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Garmaa G, Bunduc S, Kói T, Hegyi P, Csupor D, Ganbat D, Dembrovszky F, Meznerics FA, Nasirzadeh A, Barbagallo C, Kökény G. A Systematic Review and Meta-Analysis of microRNA Profiling Studies in Chronic Kidney Diseases. Noncoding RNA 2024; 10:30. [PMID: 38804362 PMCID: PMC11130806 DOI: 10.3390/ncrna10030030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/24/2024] [Accepted: 04/28/2024] [Indexed: 05/29/2024] Open
Abstract
Chronic kidney disease (CKD) represents an increasing health burden. Evidence suggests the importance of miRNA in diagnosing CKD, yet the reports are inconsistent. This study aimed to determine novel miRNA biomarkers and potential therapeutic targets from hypothesis-free miRNA profiling studies in human and murine CKDs. Comprehensive literature searches were conducted on five databases. Subgroup analyses of kidney diseases, sample types, disease stages, and species were conducted. A total of 38 human and 12 murine eligible studies were analyzed using Robust Rank Aggregation (RRA) and vote-counting analyses. Gene set enrichment analyses of miRNA signatures in each kidney disease were conducted using DIANA-miRPath v4.0 and MIENTURNET. As a result, top target genes, Gene Ontology terms, the interaction network between miRNA and target genes, and molecular pathways in each kidney disease were identified. According to vote-counting analysis, 145 miRNAs were dysregulated in human kidney diseases, and 32 were dysregulated in murine CKD models. By RRA, miR-26a-5p was significantly reduced in the kidney tissue of Lupus nephritis (LN), while miR-107 was decreased in LN patients' blood samples. In both species, epithelial-mesenchymal transition, Notch, mTOR signaling, apoptosis, G2/M checkpoint, and hypoxia were the most enriched pathways. These miRNA signatures and their target genes must be validated in large patient cohort studies.
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Affiliation(s)
- Gantsetseg Garmaa
- Institute of Translational Medicine, Semmelweis University, Nagyvárad tér 4, 1089 Budapest, Hungary; (G.G.); (A.N.)
- Center for Translational Medicine, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (S.B.); (T.K.); (P.H.); (D.C.); (F.D.); (F.A.M.)
- Department of Pathology, School of Medicine, Mongolian National University of Medical Sciences, Ulan-Bator 14210, Mongolia;
| | - Stefania Bunduc
- Center for Translational Medicine, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (S.B.); (T.K.); (P.H.); (D.C.); (F.D.); (F.A.M.)
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Dionisie Lupu Street 37, 020021 Bucharest, Romania
- Fundeni Clinical Institute, Fundeni Street 258, 022328 Bucharest, Romania
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Baross út 22-24, 1085 Budapest, Hungary
| | - Tamás Kói
- Center for Translational Medicine, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (S.B.); (T.K.); (P.H.); (D.C.); (F.D.); (F.A.M.)
- Department of Stochastics, Institute of Mathematics, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary
| | - Péter Hegyi
- Center for Translational Medicine, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (S.B.); (T.K.); (P.H.); (D.C.); (F.D.); (F.A.M.)
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Baross út 22-24, 1085 Budapest, Hungary
- Institute for Translational Medicine, Medical School, University of Pécs, 7624 Pécs, Hungary
| | - Dezső Csupor
- Center for Translational Medicine, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (S.B.); (T.K.); (P.H.); (D.C.); (F.D.); (F.A.M.)
- Institute for Translational Medicine, Medical School, University of Pécs, 7624 Pécs, Hungary
- Institute of Clinical Pharmacy, University of Szeged, Szikra utca 8, 6725 Szeged, Hungary
| | - Dariimaa Ganbat
- Department of Pathology, School of Medicine, Mongolian National University of Medical Sciences, Ulan-Bator 14210, Mongolia;
- Department of Public Health, Graduate School of Medicine, International University of Health and Welfare, Tokyo 107-840, Japan
| | - Fanni Dembrovszky
- Center for Translational Medicine, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (S.B.); (T.K.); (P.H.); (D.C.); (F.D.); (F.A.M.)
