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Manoharan J, Rana R, Kuenze G, Gupta D, Elwakiel A, Ambreen S, Wang H, Banerjee K, Zimmermann S, Singh K, Gupta A, Fatima S, Kretschmer S, Schaefer L, Zeng-Brouwers J, Schwab C, Al-Dabet MM, Gadi I, Altmann H, Koch T, Poitz DM, Baber R, Kohli S, Shahzad K, Geffers R, Lee-Kirsch MA, Kalinke U, Meiler J, Mackman N, Isermann B. Tissue factor binds to and inhibits interferon-α receptor 1 signaling. Immunity 2024; 57:68-85.e11. [PMID: 38141610 DOI: 10.1016/j.immuni.2023.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 08/02/2023] [Accepted: 11/28/2023] [Indexed: 12/25/2023]
Abstract
Tissue factor (TF), which is a member of the cytokine receptor family, promotes coagulation and coagulation-dependent inflammation. TF also exerts protective effects through unknown mechanisms. Here, we showed that TF bound to interferon-α receptor 1 (IFNAR1) and antagonized its signaling, preventing spontaneous sterile inflammation and maintaining immune homeostasis. Structural modeling and direct binding studies revealed binding of the TF C-terminal fibronectin III domain to IFNAR1, which restricted the expression of interferon-stimulated genes (ISGs). Podocyte-specific loss of TF in mice (PodΔF3) resulted in sterile renal inflammation, characterized by JAK/STAT signaling, proinflammatory cytokine expression, disrupted immune homeostasis, and glomerulopathy. Inhibiting IFNAR1 signaling or loss of Ifnar1 expression in podocytes attenuated these effects in PodΔF3 mice. As a heteromer, TF and IFNAR1 were both inactive, while dissociation of the TF-IFNAR1 heteromer promoted TF activity and IFNAR1 signaling. These data suggest that the TF-IFNAR1 heteromer is a molecular switch that controls thrombo-inflammation.
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Affiliation(s)
- Jayakumar Manoharan
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
| | - Rajiv Rana
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
| | - Georg Kuenze
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Dheerendra Gupta
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
| | - Ahmed Elwakiel
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
| | - Saira Ambreen
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
| | - Hongjie Wang
- Department of Cardiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kuheli Banerjee
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
| | - Silke Zimmermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
| | - Kunal Singh
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
| | - Anubhuti Gupta
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
| | - Sameen Fatima
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
| | - Stefanie Kretschmer
- Department of Pediatrics, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Liliana Schaefer
- Institute of Pharmacology and Toxicology, Goethe University, Frankfurt am Main, Germany
| | - Jinyang Zeng-Brouwers
- Institute of Pharmacology and Toxicology, Goethe University, Frankfurt am Main, Germany
| | - Constantin Schwab
- Tissue Bank of the National Center for Tumor Diseases, Heidelberg, Germany
| | - Moh'd Mohanad Al-Dabet
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
| | - Ihsan Gadi
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
| | - Heidi Altmann
- Dresden Integrated Liquid Biobank, Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany; Medical Department I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Thea Koch
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - David M Poitz
- Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Ronny Baber
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany; Leipzig Medical Biobank, Leipzig University, Leipzig, Germany
| | - Shrey Kohli
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
| | - Khurrum Shahzad
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
| | - Robert Geffers
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, 30625 Hannover, Germany
| | - Jens Meiler
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Nigel Mackman
- Division of Hematology, Department of Medicine, UNC Blood Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany.
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DiSabato DJ, Marion CM, Mifflin KA, Alfredo AN, Rodgers KA, Kigerl KA, Popovich PG, McTigue DM. System failure: Systemic inflammation following spinal cord injury. Eur J Immunol 2024; 54:e2250274. [PMID: 37822141 PMCID: PMC10919103 DOI: 10.1002/eji.202250274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/13/2023]
Abstract
Spinal cord injury (SCI) affects hundreds of thousands of people in the United States, and while some effects of the injury are broadly recognized (deficits to locomotion, fine motor control, and quality of life), the systemic consequences of SCI are less well-known. The spinal cord regulates systemic immunological and visceral functions; this control is often disrupted by the injury, resulting in viscera including the gut, spleen, liver, bone marrow, and kidneys experiencing local tissue inflammation and physiological dysfunction. The extent of pathology depends on the injury level, severity, and time post-injury. In this review, we describe immunological and metabolic consequences of SCI across several organs. Since infection and metabolic disorders are primary reasons for reduced lifespan after SCI, it is imperative that research continues to focus on these deleterious aspects of SCI to improve life span and quality of life for individuals with SCI.
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Affiliation(s)
- Damon J. DiSabato
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Belford Center for Spinal Cord Injury, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Center for Brain and Spinal Cord Repair, The Ohio State University, Columbus, Ohio, USA
| | - Christina M. Marion
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Belford Center for Spinal Cord Injury, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Center for Brain and Spinal Cord Repair, The Ohio State University, Columbus, Ohio, USA
| | - Katherine A. Mifflin
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Belford Center for Spinal Cord Injury, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Center for Brain and Spinal Cord Repair, The Ohio State University, Columbus, Ohio, USA
| | - Anthony N. Alfredo
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Kyleigh A. Rodgers
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Kristina A. Kigerl
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Belford Center for Spinal Cord Injury, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Center for Brain and Spinal Cord Repair, The Ohio State University, Columbus, Ohio, USA
| | - Phillip G. Popovich
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Belford Center for Spinal Cord Injury, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Center for Brain and Spinal Cord Repair, The Ohio State University, Columbus, Ohio, USA
| | - Dana M. McTigue
- Department of Neuroscience, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Belford Center for Spinal Cord Injury, College of Medicine, The Ohio State University, Columbus, Ohio, USA
- Center for Brain and Spinal Cord Repair, The Ohio State University, Columbus, Ohio, USA
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Kobayashi H, Satake E, Murata Y, Otsuka H, Tsunemi A, Azuma M, Nakamura Y, Saito T, Abe M. Neuroblastoma suppressor of tumorigenicity 1 is associated with the severity of interstitial fibrosis and kidney function decline in IgA nephropathy. J Nephrol 2023; 36:2245-2256. [PMID: 37436574 DOI: 10.1007/s40620-023-01704-x] [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: 12/23/2022] [Accepted: 06/09/2023] [Indexed: 07/13/2023]
Abstract
INTRODUCTION Recently, circulating neuroblastoma suppressor of tumorigenicity 1 (NBL1) was shown to be strongly associated with kidney disease progression and histological lesions in patients with diabetic kidney disease. This study aimed to examine whether serum NBL1 level was also associated with kidney function and renal histological findings in patients with IgA nephropathy. METHODS We evaluated the levels of NBL1 in 109 patients with newly diagnosed biopsy-proven primary IgAN, between 2009 and 2018, at the Nihon University School of Medicine Itabashi Hospital, Tokyo, Japan, using serum obtained immediately before the renal biopsy, and examined the relationship between serum NBL1, renal function and renal histological findings assessed using the Oxford Classification (MEST score). Furthermore, we analyzed the association of serum NBL1 with kidney function decline over time in patients with IgA nephropathy who had follow-up data on the estimated glomerular filtration rate (n = 76). RESULTS Serum NBL1 levels in patients with newly diagnosed IgA nephropathy were elevated, as compared to those in healthy individuals (n = 93). Logistic regression analysis demonstrated that the serum NBL1 level was independently and significantly associated with tubular atrophy/interstitial fibrosis. Immunohistochemical staining revealed that NBL1 was highly expressed in the tubulointerstitium. Furthermore, Spearman's rank correlation identified a significant correlation between serum NBL1 level and estimated glomerular filtration rate slope. CONCLUSIONS The serum NBL1 level was significantly associated with the severity of renal interstitial fibrosis and kidney disease progression in patients with newly diagnosed IgA nephropathy. Thus, circulating NBL1 may serve as a good biomarker for evaluating renal interstitial fibrosis and the risk of kidney disease progression.
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Affiliation(s)
- Hiroki Kobayashi
- Department of Internal Medicine, Division of Nephrology, Hypertension, and Endocrinology, Nihon University School of Medicine, 30-1 Oyaguchi Kami-chou, Itabashi-ku, Tokyo, 173-8610, Japan.
| | - Eiichiro Satake
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Yusuke Murata
- Department of Internal Medicine, Division of Nephrology, Hypertension, and Endocrinology, Nihon University School of Medicine, 30-1 Oyaguchi Kami-chou, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Hiromasa Otsuka
- Department of Emergency Room and General Medicine, Ageo Central General Hospital, Saitama, Japan
- Department of Internal Medicine, Hatogaya Hospital, Saitama, Japan
| | - Akiko Tsunemi
- Department of Internal Medicine, Division of Nephrology, Hypertension, and Endocrinology, Nihon University School of Medicine, 30-1 Oyaguchi Kami-chou, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Masaki Azuma
- Department of Internal Medicine, Hatogaya Hospital, Saitama, Japan
| | - Yoshihiro Nakamura
- Department of Internal Medicine, Division of Nephrology, Hypertension, and Endocrinology, Nihon University School of Medicine, 30-1 Oyaguchi Kami-chou, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Tomoyuki Saito
- Department of Internal Medicine, Division of Nephrology, Hypertension, and Endocrinology, Nihon University School of Medicine, 30-1 Oyaguchi Kami-chou, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Masanori Abe
- Department of Internal Medicine, Division of Nephrology, Hypertension, and Endocrinology, Nihon University School of Medicine, 30-1 Oyaguchi Kami-chou, Itabashi-ku, Tokyo, 173-8610, Japan
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Schanz M, Kimmel M, Alscher MD, Amann K, Daniel C. TIMP-2 and IGFBP7 in human kidney biopsies in renal disease. Clin Kidney J 2023; 16:1434-1446. [PMID: 37664566 PMCID: PMC10468751 DOI: 10.1093/ckj/sfad010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Indexed: 09/05/2023] Open
Abstract
Background Tissue inhibitor of matrix metalloproteinase-2 (TIMP-2) and insulin-like growth factor binding protein 7 (IGFBP7) are markers of tubular stress and urinary [TIMP-2]*[IGFBP7] is an established biomarker for risk assessment of acute kidney injury. There are no studies of expression profiles or localization of these markers in human renal tissue with confirmed renal disease. Methods We analysed 37 kidney biopsies of patients with renal disease and 10 non-diseased control biopsies for TIMP-2 and IGFBP7 expression using immunohistochemistry. Changes in glomerular morphology were evaluated by a semi-quantitative glomerulosclerosis score (GSI) and tubular interstitial changes were graded by the tubular injury score (TSI) using periodic acid-Schiff-stained paraffin sections. Interstitial fibrosis and tubular atrophy (IF/TA) were graded according to the Banff classification. Urinary [TIMP-2]*[IGFBP7] was collected at the time of biopsy. Results TIMP-2 and IGFBP7 had significantly greater expression in kidney biopsies from patients with renal disease compared with control tissue, especially in the tubular compartment. Here, IGFBP7 was detected in proximal and distal tubules while TIMP-2 was predominantly localized in the collecting ducts. Renal injury significantly correlated with staining intensity for TIMP-2 and IGFBP7: GSI weakly correlated with glomerular TIMP-2 (r = 0.36) and IGFBP7 (r = 0.35) and TSI correlated with tubular TIMP-2 (r = 0.41) and IGFBP7 (r = 0.43). Urinary [TIMP-2]*[IGFBP7] correlated weakly with the histopathological damage score but not with glomerular and tubular expression. Conclusion Our findings underline the role of TIMP-2/IGFBP7 as an unspecific marker of renal injury that is already in use for early detection of acute kidney injury.
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Affiliation(s)
- Moritz Schanz
- Department of Internal Medicine, Division of General Internal Medicine and Nephrology, Robert-Bosch Hospital Stuttgart, Germany
| | - Martin Kimmel
- Department of Internal Medicine, Division of Nephrology, Hypertension and Autoimmune Disorders, Alb-Fils Kliniken, Göppingen, Germany
| | - Mark Dominik Alscher
- Department of Internal Medicine, Division of General Internal Medicine and Nephrology, Robert-Bosch Hospital Stuttgart, Germany
| | - Kerstin Amann
- Department of Nephropathology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christoph Daniel
- Department of Nephropathology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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Zanoni F, Abinti M, Belingheri M, Castellano G. Present and Future of IgA Nephropathy and Membranous Nephropathy Immune Monitoring: Insights from Molecular Studies. Int J Mol Sci 2023; 24:13134. [PMID: 37685941 PMCID: PMC10487514 DOI: 10.3390/ijms241713134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
IgA Nephropathy (IgAN) and Membranous Nephropathy (MN) are primary immune-mediated glomerular diseases with highly variable prognosis. Current guidelines recommend that greater immunologic activity and worse prognosis should guide towards the best treatment in an individualized approach. Nevertheless, proteinuria and glomerular filtration rate, the current gold standards for prognosis assessment and treatment guidance in primary glomerular diseases, may be altered with chronic damage and nephron scarring, conditions that are not related to immune activity. In recent years, thanks to the development of new molecular technologies, among them genome-wide genotyping, RNA sequencing techniques, and mass spectrometry, we have witnessed an outstanding improvement in understanding the pathogenesis of IgAN and MN. In addition, recent genome-wide association studies have suggested potential targets for immunomodulating agents, stressing the need for the identification of specific biomarkers of immune activity. In this work, we aim to review current evidence and recent progress, including the more recent use of omics techniques, in the identification of potential biomarkers for immune monitoring in IgAN and MN.
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Affiliation(s)
- Francesca Zanoni
- Division of Nephrology, Dialysis and Kidney Transplantation, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.A.); (M.B.); (G.C.)
| | - Matteo Abinti
- Division of Nephrology, Dialysis and Kidney Transplantation, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.A.); (M.B.); (G.C.)
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, 20122 Milan, Italy
| | - Mirco Belingheri
- Division of Nephrology, Dialysis and Kidney Transplantation, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.A.); (M.B.); (G.C.)
| | - Giuseppe Castellano
- Division of Nephrology, Dialysis and Kidney Transplantation, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.A.); (M.B.); (G.C.)
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, 20122 Milan, Italy
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Liu B, Jie X, Deng J, Zhang S, Lu F, Liu X, Zhang D. Bupi Yishen formula may prevent kidney fibrosis by modulating fatty acid metabolism in renal tubules. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 114:154767. [PMID: 37001297 DOI: 10.1016/j.phymed.2023.154767] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/19/2023] [Accepted: 03/12/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Bupi Yishen formula (BYF), a traditional Chinese herbal mixture, has demonstrated better effectiveness than Losartan in preserving renal function and preventing composite severe adverse outcomes in patients with advanced chronic kidney disease (CKD) in a recent randomized controlled trial. Prior studies have shown that BYF exerts anti-inflammatory and anti-fibrotic effects in the kidneys of CKD models, but the underlying mechanisms have not been fully elucidated. PURPOSE The aim of this study was to investigate the protective effects of BYF administration on profibrotic phenotypic changes in the kidney and to elucidate its fundamental mechanisms of action. METHODS Adenine and 5/6 nephrectomy rat models were administered with two doses of BYF extract (15 or 30 g/kg/d) by intragastric administration, and Losartan treatment was used as a positive control group. The relationship between BYF renoprotection and restoration of fatty acid dysregulation was examined using the two fibrosis models and TGFb1-induced human tubular HK2 cells. Transcriptomic profiles of the fibrotic kidneys obtained from adenine-induced CKD rats were used to identify the key mechanisms that are affected by BYF intervention. Human relevance and clinical implications were established by re-analysis of the microarray databases of CKD patients and immunostaining on human biopsy specimens. RESULTS BYF effectively prevented kidney histological damage and ameliorated renal malfunction in the adenine rat model of CKD. BYF robustly attenuated the significant increase in profibrotic and proapoptotic markers in fibrotic kidneys of adenine-induced CKD rats. Transcriptomic analyses of the fibrotic kidneys of the adenine rats identified fatty acid metabolism as the key dysregulated pathway affected by BYF prevention. BYF significantly reversed defective fatty acid oxidation (FAO) and the intracellular lipids accumulation in the fibrotic kidneys induced by 5/6 nephrectomy. Furthermore, BYF prevented dysfunctional fatty acid metabolism, which were associated with the significant improvement of TGFb1-induced profibrotic changes in HK2 human proximal tubular cells. Furthermore, analyses of kidney microarray databases and biopsy specimens of CKD patients suggested that FAO defect is common in CKD in humans. CONCLUSION Our exploratory study found that BYF may exert protective effects on renal fibrosis by regulating the fatty acid metabolism of renal tubular cells, which may be a key mechanism for preventing kidney fibrosis in CKD.
