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Unger Avila P, Padvitski T, Leote AC, Chen H, Saez-Rodriguez J, Kann M, Beyer A. Gene regulatory networks in disease and ageing. Nat Rev Nephrol 2024; 20:616-633. [PMID: 38867109 DOI: 10.1038/s41581-024-00849-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2024] [Indexed: 06/14/2024]
Abstract
The precise control of gene expression is required for the maintenance of cellular homeostasis and proper cellular function, and the declining control of gene expression with age is considered a major contributor to age-associated changes in cellular physiology and disease. The coordination of gene expression can be represented through models of the molecular interactions that govern gene expression levels, so-called gene regulatory networks. Gene regulatory networks can represent interactions that occur through signal transduction, those that involve regulatory transcription factors, or statistical models of gene-gene relationships based on the premise that certain sets of genes tend to be coexpressed across a range of conditions and cell types. Advances in experimental and computational technologies have enabled the inference of these networks on an unprecedented scale and at unprecedented precision. Here, we delineate different types of gene regulatory networks and their cell-biological interpretation. We describe methods for inferring such networks from large-scale, multi-omics datasets and present applications that have aided our understanding of cellular ageing and disease mechanisms.
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Affiliation(s)
- Paula Unger Avila
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Tsimafei Padvitski
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Ana Carolina Leote
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - He Chen
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Martin Kann
- Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Andreas Beyer
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
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Zhao R, Fan R, Pan Y, Han Y, Wang Y, Chen W. Fruquintinib-induced renal-limited thrombotic microangiopathy: a case report. BMC Nephrol 2024; 25:170. [PMID: 38762494 PMCID: PMC11102188 DOI: 10.1186/s12882-024-03598-8] [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: 01/12/2024] [Accepted: 05/03/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND Fruquintinib is a highly selective inhibitor of vascular endothelial growth factor receptor (VEGFR). Currently, there are no reported cases of fruquintinib causing kidney-restrictive thrombotic microangiopathy (TMA) in the available Chinese and foreign literature. CASE PRESENTATION In this case report, we presented a 73-year-old patient receiving fruquintinib for metastatic colon cancer, manifesting abundant proteinuria, in which kidney-restrictive TMA was also diagnosed through renal biopsy. As far as we were concerned, this was the frst reported in terms of fruquintinib-induced kidney-restrictive TMA confrmed by renal biopsy. CONCLUSION This case indicates that fruquintinib may result in kidney-restrictive TMA, which is a rare but life-threatening complication of cancer treatment drug. Therefore, regular monitoring of proteinuria and blood pressure is imperative for all patients undergoing anti-VEGF drug therapy. And renal biopsy should be promptly conducted to facilitate early detection of thrombotic microangiopathy.
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Affiliation(s)
- Ruiping Zhao
- Department of Nephrology, the First Affiliated Hospital of Bengbu Medical University, Bengbu, China
| | - Ruichen Fan
- Department of Pharmacy, the First Affiliated Hospital of Bengbu Medical University, Bengbu, China
| | - Yan Pan
- Department of Nephrology, the First Affiliated Hospital of Bengbu Medical University, Bengbu, China
| | - Yuze Han
- Department of Nephrology, the First Affiliated Hospital of Bengbu Medical University, Bengbu, China
| | - Ying Wang
- Department of Nephrology, the First Affiliated Hospital of Bengbu Medical University, Bengbu, China
| | - Weidong Chen
- Department of Nephrology, the First Affiliated Hospital of Bengbu Medical University, Bengbu, China.
