in DKD research to assist researchers in further understanding the subject.
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Affiliation(s)
- Yi Wei
- Department of Nephrology, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Er Heng Road, Guangzhou, 510655, China
| | - Zongpei Jiang
- Department of Nephrology, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Er Heng Road, Guangzhou, 510655, China.
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