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Affiliation(s)
- Bingran Liu
- The Second Clinical College of Guangzhou University of Chinese Medicine, No.111 Dade Road, Guangzhou 510405, China; Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, No.111 Dade Road, Guangzhou 510120, China
| | - Xina Jie
- The Second Clinical College of Guangzhou University of Chinese Medicine, No.111 Dade Road, Guangzhou 510405, China; Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, No.111 Dade Road, Guangzhou 510120, China
| | - Jiankun Deng
- The Second Clinical College of Guangzhou University of Chinese Medicine, No.111 Dade Road, Guangzhou 510405, China
| | - Simeng Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, No.111 Dade Road, Guangzhou 510405, China
| | - Fuhua Lu
- The Second Clinical College of Guangzhou University of Chinese Medicine, No.111 Dade Road, Guangzhou 510405, China; Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, No.111 Dade Road, Guangzhou 510120, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xusheng Liu
- The Second Clinical College of Guangzhou University of Chinese Medicine, No.111 Dade Road, Guangzhou 510405, China; Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, No.111 Dade Road, Guangzhou 510120, China.
| | - Difei Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, No.111 Dade Road, Guangzhou 510405, China; Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, No.111 Dade Road, Guangzhou 510120, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, China.
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7
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Mucha K, Pac M, Pączek L. Omics are Getting Us Closer to Understanding IgA Nephropathy. Arch Immunol Ther Exp (Warsz) 2023; 71:12. [PMID: 37060455 PMCID: PMC10105675 DOI: 10.1007/s00005-023-00677-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 03/02/2023] [Indexed: 04/16/2023]
Abstract
During the last decade, thanks to omics technologies, new light has been shed on the pathogenesis of many diseases. Genomics, epigenomics, transcriptomics, and proteomics have helped to provide a better understanding of the origin and heterogeneity of several diseases. However, the risk factors for most autoimmune diseases remain unknown. The successes and pitfalls of omics have also been observed in nephrology, including immunoglobulin A nephropathy (IgAN), the most common form of glomerulonephritis and a principal cause of end-stage renal disease worldwide. Unfortunately, the immense progress in basic research has not yet been followed by the satisfactory development of a targeted treatment. Although, most omics studies describe changes in the immune system, there is still insufficient data to apply their results in the constantly evolving multi-hit pathogenesis model and thus do to provide a complete picture of the disease. Here, we describe recent findings regarding the pathophysiology of IgAN and link omics studies with immune system dysregulation. This review provides insights into specific IgAN markers, which may lead to the identification of potential targets for personalised treatment in the future.
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Affiliation(s)
- Krzysztof Mucha
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland.
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Michał Pac
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Leszek Pączek
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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Liu S, Zhao Y, Lu S, Zhang T, Lindenmeyer MT, Nair V, Gies SE, Wu G, Nelson RG, Czogalla J, Aypek H, Zielinski S, Liao Z, Schaper M, Fermin D, Cohen CD, Delic D, Krebs CF, Grahammer F, Wiech T, Kretzler M, Meyer-Schwesinger C, Bonn S, Huber TB. Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy. Genome Med 2023; 15:2. [PMID: 36627643 PMCID: PMC9830686 DOI: 10.1186/s13073-022-01145-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/24/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Diabetic nephropathy (DN) is the leading cause of end-stage renal disease, and histopathologic glomerular lesions are among the earliest structural alterations of DN. However, the signaling pathways that initiate these glomerular alterations are incompletely understood. METHODS To delineate the cellular and molecular basis for DN initiation, we performed single-cell and bulk RNA sequencing of renal cells from type 2 diabetes mice (BTBR ob/ob) at the early stage of DN. RESULTS Analysis of differentially expressed genes revealed glucose-independent responses in glomerular cell types. The gene regulatory network upstream of glomerular cell programs suggested the activation of mechanosensitive transcriptional pathway MRTF-SRF predominantly taking place in mesangial cells. Importantly, activation of MRTF-SRF transcriptional pathway was also identified in DN glomeruli in independent patient cohort datasets. Furthermore, ex vivo kidney perfusion suggested that the regulation of MRTF-SRF is a common mechanism in response to glomerular hyperfiltration. CONCLUSIONS Overall, our study presents a comprehensive single-cell transcriptomic landscape of early DN, highlighting mechanosensitive signaling pathways as novel targets of diabetic glomerulopathy.
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Affiliation(s)
- Shuya Liu
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Yu Zhao
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shun Lu
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tianran Zhang
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja T Lindenmeyer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Viji Nair
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Sydney E Gies
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guochao Wu
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | - Jan Czogalla
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hande Aypek
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephanie Zielinski
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Cellular and Integrative Physiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Zhouning Liao
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Melanie Schaper
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Damian Fermin
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Clemens D Cohen
- Nephrological Center, Medical Clinic and Policlinic IV, University of Munich, Munich, Germany
| | - Denis Delic
- Boehringer Ingelheim Pharma GmbH & Co. KG, Translational Medicine & Clinical Pharmacology, Birkendorferstr. 65, 88397, Biberach, Germany
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Christian F Krebs
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Division of Translational Immunology, III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Grahammer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Wiech
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Pathology, Nephropathology Section, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Kretzler
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Catherine Meyer-Schwesinger
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Cellular and Integrative Physiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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9
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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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10
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Lausecker F, Lennon R, Randles MJ. The kidney matrisome in health, aging, and disease. Kidney Int 2022; 102:1000-1012. [PMID: 35870643 DOI: 10.1016/j.kint.2022.06.029] [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: 01/21/2022] [Revised: 06/15/2022] [Accepted: 06/24/2022] [Indexed: 02/06/2023]
Abstract
Dysregulated extracellular matrix is the hallmark of fibrosis, and it has a profound impact on kidney function in disease. Furthermore, perturbation of matrix homeostasis is a feature of aging and is associated with declining kidney function. Understanding these dynamic processes, in the hope of developing therapies to combat matrix dysregulation, requires the integration of data acquired by both well-established and novel technologies. Owing to its complexity, the extracellular proteome, or matrisome, still holds many secrets and has great potential for the identification of clinical biomarkers and drug targets. The molecular resolution of matrix composition during aging and disease has been illuminated by cutting-edge mass spectrometry-based proteomics in recent years, but there remain key questions about the mechanisms that drive altered matrix composition. Basement membrane components are particularly important in the context of kidney function; and data from proteomic studies suggest that switches between basement membrane and interstitial matrix proteins are likely to contribute to organ dysfunction during aging and disease. Understanding the impact of such changes on physical properties of the matrix, and the subsequent cellular response to altered stiffness and viscoelasticity, is of critical importance. Likewise, the comparison of proteomic data sets from multiple organs is required to identify common matrix biomarkers and shared pathways for therapeutic intervention. Coupled with single-cell transcriptomics, there is the potential to identify the cellular origin of matrix changes, which could enable cell-targeted therapy. This review provides a contemporary perspective of the complex kidney matrisome and draws comparison to altered matrix in heart and liver disease.
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Affiliation(s)
- Franziska Lausecker
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK; Department of Paediatric Nephrology, Royal Manchester Children's Hospital, Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Michael J Randles
- Chester Medical School, Faculty of Medicine and Life Sciences, University of Chester, Chester, UK.
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11
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Identification of key candidate genes for IgA nephropathy using machine learning and statistics based bioinformatics models. Sci Rep 2022; 12:13963. [PMID: 35978028 PMCID: PMC9385868 DOI: 10.1038/s41598-022-18273-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/08/2022] [Indexed: 11/08/2022] Open
Abstract
Immunoglobulin-A-nephropathy (IgAN) is a kidney disease caused by the accumulation of IgAN deposits in the kidneys, which causes inflammation and damage to the kidney tissues. Various bioinformatics analysis-based approaches are widely used to predict novel candidate genes and pathways associated with IgAN. However, there is still some scope to clearly explore the molecular mechanisms and causes of IgAN development and progression. Therefore, the present study aimed to identify key candidate genes for IgAN using machine learning (ML) and statistics-based bioinformatics models. First, differentially expressed genes (DEGs) were identified using limma, and then enrichment analysis was performed on DEGs using DAVID. Protein-protein interaction (PPI) was constructed using STRING and Cytoscape was used to determine hub genes based on connectivity and hub modules based on MCODE scores and their associated genes from DEGs. Furthermore, ML-based algorithms, namely support vector machine (SVM), least absolute shrinkage and selection operator (LASSO), and partial least square discriminant analysis (PLS-DA) were applied to identify the discriminative genes of IgAN from DEGs. Finally, the key candidate genes (FOS, JUN, EGR1, FOSB, and DUSP1) were identified as overlapping genes among the selected hub genes, hub module genes, and discriminative genes from SVM, LASSO, and PLS-DA, respectively which can be used for the diagnosis and treatment of IgAN.
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12
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Li B, Li S, Fan Y, Diao H, Ye S, Peng H, Chen W. Computational Analysis Reveals the Characteristics of Immune Cells in Glomerular and Tubulointerstitial Compartments in IgA Nephropathy Patients. Front Genet 2022; 13:838863. [PMID: 35601494 PMCID: PMC9116531 DOI: 10.3389/fgene.2022.838863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 04/06/2022] [Indexed: 01/20/2023] Open
Abstract
Objective: The commonalities and differences regarding immune states between glomerular and tubulointerstitial compartments of IgA nephropathy (IgAN) remains largely undetermined. We aim to perform bioinformatic analysis for providing a comprehensive insight into the characteristics of immune cells and associated molecular mechanisms in IgAN. Materials and Methods: We performed integrated bioinformatic analyses by using IgAN-related datasets from the Gene Expression Omnibus database. First, the differentially expressed genes (DEGs) were identified and subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Then, CIBERSORT was employed to determine the landscape of infiltrating immune cells in both glomerular and tubulointerstitial compartments of IgAN patients, followed by Pearson’s correlation analysis and principal component analysis (PCA). Finally, commonly shared DEGs between glomerular and tubulointerstitial entities were recognized, followed by correlation analyses to identify the dominant commonly shared DEGs associated with immune cell infiltration in IgAN. Results: GO and KEGG enrichment analyses showed apparently distinct biological processes in the glomerular and tubulointerstitial compartments of IgAN. In addition, CIBERSORT analyses revealed a clear trend of increasing proportions of M1 macrophage and M2 macrophage in the glomerular compartment while noticeably higher proportions of resting CD4+ memory T cells and M2 macrophages in the tubulointerstitial compartments. The PCA analyses showed that the varying composition of immune cells in both glomerular and tubulointerstitial entities was compelling to distinguish IgAN patients from healthy living controls. In addition, 21 commonly shared DEGs between glomerular and tubulointerstitial entities were recognized as key regulators in the pathogenesis of IgAN, among which the enhanced hemoglobin subunit beta (HBB) gene expression was found to be positively associated with M2 macrophage in the glomerular compartment and resting CD4+ memory T cells in the tubulointerstitial compartment. Most importantly, FBJ murine osteosarcoma viral oncogene homolog B (FOSB) gene deficiency was recognized as the dominant alteration in promoting M2 macrophage infiltration in the glomerular compartment of IgAN. Conclusion: The findings from our current study for the first time reveal commonalities and differences regarding immune states between glomerular and tubulointerstitial compartments, as well as decode the essential role of M2 macrophages and associated molecular patterns within the microenvironments of IgAN.
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Affiliation(s)
- Bin Li
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University), Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, China
| | - Suchun Li
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University), Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, China
| | - Yuting Fan
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University), Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, China
| | - Hui Diao
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University), Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, China
| | - Siyang Ye
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University), Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, China
| | - Huajing Peng
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University), Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, China
| | - Wei Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-Sen University), Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, China
- *Correspondence: Wei Chen,
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13
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Xu J, Shen X, Wei X, Ding J, Yuan J, Weng Z, He Y. Identification of blood-based key biomarker and immune infiltration in Immunoglobulin A nephropathy by comprehensive bioinformatics analysis and a cohort validation. J Transl Med 2022; 20:145. [PMID: 35351150 PMCID: PMC8966267 DOI: 10.1186/s12967-022-03330-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/03/2022] [Indexed: 12/28/2022] Open
Abstract
Abstract
Background
To identify the critical genes in the onset and progression of Immunoglobulin A nephropathy (IgAN) and to explore its immune cell infiltration feature.
Methods
Differentially expressed genes (DEGs) were firstly screened from 1 blood-derived dataset GSE73953 and a glomerulus derived dataset GSE93798 through limma analysis, overlap genes omitting and weighted gene correlation network analysis (WGCNA) and further reduced according to expression pattern and correlation with the clinical features: eGFR and proteinuria, followed by external validation using the GSE37460 dataset and an IgAN cohort. In addition, the CIBERSORT tool for immune cell infiltration analysis, ceRNA network construction and Connectivity Map (CMAP) were also performed.
Results
A total of 195 DEGs were found, and among them, 3 upregulated (ORMDL2, NRP1, and COL4A1) and 3 downregulated genes (ST13, HSPA8 and PKP4) are verified to correlate clinically, and finally ORMDL2, NRP1 and COL4A1 were validated in patient cohort and with the ability of IgAN discrimination (highest AUC was COL4A1: 97.14%). The immune cell infiltration results revealed that significant differences could be found on resting memory CD4 T cells, activated NK cells, and M2 macrophages between control and IgAN.
Conclusions
Our results demonstrated here that significantly upregulated DEGs: ORMDL2, NRP1 and COL4A1, could be served as the diagnostic marker for IgAN, and dysregulated immune cell infiltration hinted possible the immune system intervention point in the setting of IgAN.
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14
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Clr-f expression regulates kidney immune and metabolic homeostasis. Sci Rep 2022; 12:4834. [PMID: 35318366 PMCID: PMC8940912 DOI: 10.1038/s41598-022-08547-9] [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: 11/19/2021] [Accepted: 03/09/2022] [Indexed: 11/25/2022] Open
Abstract
The C-type lectin-related protein, Clr-f, encoded by Clec2h in the mouse NK gene complex (NKC), is a member of a family of immune regulatory lectins that guide immune responses at distinct tissues of the body. Clr-f is highly expressed in the kidney; however, its activity in this organ is unknown. To assess the requirement for Clr-f in kidney health and function, we generated a Clr-f-deficient mouse (Clr-f−/−) by targeted deletions in the Clec2h gene. Mice lacking Clr-f exhibited glomerular and tubular lesions, immunoglobulin and C3 complement protein renal deposits, and significant abdominal and ectopic lipid accumulation. Whole kidney transcriptional profile analysis of Clr-f−/− mice at 7, 13, and 24 weeks of age revealed a dynamic dysregulation in lipid metabolic processes, stress responses, and inflammatory mediators. Examination of the immune contribution to the pathologies of Clr-f−/− mouse kidneys identified elevated IL-12 and IFNγ in cells of the tubulointerstitium, and an infiltrating population of neutrophils and T and B lymphocytes. The presence of these insults in a Rag1−/−Clr-f−/− background reveals that Clr-f−/− mice are susceptible to a T and B lymphocyte-independent renal pathogenesis. Our data reveal a role for Clr-f in the maintenance of kidney immune and metabolic homeostasis.