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Baross út 22-24, 1085 Budapest, Hungary
| | - Fanni Adél Meznerics
- Center for Translational Medicine, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary; (S.B.); (T.K.); (P.H.); (D.C.); (F.D.); (F.A.M.)
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Mária utca 41, 1085 Budapest, Hungary
| | - Ailar Nasirzadeh
- Institute of Translational Medicine, Semmelweis University, Nagyvárad tér 4, 1089 Budapest, Hungary; (G.G.); (A.N.)
| | - Cristina Barbagallo
- Section of Biology and Genetics “G. Sichel”, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy;
| | - Gábor Kökény
- Institute of Translational Medicine, Semmelweis University, Nagyvárad tér 4, 1089 Budapest, Hungary; (G.G.); (A.N.)
- International Nephrology Research and Training Center, Semmelweis University, Nagyvárad tér 4, 1089 Budapest, Hungary
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Liu C, Zhang Y, Guo J, Sun W, Ji Y, Wang Y, Liu J, Kong X. Overexpression of microRNA-93-5p and microRNA-374a-5p Suppresses the Osteogenic Differentiation and Mineralization of Human Aortic Valvular Interstitial Cells Through the BMP2/Smad1/5/RUNX2 Signaling Pathway. J Cardiovasc Pharmacol 2023; 82:138-147. [PMID: 37232560 DOI: 10.1097/fjc.0000000000001440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/14/2023] [Indexed: 05/27/2023]
Abstract
ABSTRACT Aortic valve calcification commonly occurs in patients with chronic kidney disease (CKD). However, the regulatory functions of microRNAs (miRNAs/miRs) in the osteogenic differentiation of human aortic valvular interstitial cells (hAVICs) in patients with CKD remain largely unknown. This study aimed to explore the functional role and underlying mechanisms of miR-93-5p and miR-374a-5p in the osteogenic differentiation of hAVICs. For this purpose, hAVICs calcification was induced with high-calcium/high-phosphate medium and the expression levels of miR-93-5p and miR-374a-5p were determined using bioinformatics assay. Alizarin red staining, intracellular calcium content, and alkaline phosphatase activity were used to evaluate calcification. The expression levels of bone morphogenetic protein-2 (BMP2), runt-related transcription factor 2 (Runx2), and phosphorylated (p)-Smad1/5 were detected by luciferase reporter assay, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and western blot analysis. The results revealed that the expression levels of miR-93-5p and miR-374a-5p were significantly decreased in hAVICs in response to high-calcium/high-phosphate medium. The overexpression of miR-93-5p and miR-374a-5p effectively suppressed the high-calcium/high-phosphate-induced calcification and osteogenic differentiation makers. Mechanistically, the overexpression of miR-93-5p and miR-374a-5p inhibits osteogenic differentiation by regulating the BMP2/Smad1/5/Runx2 signaling pathway. Taken together, this study indicates that miR-93-5p and miR-374a-5p suppress the osteogenic differentiation of hAVICs associated with calcium-phosphate metabolic dyshomeostasis through the inhibition of the BMP2/Smad1/5/Runx2 signaling pathway.