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Li J, Li XL, Li CQ. Immunoregulation mechanism of VEGF signaling pathway inhibitors and its efficacy on the kidney. Am J Med Sci 2023; 366:404-412. [PMID: 37699444 DOI: 10.1016/j.amjms.2023.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/10/2023] [Accepted: 09/07/2023] [Indexed: 09/14/2023]
Abstract
Angiogenesis and immunosuppression are closely related pathophysiologic processes. Widely prescribed in malignant tumor and proliferative retinal lesions, VEGF signaling pathway inhibitors may cause hypertension and renal injury in some patients, presenting with proteinuria, nephrotic syndrome, renal failure and thrombotic microangiopathy. VEGF signaling pathway inhibitors block the action of both VEGF-A and VEGF-C. However, VEGF-A and VEGF-C produced by podocytes are vital to maintain the physiological function of glomerular endothelial cells and podocytes. There is still no effective treatment for kidney disease associated with VEGF signaling pathway inhibitors and some patients have progressive renal failure even after withdrawal of the drug. Recent studies reveal that blocking of VEGF-A and VEGF-C can activate CD4 +and CD8+ T cells, augment antigen-presenting function of dendritic cells, enhance cytotoxicity of macrophages and initiate complement cascade activation. VEGF and VEGFR are expressed in immune cells, which are involved in the immunosuppression and cross-talk among immune cells. This review summarizes the expression and function of VEGF-A and VEGF-C in the kidney. The current immunoregulation mechanisms of VEGF signaling pathway inhibitors are reviewed. Finally, combinate strategies are summarized to highlight the proposal for VEGF signaling pathway inhibitors.
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Affiliation(s)
- Jun Li
- Department of Nephrology, Affiliated Hospital of Jiangnan University, Jiangsu, China; Wuxi School of Medicine, Jiangnan University, Jiangsu, China.
| | - Xiao-Lin Li
- Wuxi School of Medicine, Jiangnan University, Jiangsu, China
| | - Chun-Qing Li
- Department of Nephrology, Affiliated Hospital of Jiangnan University, Jiangsu, China
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Salfi G, Casiraghi F, Remuzzi G. Current understanding of the molecular mechanisms of circulating permeability factor in focal segmental glomerulosclerosis. Front Immunol 2023; 14:1247606. [PMID: 37795085 PMCID: PMC10546017 DOI: 10.3389/fimmu.2023.1247606] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/05/2023] [Indexed: 10/06/2023] Open
Abstract
The pathogenetic mechanisms underlying the onset and the post-transplant recurrence of primary focal segmental glomerulosclerosis (FSGS) are complex and remain yet to be fully elucidated. However, a growing body of evidence emphasizes the pivotal role of the immune system in both initiating and perpetuating the disease. Extensive investigations, encompassing both experimental models and patient studies, have implicated T cells, B cells, and complement as crucial actors in the pathogenesis of primary FSGS, with various molecules being proposed as potential "circulating factors" contributing to the disease and its recurrence post kidney-transplantation. In this review, we critically assessed the existing literature to identify essential pathways for a comprehensive characterization of the pathogenesis of FSGS. Recent discoveries have shed further light on the intricate interplay between these mechanisms. We present an overview of the current understanding of the engagement of distinct molecules and immune cells in FSGS pathogenesis while highlighting critical knowledge gaps that require attention. A thorough characterization of these intricate immune mechanisms holds the potential to identify noninvasive biomarkers that can accurately identify patients at high risk of post-transplant recurrence. Such knowledge can pave the way for the development of targeted and personalized therapeutic approaches in the management of FSGS.
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Affiliation(s)
| | - Federica Casiraghi
- Istituto di Ricerche Farmacologiche Mario Negri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Bergamo, Italy
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Luo J, Tugade T, Sun E, Pena Diaz AM, O’Gorman DB. Sustained AWT1 expression by Dupuytren's disease myofibroblasts promotes a proinflammatory milieu. J Cell Commun Signal 2022; 16:677-690. [PMID: 35414143 PMCID: PMC9733761 DOI: 10.1007/s12079-022-00677-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/22/2022] [Indexed: 12/13/2022] Open
Abstract
Palmar fibromatosis, also known as Dupuytren's disease (DD), is a common and heritable fibrosis of the hand. It is characterized by the formation of myofibroblastic nodules that can progress to palmar-digital contractures and permanent loss of dexterity. The presence of inflammatory cell infiltrate within these nodules has been interpreted to suggest a pathogenesis mediated by a proinflammatory microenvironment. However, the molecular mechanisms driving the formation of pro-fibrotic microenvironments in this and other fibroses remain unclear. To gain insights into this process, we have assessed the contributions of an alternatively spliced, multi-functional transcription factor, Wilms Tumor 1 (WT1), previously shown to be upregulated in primary myofibroblasts derived from DD tissues. Proinflammatory cytokine stimuli of DD myofibroblasts enhanced the expression of several distinct WT1 variants, the most sustained being a 5' truncated version of WT1, alternative WT1 (AWT1). Constitutive adenoviral expression of AWT1 in myofibroblasts derived from phenotypically non-fibrotic palmar fascia significantly induced the expression and secretion of proinflammatory cytokines, including some with potential as novel therapeutic targets. In summary, these data implicate roles for sustained AWT1 expression in DD as a transcriptional driver of a proinflammatory fascial milieu.