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15
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Villalvazo P, Carriazo S, Martin-Cleary C, Ortiz A. Aguascalientes: one of the hottest chronic kidney disease (CKD) hotspots in Mexico and a CKD of unknown aetiology mystery to be solved. Clin Kidney J 2021; 14:2285-2294. [PMID: 34754425 PMCID: PMC8573004 DOI: 10.1093/ckj/sfab136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/05/2023] Open
Abstract
In a recent issue of Clinical Kidney Journal (CKJ), Gutierrez-Peña et al. reported a high incidence and prevalence of advanced chronic kidney disease (CKD) in Aguascalientes, Mexico. This contradicts Global Burden of Disease estimates, which should be updated. A key component of this high burden of CKD relates to young people ages 20-40 years in whom the cause of CKD was unknown [CKD of unknown aetiology (CKDu)]. The incidence of kidney replacement therapy in this age group in Aguascalientes is among the highest in the world, second only to Taiwan. However, high-altitude Aguascalientes, with a year-round average temperature of 19°C, does not fit the geography of other CKDu hotspots. Furthermore, kidney biopsies in young people showed a high prevalence of focal segmental glomerulosclerosis. Potential causes of CKDu in Aguascalientes include the genetic background (no evidence, although podocytopathy genes should be explored) and environmental factors. The highest prevalence of CKD was found in Calvillo, known for guava farming. Thus guava itself, known to contain bioactive, potentially nephrotoxic molecules and pesticides, should be explored. Additionally, there are reports of water sources in Aguascalientes contaminated with heavy metals and/or pesticides. These include fluoride (increased levels found in Calvillo drinking water) as well as naturally occurring arsenic, among others. Fluoride may accumulate in bone and cause kidney disease years later, and maternal exposure to excess fluoride may cause kidney disease in offspring. We propose a research agenda to clarify the cause of CKDu in Aguascalientes that should involve international funders. The need for urgent action to identify and stem the cause of the high incidence of CKD extends to other CKD hotspots in Mexico, including Tierra Blanca in Veracruz and Poncitlan in Jalisco.
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Affiliation(s)
| | - Sol Carriazo
- IIS-Fundacion Jimenez Diaz UAM and School of Medicine, UAM, Madrid, Spain
| | | | - Alberto Ortiz
- IIS-Fundacion Jimenez Diaz UAM and School of Medicine, UAM, Madrid, Spain
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16
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The molecular mechanisms of inflammation and scarring in the kidneys of immunoglobulin A nephropathy : Gene involvement in the mechanisms of inflammation and scarring in kidney biopsy of IgAN patients. Semin Immunopathol 2021; 43:691-705. [PMID: 34674036 PMCID: PMC8551145 DOI: 10.1007/s00281-021-00891-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/14/2021] [Indexed: 10/26/2022]
Abstract
Kidney biopsy is the cornerstone for the diagnosis of immunoglobulin A nephropathy (IgAN). The immunofluorescence technique evidences the IgA deposits in the glomeruli; the routine histology shows degree of active and chronic renal lesions. The spectrum of renal lesions is highly variable, ranging from minor or no detectable lesions to diffuse proliferative or crescentic lesions. Over the past three decades, renal transcriptomic studies have been performed on fresh or frozen renal tissue, and formalin-fixed paraffin-embedded kidney tissue specimens obtained from archival histological repositories. This paper aims to describe (1) the transcriptomic profiles of the kidney biopsy and (2) the potential urinary biomarkers that can be used to monitor the follow-up of IgAN patients. The use of quantitative Real-Time Polymerase Chain Reaction (qRT-PCR), microarrays and RNA-sequencing (RNA-seq) techniques on renal tissue and separated compartments of the nephron such as glomeruli and tubule-interstitium has clarified many aspects of the renal damage in IgAN. Recently, the introduction of the single-cell RNA-seq techniques has overcome the limitations of the previous methods, making that it is possible to study the whole renal tissue without the dissection of the nephron segments; it also allows better analysis of the cell-specific gene expression involved in cell differentiation. These gene products could represent effective candidates for urinary biomarkers for clinical decision making. Finally, some of these molecules may be the targets of old drugs, such as corticosteroids, renin-angiotensin-aldosterone blockers, and new drugs such as monoclonal antibodies. In the era of personalized medicine and precision therapy, high-throughput technologies may better characterize different renal patterns of IgAN and deliver targeted treatments to individual patients.
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17
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Martin CE, Jones N. ShcA expression in podocytes is dispensable for glomerular development but its upregulation is associated with kidney disease. Am J Transl Res 2021; 13:9874-9882. [PMID: 34540124 PMCID: PMC8430102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/18/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND ShcA (SHC1) is a phosphotyrosine adaptor protein which plays broad signaling roles within the cell. Systemic loss of ShcA during embryogenesis is lethal, while its aberrant expression contributes to disease. We recently demonstrated that ShcA is highly expressed during glomerular development and that it is upregulated within podocytes in experimental kidney injury and chronic kidney disease. The objective of this study was to analyze the in vivo role of ShcA in podocytes. METHODS We selectively deleted all three isoforms of ShcA from mouse kidney podocytes using the Cre/lox system driven by the podocyte-specific podocin promoter (Nphs2). Immunostaining of kidney sections was used to confirm ShcA deletion in podocytes. Coomassie blue staining of protein gels was used to detect urinary albumin. Light and electron microscopy were used to assess glomerular morphology. Transcript levels of SHC1 in human renal disease were assessed using the Nephroseq database. RESULTS Mice lacking podocyte ShcA were born at the expected Mendelian frequency and did not display overt renal impairment or changes in podocyte architecture beyond one year of age. In parallel, we correlated increased ShcA mRNA expression in the human kidney with proteinuria and reduced glomerular filtration rate. CONCLUSION Our studies reveal that ShcA is dispensable for normal kidney function, but its upregulation is associated with disease.
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Affiliation(s)
- Claire E Martin
- Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
| | - Nina Jones
- Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
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18
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Matías-García PR, Wilson R, Guo Q, Zaghlool SB, Eales JM, Xu X, Charchar FJ, Dormer J, Maalmi H, Schlosser P, Elhadad MA, Nano J, Sharma S, Peters A, Fornoni A, Mook-Kanamori DO, Winkelmann J, Danesh J, Di Angelantonio E, Ouwehand WH, Watkins NA, Roberts DJ, Petrera A, Graumann J, Koenig W, Hveem K, Jonasson C, Köttgen A, Butterworth A, Prunotto M, Hauck SM, Herder C, Suhre K, Gieger C, Tomaszewski M, Teumer A, Waldenberger M. Plasma Proteomics of Renal Function: A Transethnic Meta-Analysis and Mendelian Randomization Study. J Am Soc Nephrol 2021; 32:1747-1763. [PMID: 34135082 PMCID: PMC8425654 DOI: 10.1681/asn.2020071070] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 02/24/2021] [Accepted: 03/22/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Studies on the relationship between renal function and the human plasma proteome have identified several potential biomarkers. However, investigations have been conducted largely in European populations, and causality of the associations between plasma proteins and kidney function has never been addressed. METHODS A cross-sectional study of 993 plasma proteins among 2882 participants in four studies of European and admixed ancestries (KORA, INTERVAL, HUNT, QMDiab) identified transethnic associations between eGFR/CKD and proteomic biomarkers. For the replicated associations, two-sample bidirectional Mendelian randomization (MR) was used to investigate potential causal relationships. Publicly available datasets and transcriptomic data from independent studies were used to examine the association between gene expression in kidney tissue and eGFR. RESULTS In total, 57 plasma proteins were associated with eGFR, including one novel protein. Of these, 23 were additionally associated with CKD. The strongest inferred causal effect was the positive effect of eGFR on testican-2, in line with the known biological role of this protein and the expression of its protein-coding gene (SPOCK2) in renal tissue. We also observed suggestive evidence of an effect of melanoma inhibitory activity (MIA), carbonic anhydrase III, and cystatin-M on eGFR. CONCLUSIONS In a discovery-replication setting, we identified 57 proteins transethnically associated with eGFR. The revealed causal relationships are an important stepping stone in establishing testican-2 as a clinically relevant physiological marker of kidney disease progression, and point to additional proteins warranting further investigation.
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Affiliation(s)
- Pamela R. Matías-García
- Research Unit Molecular Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- TUM School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Cardiovascular Research, Munich, Germany
| | - Rory Wilson
- Research Unit Molecular Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
| | - Qi Guo
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Shaza B. Zaghlool
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - James M. Eales
- Division of Cardiovascular Sciences, University of Manchester, Manchester, United Kingdom
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, University of Manchester, Manchester, United Kingdom
| | - Fadi J. Charchar
- School of Health and Life Sciences, Federation University Australia, Ballarat, Australia
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- Department of Physiology, University of Melbourne, Melbourne, Australia
| | - John Dormer
- Department of Cellular Pathology, University Hospitals of Leicester National Health Service Trust, Leicester, United Kingdom
| | - Haifa Maalmi
- Institute for Clinical Diabetology, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Pascal Schlosser
- Department of Data-Driven Medicine, Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Mohamed A. Elhadad
- Research Unit Molecular Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research, Munich, Germany
| | - Jana Nano
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Sapna Sharma
- Research Unit Molecular Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research, Munich, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
| | - Alessia Fornoni
- Department of Medicine, Katz Family Division of Nephrology and Hypertension, University of Miami Miller School of Medicine, Miami, Florida
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Juliane Winkelmann
- Institute of Neurogenomics, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Neurogenetics and Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - John Danesh
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, United Kingdom
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, United Kingdom
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, United Kingdom
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, United Kingdom
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Emanuele Di Angelantonio
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, United Kingdom
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, United Kingdom
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, United Kingdom
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, United Kingdom
| | - Willem H. Ouwehand
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Nicholas A. Watkins
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, United Kingdom
| | - David J. Roberts
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, United Kingdom
- National Health Service Blood and Transplant Oxford Centre, Oxford, United Kingdom
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Agnese Petrera
- Research Unit Protein Science and Metabolomics and Proteomics Core Facility, Helmholtz Zentrum Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Graumann
- Scientific Service Group Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Max Planck Institute of Heart and Lung Research, Bad Nauheim, Germany
| | - Wolfgang Koenig
- German Center for Cardiovascular Research, Munich, Germany
- Klinik für Herz-Kreislauferkrankungen, Deutsches Herzzentrum München, Technical University of Munich, Munich, Germany
- Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm, Germany
| | - Kristian Hveem
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- Nord-Trøndelag Health Study HUNT Research Centre, Faculty of Medicine, Norwegian University of Science and Technology, Levanger, Norway
| | - Christian Jonasson
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- Nord-Trøndelag Health Study HUNT Research Centre, Faculty of Medicine, Norwegian University of Science and Technology, Levanger, Norway
| | - Anna Köttgen
- Department of Data-Driven Medicine, Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Adam Butterworth
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Marco Prunotto
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Stefanie M. Hauck
- Research Unit Protein Science and Metabolomics and Proteomics Core Facility, Helmholtz Zentrum Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Herder
- Institute for Clinical Diabetology, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research, München-Neuherberg, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Christian Gieger
- Research Unit Molecular Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research, Munich, Germany
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, University of Manchester, Manchester, United Kingdom
- Manchester Heart Centre and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Alexander Teumer
- Department SHIP/Clinical-Epidemiological Research, Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- German Center for Cardiovascular Research, partner site Greifswald, Greifswald, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research, Munich, Germany
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19
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Randles MJ, Lausecker F, Kong Q, Suleiman H, Reid G, Kolatsi-Joannou M, Davenport B, Tian P, Falcone S, Potter P, Van Agtmael T, Norman JT, Long DA, Humphries MJ, Miner JH, Lennon R. Identification of an Altered Matrix Signature in Kidney Aging and Disease. J Am Soc Nephrol 2021; 32:1713-1732. [PMID: 34049963 PMCID: PMC8425653 DOI: 10.1681/asn.2020101442] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Accumulation of extracellular matrix in organs and tissues is a feature of both aging and disease. In the kidney, glomerulosclerosis and tubulointerstitial fibrosis accompany the decline in function, which current therapies cannot address, leading to organ failure. Although histologic and ultrastructural patterns of excess matrix form the basis of human disease classifications, a comprehensive molecular resolution of abnormal matrix is lacking. METHODS Using mass spectrometry-based proteomics, we resolved matrix composition over age in mouse models of kidney disease. We compared the changes in mice with a global characterization of human kidneymatrix during aging and to existing kidney disease datasets to identify common molecular features. RESULTS Ultrastructural changes in basement membranes are associated with altered cell adhesion and metabolic processes and with distinct matrix proteomes during aging and kidney disease progression in mice. Within the altered matrix, basement membrane components (laminins, type IV collagen, type XVIII collagen) were reduced and interstitial matrix proteins (collagens I, III, VI, and XV; fibrinogens; and nephronectin) were increased, a pattern also seen in human kidney aging. Indeed, this signature of matrix proteins was consistently modulated across all age and disease comparisons, and the increase in interstitial matrix was also observed in human kidney disease datasets. CONCLUSIONS This study provides deep molecular resolution of matrix accumulation in kidney aging and disease, and identifies a common signature of proteins that provides insight into mechanisms of response to kidney injury and repair.
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Affiliation(s)
- Michael J. Randles
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Franziska Lausecker
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Qingyang Kong
- Department of Renal Medicine, University College London, London, United Kingdom
| | - Hani Suleiman
- Renal Division, Washington University School of Medicine, Saint Louis, Missouri
| | - Graeme Reid
- Department of Histopathology, Manchester Royal Infirmary, Manchester University Hospitals National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Maria Kolatsi-Joannou
- Developmental Biology and Cancer Programme, Great Ormond Institute of Child Health, University College London, London, United Kingdom
| | - Bernard Davenport
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Pinyuan Tian
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Sara Falcone
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Paul Potter
- Department Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Tom Van Agtmael
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jill T. Norman
- Department of Renal Medicine, University College London, London, United Kingdom
| | - David A. Long
- Developmental Biology and Cancer Programme, Great Ormond Institute of Child Health, University College London, London, United Kingdom
| | - Martin J. Humphries
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Jeffrey H. Miner
- Renal Division, Washington University School of Medicine, Saint Louis, Missouri
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom,Department of Paediatric Nephrology, Royal Manchester Children’s Hospital, Manchester University Hospitals National Health Service Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
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20
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Gene Expression as a Guide to the Development of Novel Therapies in Primary Glomerular Diseases. J Clin Med 2021; 10:jcm10112262. [PMID: 34073694 PMCID: PMC8197155 DOI: 10.3390/jcm10112262] [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: 04/07/2021] [Revised: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 11/17/2022] Open
Abstract
Despite improvements in understanding the pathogenic mechanisms of primary glomerular diseases, therapy still remains nonspecific. We sought to identify novel therapies targeting kidney-intrinsic injury of distinct primary glomerulonephritides through computational systems biology approaches. We defined the unique transcriptional landscape within kidneys from patients with focal segmental glomerulosclerosis (FSGS), minimal change disease (MCD), immunoglobulin A nephropathy (IgAN), membranous nephropathy (MN) and thin basement membrane nephropathy (TBMN). Differentially expressed genes were functionally annotated with enrichment analysis, and distinct biological processes and pathways implicated in each primary glomerular disease were uncovered. Finally, we identified novel drugs and small-molecule compounds that may reverse each glomerulonephritis phenotype, suggesting they should be further tested as precise therapy in primary glomerular diseases.