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Affiliation(s)
- Cuiying Liu
- Department of Cardiovascular Medicine, Medical School of Southeast University, Nanjing, China
| | - Yajie Zhang
- Central Laboratory, Nanjing Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Jing Guo
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China; and
| | - Wei Sun
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China; and
| | - Yue Ji
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China; and
| | - Yaqing Wang
- Department of Cardiology, Geriatric Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Liu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China; and
| | - Xiangqing Kong
- Department of Cardiovascular Medicine, Medical School of Southeast University, Nanjing, China
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Sargazi S, Mollashahi B, Sargazi S, Heidari Nia M, Saravani R, Mirinejad S, Alidadi A. Prevalence of miR146a Gene Polymorphisms in Diabetic and Non-diabetic Patients with Chronic Kidney Disease. IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY, TRANSACTIONS A: SCIENCE 2021. [DOI: 10.1007/s40995-021-01229-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Construction and Validation of Predictive Model to Identify Critical Genes Associated with Advanced Kidney Disease. Int J Genomics 2020; 2020:7524057. [PMID: 33274190 PMCID: PMC7676934 DOI: 10.1155/2020/7524057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/21/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022] Open
Abstract
Background Chronic kidney disease (CKD) is characterized by progressive renal function loss, which may finally lead to end-stage renal disease (ESRD). The study is aimed at identifying crucial genes related to CKD progressive and constructing a disease prediction model to investigate risk factors. Methods GSE97709 and GSE37171 datasets were downloaded from the GEO database including peripheral blood samples from subjects with CKD, ESRD, and healthy controls. Differential expressed genes (DEGs) were identified and functional enrichment analysis. Machine learning algorithm-based prediction model was constructed to identify crucial functional feature genes related to ESRD. Results A total of 76 DEGs were screened from CDK vs. normal samples while 10,114 DEGs were identified from ESRD vs. CDK samples. For numerous genes related to ESRD, several GO biological terms and 141 signaling pathways were identified including markedly upregulated olfactory transduction and downregulated platelet activation pathway. The DEGs were clustering in three modules according to WGCNA access, namely, ME1, ME2, and ME3. By construction of the XGBoost model and dataset validation, we screened cohorts of genes associated with progressive CKD, such as FZD10, FOXD4, and FAM215A. FZD10 represented the highest score (F score = 21) in predictive model. Conclusion Our results demonstrated that FZD10, FOXD4, PPP3R1, and UCP2 might be critical genes in CKD progression.
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Ren Q, Cheng L, Yi J, Ma L, Pan J, Gou SJ, Fu P. Toll-like Receptors as Potential Therapeutic Targets in Kidney Diseases. Curr Med Chem 2020; 27:5829-5854. [PMID: 31161985 DOI: 10.2174/0929867325666190603110907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/15/2019] [Accepted: 05/13/2019] [Indexed: 02/08/2023]
Abstract
Toll-like Receptors (TLRs) are members of pattern recognition receptors and serve a pivotal role in host immunity. TLRs response to pathogen-associated molecular patterns encoded by pathogens or damage-associated molecular patterns released by dying cells, initiating an inflammatory cascade, where both beneficial and detrimental effects can be exerted. Accumulated evidence has revealed that TLRs are closely associated with various kidney diseases but their roles are still not well understood. This review updated evidence on the roles of TLRs in the pathogenesis of kidney diseases including urinary tract infection, glomerulonephritis, acute kidney injury, transplant allograft dysfunction and chronic kidney diseases.
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Affiliation(s)
- Qian Ren
- Kidney Research Laboratory, Division of Nephrology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Lu Cheng
- Kidney Research Laboratory, Division of Nephrology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Jing Yi
- Kidney Research Laboratory, Division of Nephrology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Liang Ma
- Kidney Research Laboratory, Division of Nephrology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Jing Pan
- Kidney Research Laboratory, Division of Nephrology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Shen-Ju Gou
- Kidney Research Laboratory, Division of Nephrology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Ping Fu
- Kidney Research Laboratory, Division of Nephrology, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
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Ponsuksili S, Reyer H, Hadlich F, Weber F, Trakooljul N, Oster M, Siengdee P, Muráni E, Rodehutscord M, Camarinha-Silva A, Bennewitz J, Wimmers K. Identification of the Key Molecular Drivers of Phosphorus Utilization Based on Host miRNA-mRNA and Gut Microbiome Interactions. Int J Mol Sci 2020; 21:E2818. [PMID: 32316683 PMCID: PMC7215353 DOI: 10.3390/ijms21082818] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/06/2020] [Accepted: 04/16/2020] [Indexed: 12/13/2022] Open
Abstract
Phosphorus is an essential mineral for all living organisms and a limited resource worldwide. Variation and heritability of phosphorus utilization (PU) traits were observed, indicating the general possibility of improvement. Molecular mechanisms of PU, including host and microbial effects, are still poorly understood. The most promising molecules that interact between the microbiome and host are microRNAs. Japanese quail representing extremes for PU were selected from an F2 population for miRNA profiling of the ileal tissue and subsequent association with mRNA and microbial data of the same animals. Sixty-nine differentially expressed miRNAs were found, including 21 novel and 48 known miRNAs. Combining miRNAs and mRNAs based on correlated expression and target prediction revealed enrichment of transcripts in functional pathways involved in phosphate or bone metabolism such as RAN, estrogen receptor and Wnt signaling, and immune pathways. Out of 55 genera of microbiota, seven were found to be differentially abundant between PU groups. The study reveals molecular interactions occurring in the gut of quail which represent extremes for PU including miRNA-16-5p, miR-142b-5p, miR-148a-3p, CTDSP1, SMAD3, IGSF10, Bacteroides, and Alistipes as key indicators due to their trait-dependent differential expression and occurrence as hub-members of the network of molecular drivers of PU.