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Affiliation(s)
- Johnny Luo
- grid.39381.300000 0004 1936 8884Department of Biochemistry, University of Western Ontario, London, ON Canada
| | - Trisiah Tugade
- grid.39381.300000 0004 1936 8884Department of Biochemistry, University of Western Ontario, London, ON Canada
| | - Emmy Sun
- grid.39381.300000 0004 1936 8884Department of Biochemistry, University of Western Ontario, London, ON Canada
| | - Ana Maria Pena Diaz
- grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, 268 Grosvenor Street, London, ON N6A 4V2 Canada
| | - David B. O’Gorman
- grid.39381.300000 0004 1936 8884Department of Biochemistry, University of Western Ontario, London, ON Canada ,grid.39381.300000 0004 1936 8884Department of Surgery, University of Western Ontario, London, ON Canada ,grid.415847.b0000 0001 0556 2414Lawson Health Research Institute, 268 Grosvenor Street, London, ON N6A 4V2 Canada
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SAEED MOHAMEDEM, CIVES-LOSADA CANDELA, EFFERTH THOMAS. Biomarker Expression Profiling in Cervix Carcinoma Biopsies Unravels WT1 as a Target of Artesunate. Cancer Genomics Proteomics 2022; 19:727-739. [PMID: 36316038 PMCID: PMC9620444 DOI: 10.21873/cgp.20355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/01/2022] [Accepted: 09/15/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND/AIM Artemisinin and its derivatives are not only approved antimalarial drugs but also exert strong anticancer activity. Based on the clinical activity of artesunate (ART) that has been previously reported in cervix carcinoma, we investigated a panel of 12 different biomarkers and identified the Wilms Tumor 1 (WT1) protein as a potential target of ART. PATIENTS AND METHODS Matched biopsies of cervical carcinoma before, during, and after therapy from patients treated with ART were investigated for induction of apoptosis (TUNEL assay) and expression of Wilms Tumor protein 1 (WT1), 14-3-3 ζ, cluster of differentiation markers (CD4, CD8, CD56), ATP-binding cassette transporter B5 (ABCB5), glutathione S-transferase P1 (GSTP1), inducible nitric oxide synthase (iNOS), translationally controlled tumor protein (TCTP), eukaryotic elongation factor 3 (eIF3), and ADP/ATP translocase by immunohistochemistry. WT1 has been selected for more detailed analyses using molecular docking in silico, microscale thermophoresis using recombinant WT1, and cytotoxicity testing (resazurin assay) using HEK293 cells transfected with four different WT1 splice variants. RESULTS The fraction of apoptotic cells and the expression of WT1, 14-3-3 ζ, and CD4 increased upon ART treatment in tumors of patients. ART was bound in silico to a domain located at the DNA-binding site of WT1, while dihydroartemisinin (DHA) was bound with low affinity to a different site of WT1 not related to DNA-binding. The results were verified using microscale thermophoresis, where ART but not DHA bound to recombinant WT1. Transfectants overexpressing different WT1 splice variants exerted low but significant resistance to ART (≈2-fold). CONCLUSION WT1 may represent a novel target of ART in cancer cells that contribute to the response of tumor cells to this drug.
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Affiliation(s)
- MOHAMED E. M. SAEED
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - CANDELA CIVES-LOSADA
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany,Department of Physiology and Pharmacology, IBSAL, University of Salamanca, Salamanca, Spain
| | - THOMAS EFFERTH
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
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