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21
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Zhou LT, Zhang ZJ, Cao JY, Chen H, Zhu YS, Wu X, Nawabi AQ, Liu X, Shan W, Zhang Y, Zhang XR, Xue J, Hu L, Wang SS, Wang L, Sun ZX. The unique molecular mechanism of diabetic nephropathy: a bioinformatics analysis of over 250 microarray datasets. Clin Kidney J 2021; 14:1626-1638. [PMID: 34084458 PMCID: PMC8162860 DOI: 10.1093/ckj/sfaa190] [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] [Received: 05/17/2020] [Accepted: 07/20/2020] [Indexed: 11/18/2022] Open
Abstract
Background/Aims Diabetic nephropathy (DN) is one of the main causes of end-stage kidney disease worldwide. Emerging studies have suggested that its pathogenesis is distinct from nondiabetic renal diseases in many aspects. However, it still lacks a comprehensive understanding of the unique molecular mechanism of DN. Methods A total of 255 Affymetrix U133 microarray datasets (Affymetrix, Santa Calra, CA, USA) of human glomerular and tubulointerstitial tissues were collected. The 22 215 Affymetrix identifiers shared by the Human Genome U133 Plus 2.0 and U133A Array were extracted to facilitate dataset pooling. Next, a linear model was constructed and the empirical Bayes method was used to select the differentially expressed genes (DEGs) of each kidney disease. Based on these DEG sets, the unique DEGs of DN were identified and further analyzed using gene ontology and pathway enrichment analysis. Finally, the protein–protein interaction networks (PINs) were constructed and hub genes were selected to further refine the results. Results A total of 129 and 1251 unique DEGs were identified in the diabetic glomerulus (upregulated n = 83 and downregulated n = 203) and the diabetic tubulointerstitium (upregulated n = 399 and downregulated n = 874), respectively. Enrichment analysis revealed that the DEGs in the diabetic glomerulus were significantly associated with the extracellular matrix, cell growth, regulation of blood coagulation, cholesterol homeostasis, intrinsic apoptotic signaling pathway and renal filtration cell differentiation. In the diabetic tubulointerstitium, the significantly enriched biological processes and pathways included metabolism, the advanced glycation end products–receptor for advanced glycation end products signaling pathway in diabetic complications, the epidermal growth factor receptor (EGFR) signaling pathway, the FoxO signaling pathway, autophagy and ferroptosis. By constructing PINs, several nodes, such as AGR2, CSNK2A1, EGFR and HSPD1, were identified as hub genes, which might play key roles in regulating the development of DN. Conclusions Our study not only reveals the unique molecular mechanism of DN but also provides a valuable resource for biomarker and therapeutic target discovery. Some of our findings are promising and should be explored in future work.
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Affiliation(s)
- Le-Ting Zhou
- Department of Nephrology, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, Jiangsu, China
| | - Zhi-Jian Zhang
- Department of Nephrology, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, Jiangsu, China
| | - Jing-Yuan Cao
- Nephrology Department, Taizhou People's Hospital, Fifth Affiliated Hospital to Nantong University, Taizhou, Jiangsu, China
| | - Hanzhi Chen
- Department of Nephrology, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, Jiangsu, China
| | - Yu-Shan Zhu
- Department of Nephrology, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, Jiangsu, China
| | - Xi Wu
- Department of Bioinformatics, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Abdul Qadir Nawabi
- School of Medicine, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
| | - Xiaobin Liu
- Department of Nephrology, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, Jiangsu, China
| | - Weiwei Shan
- Department of Nephrology, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, Jiangsu, China
| | - Yue Zhang
- Department of Nephrology, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, Jiangsu, China
| | - Xi-Ran Zhang
- Department of Nephrology, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, Jiangsu, China
| | - Jing Xue
- Department of Nephrology, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, Jiangsu, China
| | - Ling Hu
- Department of Nephrology, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, Jiangsu, China
| | - Si-Si Wang
- Department of Nephrology, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, Jiangsu, China
| | - Liang Wang
- Department of Nephrology, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, Jiangsu, China
| | - Zhu-Xing Sun
- Department of Nephrology, Nanjing Medical University Affiliated Wuxi People's Hospital, Wuxi, Jiangsu, China
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22
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Moldoveanu Z, Suzuki H, Reily C, Satake K, Novak L, Xu N, Huang ZQ, Knoppova B, Khan A, Hall S, Yanagawa H, Brown R, Winstead CJ, O'Quinn DB, Weinmann A, Gharavi AG, Kiryluk K, Julian BA, Weaver CT, Suzuki Y, Novak J. Experimental evidence of pathogenic role of IgG autoantibodies in IgA nephropathy. J Autoimmun 2021; 118:102593. [PMID: 33508637 DOI: 10.1016/j.jaut.2021.102593] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 01/13/2023]
Abstract
BACKGROUND IgA nephropathy is thought to be an autoimmune disease wherein galactose-deficient IgA1 (Gd-IgA1) is recognized by IgG autoantibodies, resulting in formation and renal accumulation of nephritogenic immune complexes. Although this hypothesis is supported by recent findings that, in renal immunodeposits of IgA nephropathy patients, IgG is enriched for Gd-IgA1-specific autoantibodies, experimental proof is still lacking. METHODS IgG isolated from sera of IgA nephropathy patients or produced as a recombinant IgG (rIgG) was mixed with human Gd-IgA1 to form immune complexes. IgG from healthy individuals served as a control. Nude and SCID mice were injected with human IgG and Gd-IgA1, in immune complexes or individually, and their presence in kidneys was ascertained by immunofluorescence. Pathologic changes in the glomeruli were evaluated by quantitative morphometry and exploratory transcriptomic profiling was performed by RNA-Seq. RESULTS Immunodeficient mice injected with Gd-IgA1 mixed with IgG autoantibodies from patients with IgA nephropathy, but not Gd-IgA1 mixed with IgG from healthy individuals, displayed IgA, IgG, and mouse complement C3 glomerular deposits and mesangioproliferative glomerular injury with hematuria and proteinuria. Un-complexed Gd-IgA1 or IgG did not induce pathological changes. Moreover, Gd-IgA1-rIgG immune complexes injected into immunodeficient mice induced histopathological changes characteristic of human disease. Exploratory transcriptome profiling of mouse kidney tissues indicated that these immune complexes altered gene expression of multiple pathways, in concordance with the changes observed in kidney biopsies of patients with IgA nephropathy. CONCLUSIONS This study provides the first in vivo evidence for a pathogenic role of IgG autoantibodies specific for Gd-IgA1 in the pathogenesis of IgA nephropathy.
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Affiliation(s)
| | - Hitoshi Suzuki
- University of Alabama at Birmingham, Birmingham, AL, USA; Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Colin Reily
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kenji Satake
- Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Lea Novak
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nuo Xu
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Atlas Khan
- Department of Medicine, Division of Nephrology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Stacy Hall
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hiroyuki Yanagawa
- Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Rhubell Brown
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Amy Weinmann
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ali G Gharavi
- Department of Medicine, Division of Nephrology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Bruce A Julian
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Casey T Weaver
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yusuke Suzuki
- Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Jan Novak
- University of Alabama at Birmingham, Birmingham, AL, USA.
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23
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Wu J, Lin Q, Li S, Shao X, Zhu X, Zhang M, Zhou W, Ni Z. Periostin Contributes to Immunoglobulin a Nephropathy by Promoting the Proliferation of Mesangial Cells: A Weighted Gene Correlation Network Analysis. Front Genet 2021; 11:595757. [PMID: 33488671 PMCID: PMC7817997 DOI: 10.3389/fgene.2020.595757] [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: 08/28/2020] [Accepted: 11/26/2020] [Indexed: 11/13/2022] Open
Abstract
Immunoglobulin A nephropathy (IgAN) is a known cause of end-stage kidney disease, but the pathogenesis and factors affecting prognosis are not fully understood. In the present study, we carried out weighted gene correlation network analysis (WGCNA) to identify hub genes related to the occurrence of IgAN and validated candidate genes in experiments using mouse mesangial cells (MMCs) and clinical specimens (kidney tissue from IgAN patients and healthy controls). We screened the GSE37460 and GSE104948 differentially expressed genes common to both datasets and identified periostin (POSTN) as one of the five key genes using the cytoHubba plugin of Cytoscape software and by receiver-operating characteristic curve analysis. The top 25% of genes in the GSE93798 dataset showing variable expression between IgAN and healthy tissue were assessed by WGCNA. The royalblue module in WGCNA was closely related to creatinine and estimated glomerular filtration rate (eGFR) in IgAN patients. POSTN had very high module membership and gene significance values for creatinine (0.82 and 0.66, respectively) and eGFR (0.82 and -0.67, respectively), indicating that it is a co-hub gene. In MMCs, POSTN was upregulated by transforming growth factor β1, and stimulation of MMCs with recombinant POSTN protein resulted in an increase in the level of proliferating cell nuclear antigen (PCNA) and a decrease in that of B cell lymphoma-associated X protein, which were accompanied by enhanced MMC proliferation. POSTN gene knockdown had the opposite effects. Immunohistochemical analysis of kidney tissue specimens showed that POSTN and PCNA levels were elevated, whereas the rate of apoptosis was reduced in IgAN patients relative to healthy controls. POSTN level in the kidney tissue of IgAN patients was positively correlated with creatinine level and negatively correlated with eGFR. Thus, POSTN promotes the proliferation of MCs to promote renal dysfunction in IgAN.
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Affiliation(s)
- Jingkui Wu
- Department of Nephrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qisheng Lin
- Department of Nephrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Shu Li
- Department of Nephrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xinghua Shao
- Department of Nephrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xuying Zhu
- Department of Nephrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Minfang Zhang
- Department of Nephrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wenyan Zhou
- Department of Nephrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhaohui Ni
- Department of Nephrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
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24
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Smyth LJ, Patterson CC, Swan EJ, Maxwell AP, McKnight AJ. DNA Methylation Associated With Diabetic Kidney Disease in Blood-Derived DNA. Front Cell Dev Biol 2020; 8:561907. [PMID: 33178681 PMCID: PMC7593403 DOI: 10.3389/fcell.2020.561907] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/15/2020] [Indexed: 12/23/2022] Open
Abstract
A subset of individuals with type 1 diabetes will develop diabetic kidney disease (DKD). DKD is heritable and large-scale genome-wide association studies have begun to identify genetic factors that influence DKD. Complementary to genetic factors, we know that a person’s epigenetic profile is also altered with DKD. This study reports analysis of DNA methylation, a major epigenetic feature, evaluating methylome-wide loci for association with DKD. Unique features (n = 485,577; 482,421 CpG probes) were evaluated in blood-derived DNA from carefully phenotyped White European individuals diagnosed with type 1 diabetes with (cases) or without (controls) DKD (n = 677 samples). Explicitly, 150 cases were compared to 100 controls using the 450K array, with subsequent analysis using data previously generated for a further 96 cases and 96 controls on the 27K array, and de novo methylation data generated for replication in 139 cases and 96 controls. Following stringent quality control, raw data were quantile normalized and beta values calculated to reflect the methylation status at each site. The difference in methylation status was evaluated between cases and controls; resultant P-values for array-based data were adjusted for multiple testing. Genes with significantly increased (hypermethylated) and/or decreased (hypomethylated) levels of DNA methylation were considered for biological relevance by functional enrichment analysis using KEGG pathways. Twenty-two loci demonstrated statistically significant fold changes associated with DKD and additional support for these associated loci was sought using independent samples derived from patients recruited with similar inclusion criteria. Markers associated with CCNL1 and ZNF187 genes are supported as differentially regulated loci (P < 10–8), with evidence also presented for AFF3, which has been identified from a meta-analysis and subsequent replication of genome-wide association studies. Further supporting evidence for differential gene expression in CCNL1 and ZNF187 is presented from kidney biopsy and blood-derived RNA in people with and without kidney disease from NephroSeq. Evidence confirming that methylation sites influence the development of DKD may aid risk prediction tools and stimulate research to identify epigenomic therapies which might be clinically useful for this disease.
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Affiliation(s)
- Laura J Smyth
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| | | | - Elizabeth J Swan
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| | - Alexander P Maxwell
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom.,Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom
| | - Amy Jayne McKnight
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
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25
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Park S, Yang SH, Jeong CW, Moon KC, Kim DK, Joo KW, Kim YS, Lee JW, Lee H. RNA-Seq profiling of microdissected glomeruli identifies potential biomarkers for human IgA nephropathy. Am J Physiol Renal Physiol 2020; 319:F809-F821. [PMID: 32954852 DOI: 10.1152/ajprenal.00037.2020] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Few studies have examined gene expression changes occurring in the glomeruli of IgA nephropathy (IgAN) using a sensitive transcriptomic profiling method such as RNA sequencing (RNA-Seq). We collected glomeruli from biopsy specimens from patients with IgAN with relatively preserved kidney function (estimated glomerular filtration rate ≥ 60 mL·min-1·1.73 m-2 and urine protein-to-creatinine ratio < 3 g/g) and from normal kidney cortexes by hand microdissection and performed RNA-Seq. Differentially expressed genes were identified, and gene ontology term annotation and pathway analysis were performed. Immunohistochemical labeling and primary mesangial cell cultures were performed to confirm the findings of RNA-Seq analysis. Fourteen patients with IgAN and ten controls were included in this study. Glomerulus-specific genes were highly abundant. Principal component analysis showed clear separation between the IgAN and control groups. There were 2,497 differentially expressed genes, of which 1,380 were upregulated and 1,117 were downregulated (false discovery rate < 0.01). The enriched gene ontology terms included motility/migration, protein/vesicle transport, and immune system, and kinase binding was the molecular function overrepresented in IgAN. B cell signaling, chemokine signal transduction, and Fcγ receptor-mediated phagocytosis were the canonical pathways overrepresented. In vitro experiments confirmed that spleen tyrosine kinase (SYK), reported as upregulated in the IgAN transcriptome, was also upregulated in glomeruli from an independent set of patients with IgAN and that treatment with patient-derived IgA1 increased the expression of SYK in mesangial cells. In conclusion, transcriptomic profiling of the IgAN glomerulus provides insights in the intraglomerular pathophysiology of IgAN before it reaches profound kidney dysfunction. SYK may have a pathogenetic role in IgAN.
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Affiliation(s)
- Sehoon Park
- Department of Internal Medicine, Armed Forces Capital Hospital, Seoul, Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Seung Hee Yang
- Kidney Research Institute, Seoul National University, Seoul, Korea
| | - Chang Wook Jeong
- Department of Urology, Seoul National University Hospital, Seoul, Korea
| | - Kyung Chul Moon
- Department of Pathology, Seoul National University Hospital, Seoul, Korea
| | - Dong Ki Kim
- Kidney Research Institute, Seoul National University, Seoul, Korea.,Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Kwon Wook Joo
- Kidney Research Institute, Seoul National University, Seoul, Korea.,Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Yon Su Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.,Kidney Research Institute, Seoul National University, Seoul, Korea.,Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jae Wook Lee
- Kidney Research Institute, Seoul National University, Seoul, Korea.,Division of Nephrology, Department of Internal Medicine, National Cancer Center, Goyang, Korea
| | - Hajeong Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
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26
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Cox SN, Chiurlia S, Divella C, Rossini M, Serino G, Bonomini M, Sirolli V, Aiello FB, Zaza G, Squarzoni I, Gangemi C, Stangou M, Papagianni A, Haas M, Schena FP. Formalin-fixed paraffin-embedded renal biopsy tissues: an underexploited biospecimen resource for gene expression profiling in IgA nephropathy. Sci Rep 2020; 10:15164. [PMID: 32938960 PMCID: PMC7494931 DOI: 10.1038/s41598-020-72026-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 01/01/2023] Open
Abstract
Primary IgA nephropathy (IgAN) diagnosis is based on IgA-dominant glomerular deposits and histological scoring is done on formalin-fixed paraffin embedded tissue (FFPE) sections using the Oxford classification. Our aim was to use this underexploited resource to extract RNA and identify genes that characterize active (endocapillary–extracapillary proliferations) and chronic (tubulo-interstitial) renal lesions in total renal cortex. RNA was extracted from archival FFPE renal biopsies of 52 IgAN patients, 22 non-IgAN and normal renal tissue of 7 kidney living donors (KLD) as controls. Genome-wide gene expression profiles were obtained and biomarker identification was carried out comparing gene expression signatures a subset of IgAN patients with active (N = 8), and chronic (N = 12) renal lesions versus non-IgAN and KLD. Bioinformatic analysis identified transcripts for active (DEFA4,TNFAIP6,FAR2) and chronic (LTB,CXCL6, ITGAX) renal lesions that were validated by RT-PCR and IHC. Finally, two of them (TNFAIP6 for active and CXCL6 for chronic) were confirmed in the urine of an independent cohort of IgAN patients compared with non-IgAN patients and controls. We have integrated transcriptomics with histomorphological scores, identified specific gene expression changes using the invaluable repository of archival renal biopsies and discovered two urinary biomarkers that may be used for specific clinical decision making.