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Affiliation(s)
- Siriluck Ponsuksili
- Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (H.R.); (F.H.); (F.W.); (N.T.); (M.O.); (P.S.); (E.M.); (K.W.)
| | - Henry Reyer
- Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (H.R.); (F.H.); (F.W.); (N.T.); (M.O.); (P.S.); (E.M.); (K.W.)
| | - Frieder Hadlich
- Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (H.R.); (F.H.); (F.W.); (N.T.); (M.O.); (P.S.); (E.M.); (K.W.)
| | - Frank Weber
- Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (H.R.); (F.H.); (F.W.); (N.T.); (M.O.); (P.S.); (E.M.); (K.W.)
| | - Nares Trakooljul
- Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (H.R.); (F.H.); (F.W.); (N.T.); (M.O.); (P.S.); (E.M.); (K.W.)
| | - Michael Oster
- Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (H.R.); (F.H.); (F.W.); (N.T.); (M.O.); (P.S.); (E.M.); (K.W.)
| | - Puntita Siengdee
- Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (H.R.); (F.H.); (F.W.); (N.T.); (M.O.); (P.S.); (E.M.); (K.W.)
| | - Eduard Muráni
- Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (H.R.); (F.H.); (F.W.); (N.T.); (M.O.); (P.S.); (E.M.); (K.W.)
| | - Markus Rodehutscord
- Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany; (M.R.); (A.C.-S.); (J.B.)
| | - Amélia Camarinha-Silva
- Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany; (M.R.); (A.C.-S.); (J.B.)
| | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany; (M.R.); (A.C.-S.); (J.B.)
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (H.R.); (F.H.); (F.W.); (N.T.); (M.O.); (P.S.); (E.M.); (K.W.)
- Faculty of Agricultural and Environmental Sciences, University Rostock, 18059 Rostock, Germany
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Abstract
Histone deacetylation, DNA methylation, and micro-RNAs (miRNAs) are the three main epigenetic mechanisms that regulate gene expression. All the physiological processes involved in bone remodeling are tightly regulated by epigenetic factors. This review discusses the main epigenetic modifications seen in tumoral and non-tumoral bone diseases, with emphasis on miRNAs. The role for epigenetic modifications of gene expression in the most common bone diseases is illustrated by drawing on the latest publications in the field. In multifactorial bone diseases such as osteoporosis, many epigenetic biomarkers, either alone or in combination, have been associated with bone mineral density or suggested to predict osteoporotic fractures. In addition, treatments designed to modulate bone remodeling by selectively targeting the function of specific miRNAs are being evaluated. Advances in the understanding of epigenetic regulation shed new light on the pathophysiology of other non-tumoral bone diseases, including genetic conditions inherited on a Mendelian basis. Finally, in the area of primary and metastatic bone tumors, the last few years have witnessed considerable progress in elucidating the epigenetic regulation of oncogenesis and its local interactions with bone tissue. These new data may allow the development of epigenetic outcome predictors, which are in very high demand, and of innovative therapeutic agents acting via miRNA modulation.
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Affiliation(s)
- Laetitia Michou
- Division de rhumatologie, département de médecine,centre de recherche, CHU de Québec-Université Laval, R-4774 Québec, Canada; Service de rhumatologie,CHU de Québec-Université Laval, 2705, boulevard Laurier, R-4774 Québec, Canada.
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