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Affiliation(s)
- Sharon Natasha Cox
- Schena Foundation, Research Center of Kidney Diseases, Strada Provinciale Valenzano-Casamassima Km. 3.00, 70100, Valenzano, Bari, Italy. .,Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy.
| | - Samantha Chiurlia
- Schena Foundation, Research Center of Kidney Diseases, Strada Provinciale Valenzano-Casamassima Km. 3.00, 70100, Valenzano, Bari, Italy
| | - Chiara Divella
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Michele Rossini
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Grazia Serino
- National Institute of Gastroenterology "S. de Bellis", Research Hospital, 70013, Castellana Grotte, Bari, Italy
| | - Mario Bonomini
- Department of Medicine and Aging Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Vittorio Sirolli
- Department of Medicine and Aging Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Francesca B Aiello
- Department of Medicine and Aging Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Gianluigi Zaza
- Renal Unit, Department of Medicine, University-Hospital of Verona, Verona, Italy
| | - Isabella Squarzoni
- Renal Unit, Department of Medicine, University-Hospital of Verona, Verona, Italy
| | - Concetta Gangemi
- Renal Unit, Department of Medicine, University-Hospital of Verona, Verona, Italy
| | - Maria Stangou
- Department of Nephrology, Hippokration General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Aikaterini Papagianni
- Department of Nephrology, Hippokration General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mark Haas
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Francesco Paolo Schena
- Schena Foundation, Research Center of Kidney Diseases, Strada Provinciale Valenzano-Casamassima Km. 3.00, 70100, Valenzano, Bari, Italy. .,Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy.
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27
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Taylor S, Whitfield M, Barratt J, Didangelos A. The Metalloproteinase ADAMTS5 Is Expressed by Interstitial Inflammatory Cells in IgA Nephropathy and Is Proteolytically Active on the Kidney Matrix. THE JOURNAL OF IMMUNOLOGY 2020; 205:2243-2254. [PMID: 32917786 PMCID: PMC7533710 DOI: 10.4049/jimmunol.2000448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/12/2020] [Indexed: 12/29/2022]
Abstract
ADAMTS5 is upregulated in human IgA nephropathy lesions. ADAMTS5 is related to inflammatory infiltrates in affected kidneys. ADAMTS5 digests kidney matrix proteins and cleaves complement C3 and fibronectin.
In IgA nephropathy (IgAN), IgA immune complexes are deposited in the mesangium and drive inflammation and extracellular matrix (ECM) remodelling. The functional links between IgA deposition, inflammation, and matrix remodelling are not well characterized. We recently performed urine liquid chromatography–tandem mass spectrometry proteomics and identified multiple ECM glycoproteins whose expression and function in IgAN is unclear. None of the urine glycoproteins was regulated in IgAN transcriptomics, indicating that tissue remodelling rather than increased expression might contribute to their presence in urine. To investigate this, we examined the IgAN expression profile of metalloproteinases, enzymes involved in the remodelling of ECM proteins, and noted that the proteoglycanase ADAMTS5 was upregulated in IgAN kidneys. ADAMTS5 accumulated in areas of inflammation, and ADAMTS5+ cells were seen in the tubulointerstitium and glomeruli. The enzyme was expressed by CD64+ cells and its expression was increased by IL-1 and LPS. Analysis of myeloid cell transcriptomics revealed that ADAMTS5 is enriched in human classical monocytes. ADAMTS5+ cells were present in areas of matrix remodelling and associated with ECM proteins lumican, versican, and collagen-4. Liquid chromatography–tandem mass spectrometry proteomics of kidney explants digested with ADAMTS5, identified multiple kidney proteins affected by ADAMTS5 and revealed specific proteolysis of complement C3 and fibronectin associated with IgA on immune complexes. ADAMTS5 processing of immune complex proteins reduced binding to cultured mesangial cells. ADAMTS5 is associated with interstitial inflammatory cells in IgAN and other kidney lesions and fragments relevant extracellular proteins. The proteolytic enzyme might be a new translational target relevant to inflammation and scarring in kidney disease.
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Affiliation(s)
- Scott Taylor
- Mayer IgA Nephropathy Laboratory, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Molly Whitfield
- Mayer IgA Nephropathy Laboratory, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Jonathan Barratt
- Mayer IgA Nephropathy Laboratory, University of Leicester, LE1 7RH Leicester, United Kingdom
| | - Athanasios Didangelos
- Mayer IgA Nephropathy Laboratory, University of Leicester, LE1 7RH Leicester, United Kingdom
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28
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Schena FP, Serino G, Sallustio F, Falchi M, Cox SN. Omics studies for comprehensive understanding of immunoglobulin A nephropathy: state-of-the-art and future directions. Nephrol Dial Transplant 2019; 33:2101-2112. [PMID: 29905852 DOI: 10.1093/ndt/gfy130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/17/2018] [Indexed: 12/11/2022] Open
Abstract
Immunoglobulin A nephropathy (IgAN) is the most common worldwide primary glomerulonephritis with a strong autoimmune component. The disease shows variability in both clinical phenotypes and endpoints and can be potentially subdivided into more homogeneous subtypes through the identification of specific molecular biomarkers. This review focuses on the role of omics in driving the identification of potential molecular subtypes of the disease through the integration of multilevel data from genomics, transcriptomics, epigenomics, proteomics and metabolomics. First, the identification of molecular biomarkers, including mapping of the full spectrum of common and rare IgAN risk alleles, could permit a more precise stratification of IgAN patients. Second, the analysis of transcriptomic patterns and their modulation by epigenetic factors like microRNAs has the potential to increase our understanding in the pathogenic mechanisms of the disease. Third, the specificity of urinary proteomic and metabolomic signatures and the understanding of their functional relevance may contribute to the development of new non-invasive biomarkers for a better molecular characterization of the renal damage and its follow-up. All these approaches can give information for targeted therapeutic decisions and will support novel clinical decision making. In conclusion, we offer a framework of omic studies and outline barriers and potential solutions that should be used for improving the diagnosis and treatment of the disease. The ongoing decade is exploiting novel high-throughput molecular technologies and computational analyses for improving the diagnosis (precision nephrology) and treatment (personalized therapy) of the IgAN subtypes.
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Affiliation(s)
- Francesco Paolo Schena
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy.,Schena Foundation, Valenzano, Bari, Italy
| | - Grazia Serino
- National Institute of Gastroenterology 'S. de Bellis', Research Hospital, Castellana Grotte, Bari, Italy
| | - Fabio Sallustio
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sharon N Cox
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy.,Schena Foundation, Valenzano, Bari, Italy
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29
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Brittain AL, Kopchick JJ. A review of renal GH/IGF1 family gene expression in chronic kidney diseases. Growth Horm IGF Res 2019; 48-49:1-4. [PMID: 31352157 DOI: 10.1016/j.ghir.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/07/2019] [Accepted: 07/15/2019] [Indexed: 01/15/2023]
Abstract
Despite decades of study on the contribution of growth hormone (GH) to the development of kidney disease, there remains the question of the relative contribution of elevated levels of GH to kidney damage in humans, particularly in diabetic nephropathy occurring in type 1 patients. In this study, we reviewed several publicly available datasets to examine transcription of twelve genes associated with the GH/IGF1 axis in several types of human and rodent kidney diseases. Our analyses revealed downregulation of renal GHR and IGF1 gene expression in several different chronic human kidney diseases, including diabetic nephropathy, with general upregulation of IGFBP6 in the same tissues and diseases. These findings were generally supported by a review of studies in rodent models. In healthy and diseased human kidneys, increased GHR gene expression was associated with increases in glomerular filtration rate (GFR) and decreases in serum creatinine. IGFBP6 gene expression demonstrated the opposite clinical correlation. Our results suggest the kidney may exhibit GH insensitivity due to low GHR gene expression during most chronic kidney diseases.
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Affiliation(s)
- Alison L Brittain
- Edison Biotechnology Institute and Heritage College of Osteopathic Medicine, Ohio University, Konneker Research Center 206A, Athens, OH 45701, USA.
| | - John J Kopchick
- Edison Biotechnology Institute and Heritage College of Osteopathic Medicine, Ohio University, Konneker Research Center 206A, Athens, OH 45701, USA.
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30
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PKN1 kinase-negative knock-in mice develop splenomegaly and leukopenia at advanced age without obvious autoimmune-like phenotypes. Sci Rep 2019; 9:13977. [PMID: 31562379 PMCID: PMC6764976 DOI: 10.1038/s41598-019-50419-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/30/2019] [Indexed: 01/08/2023] Open
Abstract
Protein kinase N1 (PKN1) knockout (KO) mice spontaneously form germinal centers (GCs) and develop an autoimmune-like disease with age. Here, we investigated the function of PKN1 kinase activity in vivo using aged mice deficient in kinase activity resulting from the introduction of a point mutation (T778A) in the activation loop of the enzyme. PKN1[T778A] mice reached adulthood without external abnormalities; however, the average spleen size and weight of aged PKN1[T778A] mice increased significantly compared to aged wild type (WT) mice. Histologic examination and Southern blot analyses of spleens showed extramedullary hematopoiesis and/or lymphomagenesis in some cases, although without significantly different incidences between PKN1[T778A] and WT mice. Additionally, flow cytometry revealed increased numbers in B220+, CD3+, Gr1+ and CD193+ leukocytes in the spleen of aged PKN1[T778A] mice, whereas the number of lymphocytes, neutrophils, eosinophils, and monocytes was reduced in the peripheral blood, suggesting an advanced impairment of leukocyte trafficking with age. Moreover, aged PKN1[T778A] mice showed no obvious GC formation nor autoimmune-like phenotypes, such as glomerulonephritis or increased anti-dsDNA antibody titer, in peripheral blood. Our results showing phenotypic differences between aged Pkn1-KO and PKN1[T778A] mice may provide insight into the importance of PKN1-specific kinase-independent functions in vivo.
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31
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Thompson A, Carroll K, A. Inker L, Floege J, Perkovic V, Boyer-Suavet S, W. Major R, I. Schimpf J, Barratt J, Cattran DC, S. Gillespie B, Kausz A, W. Mercer A, Reich HN, H. Rovin B, West M, Nachman PH. Proteinuria Reduction as a Surrogate End Point in Trials of IgA Nephropathy. Clin J Am Soc Nephrol 2019; 14:469-481. [PMID: 30635299 PMCID: PMC6419287 DOI: 10.2215/cjn.08600718] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
IgA nephropathy (IgAN) is an important cause of ESKD for which there are no approved therapies. A challenge for evaluating treatments for IgAN is the usual long time course for progression to ESKD. The aim of this Kidney Health Initiative project was to identify surrogate end points that could serve as reliable predictors of a treatment's effect on long-term kidney outcomes in IgAN and be used as a basis for approval. Proteinuria was identified as the most widely recognized and well studied risk factor for progression to ESKD in IgAN. The workgroup performed a critical review of the data on proteinuria reduction as a surrogate end point for a treatment's effect on progression to ESKD in IgAN. Epidemiologic data indicate a strong and consistent relationship between the level and duration of proteinuria and loss of kidney function. Trial-level analyses of data from 13 controlled trials also show an association between treatment effects on percent reduction of proteinuria and treatment effects on a composite of time to doubling of serum creatinine, ESKD, or death. We conclude that data support the use of proteinuria reduction as a reasonably likely surrogate end point for a treatment's effect on progression to ESKD in IgAN. In the United States, reasonably likely surrogate end points can be used as a basis for accelerated approval of therapies intended to treat serious or life-threatening conditions, such as IgAN. The clinical benefit of products approved under this program would need to be verified in a postmarketing confirmatory trial.
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Affiliation(s)
- Aliza Thompson
- Division of Cardiovascular and Renal Products, Office of New Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | | | | | - Jürgen Floege
- Division of Nephrology, RWTH University of Aachen, Aachen, Germany
| | - Vlado Perkovic
- The George Institute for Global Health, University of New South Wales, Sydney, Australia
| | - Sonia Boyer-Suavet
- Service de Néphrologie, Hôpital Pasteur, Centre Hospitalier Universitaire de Nice, Université Nice Sophia-Antipolis, Nice, France; Departments of
| | | | | | - Jonathan Barratt
- Infection, Inflammation and Immunity, University of Leicester, Leicester, UK
| | - Daniel C. Cattran
- University Health Network, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | - Heather N. Reich
- University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Brad H. Rovin
- The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Melissa West
- American Society of Nephrology, Washington, DC; and
| | - Patrick H. Nachman
- Division of Renal Diseases and Hypertension, University of Minnesota, Minneapolis, Minnesota
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32
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Zhou LT, Lv LL, Qiu S, Yin Q, Li ZL, Tang TT, Ni LH, Feng Y, Wang B, Ma KL, Liu BC. Bioinformatics-based discovery of the urinary BBOX1 mRNA as a potential biomarker of diabetic kidney disease. J Transl Med 2019; 17:59. [PMID: 30819181 PMCID: PMC6394064 DOI: 10.1186/s12967-019-1818-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/21/2019] [Indexed: 01/15/2023] Open
Abstract
Background Diabetic kidney disease (DKD) is the leading cause of end-stage kidney disease (ESKD) in the world. Emerging evidence has shown that urinary mRNAs may serve as early diagnostic and prognostic biomarkers of DKD. In this article, we aimed to first establish a novel bioinformatics-based methodology for analyzing the “urinary kidney-specific mRNAs” and verify their potential clinical utility in DKD. Methods To select candidate mRNAs, a total of 127 Affymetrix microarray datasets of diabetic kidney tissues and other tissues from humans were compiled and analyzed using an integrative bioinformatics approach. Then, the urinary expression of candidate mRNAs in stage 1 study (n = 82) was verified, and the one with best performance moved on to stage 2 study (n = 80) for validation. To avoid potential detection bias, a one-step Taqman PCR assay was developed for quantification of the interested mRNA in stage 2 study. Lastly, the in situ expression of the selected mRNA was further confirmed using fluorescent in situ hybridization (FISH) assay and bioinformatics analysis. Results Our bioinformatics analysis identified sixteen mRNAs as candidates, of which urinary BBOX1 (uBBOX1) levels were significantly upregulated in the urine of patients with DKD. The expression of uBBOX1 was also increased in normoalbuminuric diabetes subjects, while remained unchanged in patients with urinary tract infection or bladder cancer. Besides, uBBOX1 levels correlated with glycemic control, albuminuria and urinary tubular injury marker levels. Similar results were obtained in stage 2 study. FISH assay further demonstrated that BBOX1 mRNA was predominantly located in renal tubular epithelial cells, while its expression in podocytes and urothelium was weak. Further bioinformatics analysis also suggested that tubular BBOX1 mRNA expression was quite stable in various types of kidney diseases. Conclusions Our study provided a novel methodology to identify and analyze urinary kidney-specific mRNAs. uBBOX1 might serve as a promising biomarker of DKD. The performance of the selected urinary mRNAs in monitoring disease progression needs further validation. Electronic supplementary material The online version of this article (10.1186/s12967-019-1818-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Le-Ting Zhou
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, No. 87 Dingjiaqiao Rd, Nanjing, Jiangsu, China.,Wuxi People's Hospital Affiliated To Nanjing Medical University, Wuxi, Jiangsu, China
| | - Lin-Li Lv
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, No. 87 Dingjiaqiao Rd, Nanjing, Jiangsu, China
| | - Shen Qiu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, No. 87 Dingjiaqiao Rd, Nanjing, Jiangsu, China
| | - Qing Yin
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, No. 87 Dingjiaqiao Rd, Nanjing, Jiangsu, China
| | - Zuo-Lin Li
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, No. 87 Dingjiaqiao Rd, Nanjing, Jiangsu, China
| | - Tao-Tao Tang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, No. 87 Dingjiaqiao Rd, Nanjing, Jiangsu, China
| | - Li-Hua Ni
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, No. 87 Dingjiaqiao Rd, Nanjing, Jiangsu, China
| | - Ye Feng
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, No. 87 Dingjiaqiao Rd, Nanjing, Jiangsu, China
| | - Bin Wang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, No. 87 Dingjiaqiao Rd, Nanjing, Jiangsu, China
| | - Kun-Ling Ma
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, No. 87 Dingjiaqiao Rd, Nanjing, Jiangsu, China
| | - Bi-Cheng Liu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, No. 87 Dingjiaqiao Rd, Nanjing, Jiangsu, China.
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33
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Xu X, Eales JM, Akbarov A, Guo H, Becker L, Talavera D, Ashraf F, Nawaz J, Pramanik S, Bowes J, Jiang X, Dormer J, Denniff M, Antczak A, Szulinska M, Wise I, Prestes PR, Glyda M, Bogdanski P, Zukowska-Szczechowska E, Berzuini C, Woolf AS, Samani NJ, Charchar FJ, Tomaszewski M. Molecular insights into genome-wide association studies of chronic kidney disease-defining traits. Nat Commun 2018; 9:4800. [PMID: 30467309 PMCID: PMC6250666 DOI: 10.1038/s41467-018-07260-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/17/2018] [Indexed: 02/08/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified >100 loci of chronic kidney disease-defining traits (CKD-dt). Molecular mechanisms underlying these associations remain elusive. Using 280 kidney transcriptomes and 9958 gene expression profiles from 44 non-renal tissues we uncover gene expression partners (eGenes) for 88.9% of CKD-dt GWAS loci. Through epigenomic chromatin segmentation analysis and variant effect prediction we annotate functional consequences to 74% of these loci. Our colocalisation analysis and Mendelian randomisation in >130,000 subjects demonstrate causal effects of three eGenes (NAT8B, CASP9 and MUC1) on estimated glomerular filtration rate. We identify a common alternative splice variant in MUC1 (a gene responsible for rare Mendelian form of kidney disease) and observe increased renal expression of a specific MUC1 mRNA isoform as a plausible molecular mechanism of the GWAS association signal. These data highlight the variants and genes underpinning the associations uncovered in GWAS of CKD-dt.
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Affiliation(s)
- Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - James M Eales
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Artur Akbarov
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Hui Guo
- Division of Population Health, Health Services Research and Primary Care, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Lorenz Becker
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - David Talavera
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Fehzan Ashraf
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Jabran Nawaz
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Sanjeev Pramanik
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - John Bowes
- Division of Musculoskeletal and Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Xiao Jiang
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - John Dormer
- University Hospitals of Leicester NHS Trust, Leicester, LE1 5WW, UK
| | - Matthew Denniff
- Department of Cardiovascular Sciences, University of Leicester, Leicester, LE3 9QP, UK
| | - Andrzej Antczak
- Department of Urology and Uro-oncology, Karol Marcinkowski University of Medical Sciences, Poznan, 61-285, Poland
| | - Monika Szulinska
- Department of Internal Medicine, Metabolic Disorders and Hypertension, Karol Marcinkowski University of Medical Sciences, Poznan, 60-569, Poland
| | - Ingrid Wise
- School of Health and Life Sciences, Federation University Australia, Ballarat, 3350, VIC, Australia
| | - Priscilla R Prestes
- School of Health and Life Sciences, Federation University Australia, Ballarat, 3350, VIC, Australia
| | - Maciej Glyda
- Department of Transplantology and General Surgery, District Public Hospital, University of Zielona Góra, Poznan, 65-417, Poland
| | - Pawel Bogdanski
- Department of Obesity and Metabolic Disorders Treatment and Clinical Dietetics, Karol Marcinkowski University of Medical Sciences, Poznan, 60-569, Poland
| | | | - Carlo Berzuini
- Division of Population Health, Health Services Research and Primary Care, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Adrian S Woolf
- Department of Paediatric Nephrology, Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, LE3 9QP, UK.,NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Fadi J Charchar
- Department of Cardiovascular Sciences, University of Leicester, Leicester, LE3 9QP, UK.,School of Health and Life Sciences, Federation University Australia, Ballarat, 3350, VIC, Australia.,Department of Physiology, University of Melbourne, Melbourne, 3010, VIC, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK. .,Division of Medicine, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK.
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34
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Tampe B, Tampe D, Nyamsuren G, Klöpper F, Rapp G, Kauffels A, Lorf T, Zeisberg EM, Müller GA, Kalluri R, Hakroush S, Zeisberg M. Pharmacological induction of hypoxia-inducible transcription factor ARNT attenuates chronic kidney failure. J Clin Invest 2018; 128:3053-3070. [PMID: 29664738 DOI: 10.1172/jci89632] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 04/12/2018] [Indexed: 01/05/2023] Open
Abstract
Progression of chronic kidney disease associated with progressive fibrosis and impaired tubular epithelial regeneration is still an unmet biomedical challenge because, once chronic lesions have manifested, no effective therapies are available as of yet for clinical use. Prompted by various studies across multiple organs demonstrating that preconditioning regimens to induce endogenous regenerative mechanisms protect various organs from later incurring acute injuries, we here aimed to gain insights into the molecular mechanisms underlying successful protection and to explore whether such pathways could be utilized to inhibit progression of chronic organ injury. We identified a protective mechanism controlled by the transcription factor ARNT that effectively inhibits progression of chronic kidney injury by transcriptional induction of ALK3, the principal mediator of antifibrotic and proregenerative bone morphogenetic protein-signaling (BMP-signaling) responses. We further report that ARNT expression itself is controlled by the FKBP12/YY1 transcriptional repressor complex and that disruption of such FKBP12/YY1 complexes by picomolar FK506 at subimmunosuppressive doses increases ARNT expression, subsequently leading to homodimeric ARNT-induced ALK3 transcription. Direct targeting of FKBP12/YY1 with in vivo morpholino approaches or small molecule inhibitors, including GPI-1046, was equally effective for inducing ARNT expression, with subsequent activation of ALK3-dependent canonical BMP-signaling responses and attenuated chronic organ failure in models of chronic kidney disease, and also cardiac and liver injuries. In summary, we report an organ-protective mechanism that can be pharmacologically modulated by immunophilin ligands FK506 and GPI-1046 or therapeutically targeted by in vivo morpholino approaches.
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Affiliation(s)
| | | | | | | | | | - Anne Kauffels
- Department of General, Visceral, and Pediatric Surgery, and
| | - Thomas Lorf
- Department of General, Visceral, and Pediatric Surgery, and
| | - Elisabeth M Zeisberg
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Georg August University, Göttingen, Germany.,German Center for Cardiovascular Research (DZHK), Göttingen, Germany
| | | | - Raghu Kalluri
- Department of Cancer Biology and the Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Samy Hakroush
- Institute of Pathology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Michael Zeisberg
- Department of Nephrology and Rheumatology.,German Center for Cardiovascular Research (DZHK), Göttingen, Germany
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35
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Zhou LT, Qiu S, Lv LL, Li ZL, Liu H, Tang RN, Ma KL, Liu BC. Integrative Bioinformatics Analysis Provides Insight into the Molecular Mechanisms of Chronic Kidney Disease. Kidney Blood Press Res 2018; 43:568-581. [PMID: 29642064 DOI: 10.1159/000488830] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 03/28/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Chronic kidney disease (CKD) is a worldwide public health problem. Regardless of the underlying primary disease, CKD tends to progress to end-stage kidney disease, resulting in unsatisfactory and costly treatment. Its common pathogenesis, however, remains unclear. The aim of this study was to provide an unbiased catalog of common gene-expression changes of CKD and reveal the underlying molecular mechanism using an integrative bioinformatics approach. METHODS We systematically collected over 250 Affymetrix microarray datasets from the glomerular and tubulointerstitial compartments of healthy renal tissues and those with various types of established CKD (diabetic kidney disease, hypertensive nephropathy, and glomerular nephropathy). Then, using stringent bioinformatics analysis, shared differentially expressed genes (DEGs) of CKD were obtained. These shared DEGs were further analyzed by the gene ontology (GO) and pathway enrichment analysis. Finally, the protein-protein interaction networks(PINs) were constructed to further refine our results. RESULTS Our analysis identified 176 and 50 shared DEGs in diseased glomeruli and tubules, respectively, including many transcripts that have not been previously reported to be involved in kidney disease. Enrichment analysis also showed that the glomerular and tubulointerstitial compartments underwent a wide range of unique pathological changes during chronic injury. As revealed by the GO enrichment analysis, shared DEGs in glomeruli were significantly enriched in exosomes. By constructing PINs, we identified several hub genes (e.g. OAS1, JUN, and FOS) and clusters that might play key roles in regulating the development of CKD. CONCLUSION Our study not only further reveals the unifying molecular mechanism of CKD pathogenesis but also provides a valuable resource of potential biomarkers and therapeutic targets.
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36
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Levin A, Adams E, Barrett BJ, Beanlands H, Burns KD, Chiu HHL, Chong K, Dart A, Ferera J, Fernandez N, Fowler E, Garg AX, Gilbert R, Harris H, Harvey R, Hemmelgarn B, James M, Johnson J, Kappel J, Komenda P, McCormick M, McIntyre C, Mahmud F, Pei Y, Pollock G, Reich H, Rosenblum ND, Scholey J, Sochett E, Tang M, Tangri N, Tonelli M, Turner C, Walsh M, Woods C, Manns B. Canadians Seeking Solutions and Innovations to Overcome Chronic Kidney Disease (Can-SOLVE CKD): Form and Function. Can J Kidney Health Dis 2018; 5:2054358117749530. [PMID: 29372064 PMCID: PMC5774731 DOI: 10.1177/2054358117749530] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/20/2017] [Indexed: 11/17/2022] Open
Abstract
PURPOSE OF REVIEW This article serves to describe the Can-SOLVE CKD network, a program of research projects and infrastructure that has excited patients and given them hope that we can truly transform the care they receive. ISSUE Chronic kidney disease (CKD) is a complex disorder that affects more than 4 million Canadians and costs the Canadian health care system more than $40 billion per year. The evidence base for guiding care in CKD is small, and even in areas where evidence exists, uptake of evidence into clinical practice has been slow. Compounding these complexities are the variations in outcomes for patients with CKD and difficulties predicting who is most likely to develop complications over time. Clearly these gaps in our knowledge and understanding of CKD need to be filled, but the current state of CKD research is not where it needs to be. A culture of clinical trials and inquiry into the disease is lacking, and much of the existing evidence base addresses the concerns of the researchers but not necessarily those of the patients. PROGRAM OVERVIEW The Canadian Institutes of Health Research (CIHR) has launched the national Strategy for Patient-Oriented Research (SPOR), a coalition of federal, provincial, and territorial partners dedicated to integrating research into care. Canadians Seeking Solutions and Innovations to Overcome Chronic Kidney Disease (Can-SOLVE CKD) is one of five pan-Canadian chronic kidney disease networks supported through the SPOR. The vision of Can-SOLVE CKD is that by 2020 every Canadian with or at high risk for CKD will receive the best recommended care, experience optimal outcomes, and have the opportunity to participate in studies with novel therapies, regardless of age, sex, gender, location, or ethnicity. PROGRAM OBJECTIVE The overarching objective of Can-SOLVE CKD is to accelerate the translation of knowledge about CKD into clinical research and practice. By focusing on the patient's voice and implementing relevant findings in real time, Can-SOLVE CKD will transform the care that CKD patients receive, and will improve kidney health for future generations.
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Affiliation(s)
- Adeera Levin
- The University of British Columbia, Vancouver, Canada
- BC Provincial Renal Agency, Vancouver, Canada
| | - Evan Adams
- The University of British Columbia, Vancouver, Canada
- First Nations Health Authority, West Vancouver, British Columbia, Canada
| | - Brendan J. Barrett
- Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | | | - Kevin D. Burns
- University of Ottawa, Ontario, Canada
- Ottawa Hospital Research Institute, Ontario, Canada
| | - Helen Hoi-Lun Chiu
- BC Provincial Renal Agency, Vancouver, Canada
- Providence Health Care Research Institute, Vancouver, British Columbia, Canada
- Can-SOLVE CKD Network, Vancouver, British Columbia, Canada
| | - Kate Chong
- Can-SOLVE CKD Network, Vancouver, British Columbia, Canada
| | - Allison Dart
- University of Manitoba, Winnipeg, Canada
- Children’s Hospital Research Institute of Manitoba, Winnipeg, Canada
| | - Jack Ferera
- Can-SOLVE CKD Network, Vancouver, British Columbia, Canada
| | | | | | - Amit X. Garg
- Western University, London, Ontario, Canada
- Institute for Clinical Evaluative Sciences, London, Ontario, Canada
| | - Richard Gilbert
- St. Michael’s Hospital, Toronto, Ontario, Canada
- University of Toronto, Ontario, Canada
| | - Heather Harris
- Providence Health Care Research Institute, Vancouver, British Columbia, Canada
- Can-SOLVE CKD Network, Vancouver, British Columbia, Canada
| | | | - Brenda Hemmelgarn
- University of Calgary, Alberta, Canada
- Foothills Medical Centre, Calgary, Alberta, Canada
- The Interdisciplinary Chronic Disease Collaboration, Calgary, Alberta, Canada
| | | | | | | | - Paul Komenda
- University of Manitoba, Winnipeg, Canada
- Seven Oaks General Hospital, Winnipeg, Manitoba, Canada
| | | | - Christopher McIntyre
- Western University, London, Ontario, Canada
- Lawson Health Research Institute, London, Ontario, Canada
| | - Farid Mahmud
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - York Pei
- University of Toronto, Ontario, Canada
- Toronto General Hospital, Ontario, Canada
- University Health Network, Toronto, Ontario, Canada
| | - Graham Pollock
- Providence Health Care Research Institute, Vancouver, British Columbia, Canada
- Can-SOLVE CKD Network, Vancouver, British Columbia, Canada
| | - Heather Reich
- University of Toronto, Ontario, Canada
- University Health Network, Toronto, Ontario, Canada
| | - Norman D. Rosenblum
- University of Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - James Scholey
- University of Toronto, Ontario, Canada
- University Health Network, Toronto, Ontario, Canada
| | | | - Mila Tang
- BC Provincial Renal Agency, Vancouver, Canada
- Providence Health Care Research Institute, Vancouver, British Columbia, Canada
| | - Navdeep Tangri
- University of Manitoba, Winnipeg, Canada
- Seven Oaks General Hospital, Winnipeg, Manitoba, Canada
| | - Marcello Tonelli
- University of Calgary, Alberta, Canada
- The Interdisciplinary Chronic Disease Collaboration, Calgary, Alberta, Canada
| | | | - Michael Walsh
- McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton, Ontario, Canada
| | - Cathy Woods
- Can-SOLVE CKD Network, Vancouver, British Columbia, Canada
| | - Braden Manns
- University of Calgary, Alberta, Canada
- Foothills Medical Centre, Calgary, Alberta, Canada
- The Interdisciplinary Chronic Disease Collaboration, Calgary, Alberta, Canada
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37
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Breyer MD, Kretzler M. Novel avenues for drug discovery in diabetic kidney disease. Expert Opin Drug Discov 2017; 13:65-74. [DOI: 10.1080/17460441.2018.1398731] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Matthew D. Breyer
- Lead Generation, Biotechnology Discovery Research, Eli Lilly and Company, Indianapolis, IN, USA
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
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38
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Schena FP, Nistor I, Curci C. Transcriptomics in kidney biopsy is an untapped resource for precision therapy in nephrology: a systematic review. Nephrol Dial Transplant 2017; 33:1094-1102. [DOI: 10.1093/ndt/gfx211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/03/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Ionut Nistor
- Nephrology Department, Grigore T. Popa University of Medicine and Pharmacy, Iasi, Romania
- Methods Support Team ERBP, Ghent University, Ghent, Belgium
| | - Claudia Curci
- University of Bari, Bari, Italy
- Schena Foundation, Valenzano, Italy
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39
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Cui Y, Liu S, Cui W, Gao D, Zhou W, Luo P. Identification of potential biomarkers and therapeutic targets for human IgA nephropathy and hypertensive nephropathy by bioinformatics analysis. Mol Med Rep 2017; 16:3087-3094. [PMID: 28713898 PMCID: PMC5547965 DOI: 10.3892/mmr.2017.6996] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 04/04/2017] [Indexed: 12/15/2022] Open
Abstract
In order to further elucidate the potential correlations and treatments of IgA nephropathy (IgAN) and hypertensive nephropathy (HT), bioinformatics analysis of IgAN and HT was performed. The mRNA expression profiles of human renal biopsy samples from patients with IgAN, patients with HT and pre‑transplant healthy living controls (LD) were downloaded from the Gene Expression Omnibus database. Then, the differentially expressed genes (DEGs) were identified and functions of DEGs were analyzed. Finally, the regulatory networks containing DEGs and related‑transcription factors (TFs) were constructed using Cytoscape software. When compared with the LD group, 134 and 188 DEGs were obtained in the IgAN and HT groups, respectively. A total of 39 genes were altered in the HT group when compared with the IgAN group. In addition, 66 genes were shared in the IgAN and HT groups when compared with the LD group, 6 of which [early growth response 1, activating transcription factor 3, nuclear receptor subfamily 4 group A member 2 (NR4A2), NR4A1, v‑maf avian musculoaponeurotic fibrosarcoma oncogene homolog F and Kruppel like factor 6] were identified as TFs. In addition, DEGs including interleukin (IL) 1 receptor antagonist, collagen type 4 α2 chain, IL8, FBJ murine osteosarcoma viral oncogene homolog and somatostatin were enriched in a number of inflammation‑associated biological processes, and DEGs including structural maintenance of chromosomes protein 3, v‑crk avian sarcoma virus CT10 oncogene homolog and myosin 6 were enriched in non‑inflammation‑associated biological processes. Therefore, the differentially expressed TF genes and the genes associated with inflammation may be effective as potential therapeutic targets for IgAN and HT.
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Affiliation(s)
- Yingchun Cui
- Department of Nephrology, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Shengmao Liu
- Department of Nephrology, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Wenpeng Cui
- Department of Nephrology, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Dan Gao
- Department of Nephrology, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Wenhua Zhou
- Department of Nephrology, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Ping Luo
- Department of Nephrology, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
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40
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Poveda J, Sanz AB, Carrasco S, Ruiz-Ortega M, Cannata-Ortiz P, Sanchez-Niño MD, Ortiz A. Bcl3: a regulator of NF-κB inducible by TWEAK in acute kidney injury with anti-inflammatory and antiapoptotic properties in tubular cells. Exp Mol Med 2017; 49:e352. [PMID: 28684863 PMCID: PMC5565957 DOI: 10.1038/emm.2017.89] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/21/2016] [Accepted: 01/12/2017] [Indexed: 01/09/2023] Open
Abstract
Acute kidney injury (AKI) is characterized by tubular cell death and interstitial inflammation. TWEAK promotes experimental kidney injury and activates the transcription factor NF-κB, a key regulator of genes involved in cell survival and inflammatory response. In search of potential therapeutic targets for AKI, we compared a transcriptomics database of NF-κB-related genes from murine AKI-kidneys with a transcriptomics database of TWEAK-stimulated cultured tubular cells. Four out of twenty-four (17%) genes were significantly upregulated (false discovery rate, FDR<0.05), while nine out of twenty-four (37%) genes were significantly upregulated at FDR <0.1 in both databases. Bcl3 was the top upregulated NF-κB-related gene in experimental AKI and one of the most upregulated genes in TWEAK-stimulated tubular cells. Quantitative reverse transcription PCR (qRT-PCR), western blot and immunohistochemistry confirmed Bcl3 upregulation in both experimental conditions and localized increased Bcl3 expression to tubular cells in AKI. Transcriptomics database analysis revealed increased Bcl3 expression in numerous experimental and human kidney conditions. Furthermore, systemic TWEAK administration increased kidney Bcl3 expression. In cultured tubular cells, targeting Bcl3 by siRNA resulted in the magnification of TWEAK-induced NF-κB transcriptional activity, chemokine upregulation and Klotho downregulation, and in the sensitization to cell death induced by TWEAK/TNFα/interferon-γ. In contrast, Bcl3 overexpression decreased NF-κB transcriptional activity, inflammatory response and cell death while dampening the decrease in Klotho expression. In conclusion, Bcl3 expressed in response to TWEAK stimulation decreases TWEAK-induced inflammatory and lethal responses. Therefore, therapeutic upregulation of Bcl3 activity should be explored in kidney disease because it has advantages over chemical inhibitors of NF-κB that are known to prevent inflammatory responses but can also sensitize the cells to apoptosis.
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Affiliation(s)
- Jonay Poveda
- Unidad de Dialisis, IIS-Fundación Jiménez Díaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Álvarez de Toledo-IRSIN and REDINREN, Madrid, Spain
| | - Ana B Sanz
- Unidad de Dialisis, IIS-Fundación Jiménez Díaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Álvarez de Toledo-IRSIN and REDINREN, Madrid, Spain
| | - Susana Carrasco
- Unidad de Dialisis, IIS-Fundación Jiménez Díaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Álvarez de Toledo-IRSIN and REDINREN, Madrid, Spain
| | - Marta Ruiz-Ortega
- Unidad de Dialisis, IIS-Fundación Jiménez Díaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Álvarez de Toledo-IRSIN and REDINREN, Madrid, Spain
| | - Pablo Cannata-Ortiz
- Unidad de Dialisis, IIS-Fundación Jiménez Díaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Álvarez de Toledo-IRSIN and REDINREN, Madrid, Spain
| | - Maria D Sanchez-Niño
- Unidad de Dialisis, IIS-Fundación Jiménez Díaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Álvarez de Toledo-IRSIN and REDINREN, Madrid, Spain
| | - Alberto Ortiz
- Unidad de Dialisis, IIS-Fundación Jiménez Díaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Álvarez de Toledo-IRSIN and REDINREN, Madrid, Spain
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41
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Bhreathnach U, Griffin B, Brennan E, Ewart L, Higgins D, Murphy M. Profibrotic IHG-1 complexes with renal disease associated HSPA5 and TRAP1 in mitochondria. Biochim Biophys Acta Mol Basis Dis 2017; 1863:896-906. [PMID: 28115289 DOI: 10.1016/j.bbadis.2017.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/17/2017] [Accepted: 01/19/2017] [Indexed: 01/01/2023]
Abstract
The highly conserved mitochondrial protein induced in high glucose-1 (IHG-1) functions to maintain mitochondrial quality and is associated with the development of fibrosis in diabetic nephropathy. Towards identifying novel approaches to treating diabetic kidney disease, IHG-1-protein-protein interactions were investigated using epitope-tagged immunoprecipitation analyses followed by mass spectrometry. Here we show that IHG-1 is solely expressed in mitochondria and localised to the inner mitochondrial membrane, the region where mitochondrial reactive oxygen species are generated. Chaperones HSPA5 and TRAP1 and cold shock protein YBX1 were identified as IHG-1 binding partners. All three proteins are important in the cellular response to oxidative stress and play important roles in mitochondrial transcription and DNA repair. Both redox imbalance and IHG-1 stimulate TGF-β signalling. IHG-1, HSPA5 and YBX1 all show increased expression in diabetic nephropathy, chronic kidney disease and in the Unilateral Ureteral Obstruction model of kidney fibrosis. Increased IHG-1 expression in UUO correlated with loss of TRAP1 expression. IHG-1 may target TRAP1 for degradation. When IHG-1 is no longer localised to mitochondria, it retains the ability to interact with the cold shock protein YBX1, facilitating anti-fibrotic actions in the nucleus. Targeting these proteins may offer alternative treatments for fibrotic kidney disease.
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Affiliation(s)
- Una Bhreathnach
- Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Brenda Griffin
- Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Eoin Brennan
- Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Leah Ewart
- Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Debra Higgins
- Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Madeline Murphy
- Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
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42
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Ju W, Nair V, Smith S, Zhu L, Shedden K, Song PXK, Mariani LH, Eichinger FH, Berthier CC, Randolph A, Lai JYC, Zhou Y, Hawkins JJ, Bitzer M, Sampson MG, Thier M, Solier C, Duran-Pacheco GC, Duchateau-Nguyen G, Essioux L, Schott B, Formentini I, Magnone MC, Bobadilla M, Cohen CD, Bagnasco SM, Barisoni L, Lv J, Zhang H, Wang HY, Brosius FC, Gadegbeku CA, Kretzler M. Tissue transcriptome-driven identification of epidermal growth factor as a chronic kidney disease biomarker. Sci Transl Med 2016; 7:316ra193. [PMID: 26631632 DOI: 10.1126/scitranslmed.aac7071] [Citation(s) in RCA: 275] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chronic kidney disease (CKD) affects 8 to 16% people worldwide, with an increasing incidence and prevalence of end-stage kidney disease (ESKD). The effective management of CKD is confounded by the inability to identify patients at high risk of progression while in early stages of CKD. To address this challenge, a renal biopsy transcriptome-driven approach was applied to develop noninvasive prognostic biomarkers for CKD progression. Expression of intrarenal transcripts was correlated with the baseline estimated glomerular filtration rate (eGFR) in 261 patients. Proteins encoded by eGFR-associated transcripts were tested in urine for association with renal tissue injury and baseline eGFR. The ability to predict CKD progression, defined as the composite of ESKD or 40% reduction of baseline eGFR, was then determined in three independent CKD cohorts. A panel of intrarenal transcripts, including epidermal growth factor (EGF), a tubule-specific protein critical for cell differentiation and regeneration, predicted eGFR. The amount of EGF protein in urine (uEGF) showed significant correlation (P < 0.001) with intrarenal EGF mRNA, interstitial fibrosis/tubular atrophy, eGFR, and rate of eGFR loss. Prediction of the composite renal end point by age, gender, eGFR, and albuminuria was significantly (P < 0.001) improved by addition of uEGF, with an increase of the C-statistic from 0.75 to 0.87. Outcome predictions were replicated in two independent CKD cohorts. Our approach identified uEGF as an independent risk predictor of CKD progression. Addition of uEGF to standard clinical parameters improved the prediction of disease events in diverse CKD populations with a wide spectrum of causes and stages.
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Affiliation(s)
- 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
| | - Viji Nair
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shahaan Smith
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Li Zhu
- Renal Division, Department of Internal Medicine, Peking University First Hospital, Peking University Institute of Nephrology, Beijing 100034, China
| | - Kerby Shedden
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Statistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter X K Song
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura H Mariani
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Arbor Research Collaborative for Health, Ann Arbor, MI 48104, USA
| | - Felix H Eichinger
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Celine C Berthier
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ann Randolph
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer Yi-Chun Lai
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yan Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer J Hawkins
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Markus Bitzer
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew G Sampson
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Martina Thier
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | - Corinne Solier
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | - Gonzalo C Duran-Pacheco
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | | | - Laurent Essioux
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | - Brigitte Schott
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | - Ivan Formentini
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | - Maria C Magnone
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | - Maria Bobadilla
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | - Clemens D Cohen
- Division of Nephrology, Institute of Physiology, University of Zurich, CH-8006 Zürich, Switzerland
| | - Serena M Bagnasco
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Laura Barisoni
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jicheng Lv
- Renal Division, Department of Internal Medicine, Peking University First Hospital, Peking University Institute of Nephrology, Beijing 100034, China
| | - Hong Zhang
- Renal Division, Department of Internal Medicine, Peking University First Hospital, Peking University Institute of Nephrology, Beijing 100034, China
| | - Hai-Yan Wang
- Renal Division, Department of Internal Medicine, Peking University First Hospital, Peking University Institute of Nephrology, Beijing 100034, China
| | - Frank C Brosius
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Crystal A Gadegbeku
- Temple Clinical Research Institute, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - 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
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43
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Valiño-Rivas L, Gonzalez-Lafuente L, Sanz AB, Ruiz-Ortega M, Ortiz A, Sanchez-Niño MD. Non-canonical NFκB activation promotes chemokine expression in podocytes. Sci Rep 2016; 6:28857. [PMID: 27353019 PMCID: PMC4926283 DOI: 10.1038/srep28857] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/10/2016] [Indexed: 12/13/2022] Open
Abstract
TNF-like weak inducer of apoptosis (TWEAK) receptor Fn14 is expressed by podocytes and Fn14 deficiency protects from experimental proteinuric kidney disease. However, the downstream effectors of TWEAK/Fn14 in podocytes are poorly characterized. We have explored TWEAK activation of non-canonical NFκB signaling in cultured podocytes. In cultured podocytes, TWEAK increased the expression of the chemokines CCL21, CCL19 and RANTES in a time-dependent manner. The inhibitor of canonical NFκB activation parthenolide inhibited the CCL19 and the early RANTES responses, but not the CCL21 or late RANTES responses. In this regard, TWEAK induced non-canonical NFκB activation in podocytes, characterized by NFκB2/p100 processing to NFκB2/p52 and nuclear migration of RelB/p52. Silencing by a specific siRNA of NIK, the upstream kinase of the non-canonical NFκB pathway, prevented CCL21 upregulation but did not modulate CCL19 or RANTES expression in response to TWEAK, thus establishing CCL21 as a non-canonical NFκB target in podocytes. Increased kidney Fn14 and CCL21 expression was also observed in rat proteinuric kidney disease induced by puromycin, and was localized to podocytes. In conclusion, TWEAK activates the non-canonical NFκB pathway in podocytes, leading to upregulation of CCL21 expression. The non-canonical NFκB pathway should be explored as a potential therapeutic target in proteinuric kidney disease.
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Affiliation(s)
- Lara Valiño-Rivas
- IIS-Fundación Jiménez Díaz-Universidad Autónoma de Madrid and Fundación Renal Iñigo Alvarez de Toledo-IRSIN, Madrid, Spain.,REDINREN, Madrid, Spain
| | - Laura Gonzalez-Lafuente
- IIS-Fundación Jiménez Díaz-Universidad Autónoma de Madrid and Fundación Renal Iñigo Alvarez de Toledo-IRSIN, Madrid, Spain.,REDINREN, Madrid, Spain
| | - Ana B Sanz
- IIS-Fundación Jiménez Díaz-Universidad Autónoma de Madrid and Fundación Renal Iñigo Alvarez de Toledo-IRSIN, Madrid, Spain.,REDINREN, Madrid, Spain
| | - Marta Ruiz-Ortega
- IIS-Fundación Jiménez Díaz-Universidad Autónoma de Madrid and Fundación Renal Iñigo Alvarez de Toledo-IRSIN, Madrid, Spain.,REDINREN, Madrid, Spain
| | - Alberto Ortiz
- IIS-Fundación Jiménez Díaz-Universidad Autónoma de Madrid and Fundación Renal Iñigo Alvarez de Toledo-IRSIN, Madrid, Spain.,REDINREN, Madrid, Spain
| | - Maria D Sanchez-Niño
- IIS-Fundación Jiménez Díaz-Universidad Autónoma de Madrid and Fundación Renal Iñigo Alvarez de Toledo-IRSIN, Madrid, Spain.,REDINREN, Madrid, Spain
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44
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Chun J, Chung H, Wang X, Barry R, Taheri ZM, Platnich JM, Ahmed SB, Trpkov K, Hemmelgarn B, Benediktsson H, James MT, Muruve DA. NLRP3 Localizes to the Tubular Epithelium in Human Kidney and Correlates With Outcome in IgA Nephropathy. Sci Rep 2016; 6:24667. [PMID: 27093923 PMCID: PMC4837396 DOI: 10.1038/srep24667] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/01/2016] [Indexed: 01/03/2023] Open
Abstract
Nod-like receptor pyrin domain-containing-3 (NLRP3) has been implicated in the pathogenesis of experimental renal injury, yet its characterization in human kidney disease remains largely unexplored. NLRP3 expression was evaluated in human kidney biopsies, primary renal tubular cells (HPTC) and correlated to disease outcomes in patients with IgA nephropathy (IgAN). NLRP3 localized to renal tubules in normal human kidney tissue and to mitochondria within HPTC by immunohistochemistry and immunofluorescence microscopy. Compared to control kidneys, NLRP3 gene expression was increased in biopsies of patients with IgAN. While NLRP3 expression in IgAN was detected in glomeruli, it remained largely confined to the tubular epithelial compartment. In vitro NLRP3 mRNA and protein expression were transiently induced in HPTC by TGF-β1 but subsequently diminished over time as cells lost their epithelial phenotype in a process regulated by transcription and ubiquitin-mediated degradation. Consistent with the in vitro data, low NLRP3 mRNA expression in kidney biopsies was associated with a linear trend of higher risk of composite endpoint of doubling serum creatinine and end stage renal disease in patients with IgAN. Taken together, these data show that NLRP3 is primarily a kidney tubule-expressed protein that decreases in abundance in progressive IgAN.
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Affiliation(s)
- Justin Chun
- Department of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Hyunjae Chung
- Department of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Xiangyu Wang
- Department of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Rebecca Barry
- Department of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Zohreh Mohammad Taheri
- Department of Pathology and Laboratory Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Jaye M Platnich
- Department of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Sofia B Ahmed
- Department of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Kiril Trpkov
- Department of Pathology and Laboratory Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Brenda Hemmelgarn
- Department of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Hallgrimur Benediktsson
- Department of Pathology and Laboratory Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Matthew T James
- Department of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Daniel A Muruve
- Department of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
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45
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Lovisa S, LeBleu VS, Tampe B, Sugimoto H, Vadnagara K, Carstens JL, Wu CC, Hagos Y, Burckhardt BC, Pentcheva-Hoang T, Nischal H, Allison JP, Zeisberg M, Kalluri R. Epithelial-to-mesenchymal transition induces cell cycle arrest and parenchymal damage in renal fibrosis. Nat Med 2015; 21:998-1009. [PMID: 26236991 PMCID: PMC4587560 DOI: 10.1038/nm.3902] [Citation(s) in RCA: 666] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/15/2015] [Indexed: 02/06/2023]
Abstract
Kidney fibrosis is marked by an epithelial–to–mesenchymal transition (EMT) by tubular epithelial cells (TECs). Here we find that during renal fibrosis TECs acquire a partial EMT program during which they remain associated with their basement membrane and express markers of both epithelial and mesenchymal cells. The functional consequence of EMT program during fibrotic injury is an arrest in the G2 phase of the cell cycle and lower expression of several transporters in TECs. We also found that transgenic expression of Twist or Snai1 expression is sufficient to promote prolonged TGF-β1–induced G2 arrest of TECs, limiting their potential for repair and regeneration. Also, in mouse models of experimentally-induced renal fibrosis, conditional deletion of Twist1 or Snai1 in proximal TECs resulted in inhibition of the EMT program and the maintenance of TEC integrity, while restoring proliferation, de–differentiation–associated repair and regeneration of the kidney parenchyma and attenuating interstitial fibrosis. Thus, inhibition of EMT program in TECs during chronic renal injury represents a potential anti–fibrosis therapy
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Affiliation(s)
- Sara Lovisa
- Department of Cancer Biology, Metastasis Research Center, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Valerie S LeBleu
- Department of Cancer Biology, Metastasis Research Center, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Björn Tampe
- Department of Nephrology and Rheumatology, Göttingen University Medical Center, Georg August University, Göttingen, Germany
| | - Hikaru Sugimoto
- Department of Cancer Biology, Metastasis Research Center, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Komal Vadnagara
- Department of Cancer Biology, Metastasis Research Center, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Julienne L Carstens
- Department of Cancer Biology, Metastasis Research Center, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Chia-Chin Wu
- Department of Genomic Medicine, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Yohannes Hagos
- Institute of Systemic Physiology and Pathophysiology, Göttingen University Medical Center, Georg August University, Göttingen, Germany
| | - Birgitta C Burckhardt
- Institute of Systemic Physiology and Pathophysiology, Göttingen University Medical Center, Georg August University, Göttingen, Germany
| | | | - Hersharan Nischal
- Department of Immunology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - James P Allison
- Department of Immunology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Michael Zeisberg
- Department of Nephrology and Rheumatology, Göttingen University Medical Center, Georg August University, Göttingen, Germany
| | - Raghu Kalluri
- Department of Cancer Biology, Metastasis Research Center, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
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46
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Reich HN, Sabelnykova VY, Boutros PC. Matching Kidneys and Urines: Establishing Noninvasive Surrogates of Intrarenal Events in Primary Glomerulonephritis. Semin Nephrol 2015. [PMID: 26215863 DOI: 10.1016/j.semnephrol.2015.04.005] [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: 10/23/2022]
Abstract
Kidney biopsy is the gold standard procedure for providing diagnostic and prognostic information for patients with glomerular-based diseases, however, the utility of this procedure for assessing longitudinal disease activity is limited. The intense search for noninvasive biomarkers of kidney disease activity and injury is driven in large part by the inherent risks of the kidney biopsy procedure and limited information derived from the morphologic description of biopsy findings. Furthermore, gaps in our understanding of the core intrarenal molecular processes underlying the development and progression of glomerular-based diseases has limited the development of effective targeted therapy. In this review, we discuss the potential utility of molecular analysis of the urine to provide a dynamic window into intrarenal molecular and morphologic responses. We focus on molecular analysis of the urine to identify noninvasive surrogate markers of kidney responses, with the goal of using these biomarkers as more sensitive indicators of progression and tissue-level responses to therapeutic interventions in patients with primary glomerulonephritis.
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Affiliation(s)
- Heather N Reich
- The Toronto Glomerulonephritis Registry, University Health Network, Gabor Zellerman Chair in Nephrology Research at the University of Toronto Department of Medicine, Toronto, Ontario, Canada.
| | - Veronica Y Sabelnykova
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Paul C Boutros
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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47
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Sampson MG, Hodgin JB, Kretzler M. Defining nephrotic syndrome from an integrative genomics perspective. Pediatr Nephrol 2015; 30:51-63; quiz 59. [PMID: 24890338 PMCID: PMC4241380 DOI: 10.1007/s00467-014-2857-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/06/2014] [Accepted: 05/14/2014] [Indexed: 12/15/2022]
Abstract
Nephrotic syndrome (NS) is a clinical condition with a high degree of morbidity and mortality, caused by failure of the glomerular filtration barrier, resulting in massive proteinuria. Our current diagnostic, prognostic and therapeutic decisions in NS are largely based upon clinical or histological patterns such as "focal segmental glomerulosclerosis" or "steroid sensitive". Yet these descriptive classifications lack the precision to explain the physiologic origins and clinical heterogeneity observed in this syndrome. A more precise definition of NS is required to identify mechanisms of disease and capture various clinical trajectories. An integrative genomics approach to NS applies bioinformatics and computational methods to comprehensive experimental, molecular and clinical data for holistic disease definition. A unique aspect is analysis of data together to discover NS-associated molecules, pathways, and networks. Integrating multidimensional datasets from the outset highlights how molecular lesions impact the entire individual. Data sets integrated range from genetic variation to gene expression, to histologic changes, to progression of chronic kidney disease (CKD). This review will introduce the tenets of integrative genomics and suggest how it can increase our understanding of NS from molecular and pathophysiological perspectives. A diverse group of genome-scale experiments are presented that have sought to define molecular signatures of NS. Finally, the Nephrotic Syndrome Study Network (NEPTUNE) will be introduced as an international, prospective cohort study of patients with NS that utilizes an integrated systems genomics approach from the outset. A major NEPTUNE goal is to achieve comprehensive disease definition from a genomics perspective and identify shared molecular drivers of disease.
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Affiliation(s)
- Matthew G. Sampson
- Division of Nephrology, Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, USA,to whom correspondence should be addressed: Matthew Sampson, Division of Nephrology, University of Michigan School of Medicine, 8220D MSRB III, West Medical Center Drive, Ann Arbor, MI 48109, kidneyomics.org, , Telephone and Fax: 734-647-9361. Matthias Kretzler, Medicine/Nephrology and Computational Medicine and Bioinformatics, University of Michigan, 1560 MSRB II, 1150 W. Medical Center Dr.-SPC5676, Ann Arbor, MI 48109-5676, 734-615-5757, fax: 734-763-0982,
| | - Jeffrey B. Hodgin
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA,to whom correspondence should be addressed: Matthew Sampson, Division of Nephrology, University of Michigan School of Medicine, 8220D MSRB III, West Medical Center Drive, Ann Arbor, MI 48109, kidneyomics.org, , Telephone and Fax: 734-647-9361. Matthias Kretzler, Medicine/Nephrology and Computational Medicine and Bioinformatics, University of Michigan, 1560 MSRB II, 1150 W. Medical Center Dr.-SPC5676, Ann Arbor, MI 48109-5676, 734-615-5757, fax: 734-763-0982,
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48
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Neuwirt H, Perco P, Kainz A, Mühlberger I, Leierer J, Braniff SJ, Mayer B, Mayer G, Rudnicki M. A 3-biomarker-panel predicts renal outcome in patients with proteinuric renal diseases. BMC Med Genomics 2014; 7:75. [PMID: 25540021 PMCID: PMC4301948 DOI: 10.1186/s12920-014-0075-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 12/17/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Clinical and histological parameters are valid prognostic markers in renal disease, although they may show considerable interindividual variability and sometimes limited prognostic value. Novel molecular markers and pathways have the potential to increase the predictive prognostic value of the so called "traditional markers". METHODS Transcriptomics profiles from laser-capture microdissected proximal tubular epithelial cells from routine kidney biopsies were correlated with a chronic renal damage index score (CREDI), an inflammation score (INSCO), and clinical parameters. We used data from 20 renal biopsies with various proteinuric renal diseases with a median follow-up of 49 months (discovery cohort). For validation we performed microarrays from whole kidney biopsies from a second cohort consisting of 16 patients with a median follow-up time of 28 months (validation cohort). RESULTS 562 genes correlated with the CREDI score and 285 genes correlated with the INSCO panel, respectively. 39 CREDI and 90 INSCO genes also correlated with serum creatinine at follow-up. After hierarchical clustering we identified 5 genes from the CREDI panel, and 10 genes from the INSCO panel, respectively, which showed kidney specific gene expression. After exclusion of genes, which correlated to each other by > 50% we identified VEGF-C from the CREDI panel and BMP7, THBS1, and TRIB1 from the INSCO panel. Traditional markers for chronic kidney disease progression and inflammation score predicted 44% of the serum creatinine variation at follow-up. VEGF-C did not further enhance the predictive value, but BMP7, THBS1 and TRIB1 together predicted 94% of the serum creatinine at follow up (p < 0.0001). The model was validated in a second cohort of patients yielding also a significant prediction of follow up creatinine (48%, p = 0.0115). CONCLUSION We identified and validated a panel of three genes in kidney biopsies which predicted serum creatinine at follow-up and therefore might serve as biomarkers for kidney disease progression.
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49
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Wang J, Cao J. Gene expression analysis in tubule interstitial compartments reveals candidate agents for IgA nephropathy. Kidney Blood Press Res 2014; 39:361-8. [PMID: 25322921 DOI: 10.1159/000355814] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Our aim was to explore the molecular mechanism underlying development of IgA nephropathy and discover candidate agents for IgA nephropathy. METHODS The differentially expressed genes (DEGs) between patients with IgA nephropathy and normal controls were identified by the data of GSE35488 downloaded from GEO (Gene Expression Omnibus) database. The co-expressed gene pairs among DEGs were screened to construct the gene-gene interaction network. Gene Ontology (GO) enrichment analysis was performed to analyze the functions of DEGs. The biologically active small molecules capable of targeting IgA nephropathy were identified using the Connectivity Map (cMap) database. RESULTS A total of 55 genes involved in response to organic substance, transcription factor activity and response to steroid hormone stimulus were identified to be differentially expressed in IgA nephropathy patients compared to healthy individuals. A network with 45 co-expressed gene pairs was constructed. DEGs in the network were significantly enriched in response to organic substance. Additionally, a group of small molecules were identified, such as doxorubicin and thapsigargin. CONCLUSION Our work provided a systematic insight in understanding the mechanism of IgA nephropathy. Small molecules such as thapsigargin might be potential candidate agents for the treatment of IgA nephropathy.
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Affiliation(s)
- Jinling Wang
- Department of Nephrology, the Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong Province, China
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50
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Zoja C, Abbate M, Remuzzi G. Progression of renal injury toward interstitial inflammation and glomerular sclerosis is dependent on abnormal protein filtration. Nephrol Dial Transplant 2014; 30:706-12. [PMID: 25087196 DOI: 10.1093/ndt/gfu261] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 07/03/2014] [Indexed: 11/14/2022] Open
Abstract
Chronic proteinuric renal diseases, independent from the type of the initial insult, have in common a loss of selectivity of the glomerular barrier to protein filtration. Glomerular sclerosis is the progressive lesion affecting the glomerular capillary wall, the primary site at which the protein filtration is abnormally enhanced by disease. Dysfunction of podocytes, that serve to maintain the intact barrier, is a central event in lesion development. However, glomerular injury is signalled to tubular and interstitial structures largely in advance of nephron destruction. Glomerular ultrafiltration of excessive amounts of plasma-derived proteins and associated factors incites tubulointerstitial damage and might amplify an inherent susceptibility of the kidney to become dysfunctional in several disease conditions. Thus, noxious substances in the proteinuric ultrafiltrate promote apoptotic responses and multiple changes in the phenotype of tubule cells with generation of inflammatory and fibrogenic mediators. The severity of tubular interstitial damage has long been recognized to be highly correlated to the degree of deterioration of renal failure even better than glomerular lesions. This review focuses on pathways of tubular injury and apoptosis that in turn promote nephron-by-nephron degeneration and interstitial fibrosis during proteinuria contributing to multifaceted processes of kidney scarring and function loss.
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Affiliation(s)
- Carlamaria Zoja
- IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Mauro Abbate
- IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Giuseppe Remuzzi
- IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy Unit of Nephrology and Dialysis, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
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