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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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Miao H, Zhang Y, Yu X, Zou L, Zhao Y. Membranous nephropathy: Systems biology-based novel mechanism and traditional Chinese medicine therapy. Front Pharmacol 2022; 13:969930. [PMID: 36176440 PMCID: PMC9513429 DOI: 10.3389/fphar.2022.969930] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/10/2022] [Indexed: 12/05/2022] Open
Abstract
Membranous nephropathy (MN) is a renal-limited non-inflammatory autoimmune disease in the glomerulus, which is the second or third main cause of end-stage kidney diseases in patients with primary glomerulonephritis. Substantial achievements have increased our understanding of the aetiology and pathogenesis of murine and human MN. The identification of nephritogenic autoantibodies against neutral endopeptidase, phospholipase A2 receptor (PLA2R) and thrombospondin type-1 domain-containing 7A (THSD7A) antigens provide more specific concept-driven intervention strategies for treatments by specific B cell-targeting monoclonal antibodies to inhibit antibody production and antibody-antigen immune complex deposition. Furthermore, additional antibody specificities for antigens have been discovered, but their pathogenic effects are uncertain. Although anti-PLA2R and anti-THSD7A antibodies as a diagnostic marker is widely used in MN patients, many questions including autoimmune response development, antigenic epitopes, and podocyte damage signalling pathways remain unresolved. This review describes the current available evidence regarding both established and novel molecular mechanisms based on systems biology approaches (gut microbiota, long non-coding RNAs, metabolite biomarkers and DNA methylation) in MN, with an emphasis on clinical findings. This review further summarizes the applications of traditional Chinese medicines such as Tripterygium wilfordii and Astragalus membranaceus for MN treatment. Lastly, this review considers how the identification of novel antibodies/antigens and unresolved questions and future challenges reveal the pathogenesis of MN.
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Affiliation(s)
- Hua Miao
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yamei Zhang
- Key Laboratory of Clinical Genetics & Key Disciplines of Clinical Pharmacy, Affiliated Hospital and Clinical Medical College of Chengdu University, Chengdu, Sichuan, China
| | - Xiaoyong Yu
- Department of Nephrology, Shaanxi Traditional Chinese Medicine Hospital, Xi’an, Shaanxi, China
- *Correspondence: Xiaoyong Yu, ; Liang Zou, ; Yingyong Zhao,
| | - Liang Zou
- School of Food and Bioengineering, Chengdu University, Chengdu, Sichuan, China
- *Correspondence: Xiaoyong Yu, ; Liang Zou, ; Yingyong Zhao,
| | - Yingyong Zhao
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
- Key Laboratory of Clinical Genetics & Key Disciplines of Clinical Pharmacy, Affiliated Hospital and Clinical Medical College of Chengdu University, Chengdu, Sichuan, China
- *Correspondence: Xiaoyong Yu, ; Liang Zou, ; Yingyong Zhao,
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Liu F, Chen J, Luo C, Meng X. Pathogenic Role of MicroRNA Dysregulation in Podocytopathies. Front Physiol 2022; 13:948094. [PMID: 35845986 PMCID: PMC9277480 DOI: 10.3389/fphys.2022.948094] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) participate in the regulation of various important biological processes by regulating the expression of various genes at the post-transcriptional level. Podocytopathies are a series of renal diseases in which direct or indirect damage of podocytes results in proteinuria or nephrotic syndrome. Despite decades of research, the exact pathogenesis of podocytopathies remains incompletely understood and effective therapies are still lacking. An increasing body of evidence has revealed a critical role of miRNAs dysregulation in the onset and progression of podocytopathies. Moreover, several lines of research aimed at improving common podocytopathies diagnostic tools and avoiding invasive kidney biopsies have also identified circulating and urine miRNAs as possible diagnostic and prognostic biomarkers for podocytopathies. The present review mainly aims to provide an updated overview of the recent achievements in research on the potential applicability of miRNAs involved in renal disorders related to podocyte dysfunction by laying particular emphasis on focal segmental glomerulosclerosis (FSGS), minimal change disease (MCD), membranous nephropathy (MN), diabetic kidney disease (DKD) and IgA nephropathy (IgAN). Further investigation into these dysregulated miRNAs will not only generate novel insights into the mechanisms of podocytopathies, but also might yield novel strategies for the diagnosis and therapy of this disease.
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Affiliation(s)
- Feng Liu
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiefang Chen
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Changqing Luo
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Changqing Luo, ; Xianfang Meng,
| | - Xianfang Meng
- Department of Neurobiology, Institute of Brain Research, School of Basic Medical Sciences, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Changqing Luo, ; Xianfang Meng,
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Sun IO, Bae YU, Lee H, Kim H, Jeon JS, Noh H, Choi JS, Doh KO, Kwon SH. Circulating miRNAs in extracellular vesicles related to treatment response in patients with idiopathic membranous nephropathy. J Transl Med 2022; 20:224. [PMID: 35568952 PMCID: PMC9107687 DOI: 10.1186/s12967-022-03430-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/05/2022] [Indexed: 12/29/2022] Open
Abstract
Background Extracellular vesicle (EV)-microRNAs (miRNAs) are potential biomarkers for various renal diseases. This study attempted to identify the circulating EV-miRNA signature not only for discriminating idiopathic membranous nephropathy (IMN) from idiopathic nephrotic syndrome (INS), but also to predict the treatment response of patients with IMN. Methods We prospectively enrolled 60 participants, including those with IMN (n = 19) and INS (n = 21) and healthy volunteers (HVs; n = 20) in this study. Using RNA sequencing, we assessed the serum EV-miRNA profiles of all participants. To identify the EV-miRNAs predictive of treatment response in IMN, we also analyzed EV-miRNAs among patients with IMN with and without clinical remission. Results The expression levels of 3 miRNAs differed between IMN patients, INS patients and HVs. In addition, compared to HVs, RNA sequencing revealed differential expression of 77 and 44 EV-miRNAs in patients with IMN without and with remission, respectively. We also identified statistically significant (|fold change ≥ 2, p < 0.05) differences in the expression levels of 23 miRNAs in IMN without remission. Biological pathway analysis of miRNAs in IMN without remission indicated that they are likely involved in various pathways, including renal fibrosis. Conclusion Our study identified EV-miRNAs associated with IMN as well as those associations with therapeutic response. Therefore, these circulating EV-miRNAs may be used as potential markers for the diagnosis and prediction of treatment response in patients with IMN. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03430-7.
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Affiliation(s)
- In O Sun
- Division of Nephrology, Department of Internal Medicine, Presbyterian Medical Center, Jeonju, Republic of Korea
| | - Yun-Ui Bae
- Department of Internal Medicine, Keimyung University Dongsan Hospital, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Haekyung Lee
- Division of Nephrology, Soonchunhyang University Seoul Hospital, 59 Daesagwan-ro, Youngsan-gu, Seoul, 04401, Republic of Korea
| | - Hyoungnae Kim
- Division of Nephrology, Soonchunhyang University Seoul Hospital, 59 Daesagwan-ro, Youngsan-gu, Seoul, 04401, Republic of Korea
| | - Jin Seok Jeon
- Division of Nephrology, Soonchunhyang University Seoul Hospital, 59 Daesagwan-ro, Youngsan-gu, Seoul, 04401, Republic of Korea
| | - Hyunjin Noh
- Division of Nephrology, Soonchunhyang University Seoul Hospital, 59 Daesagwan-ro, Youngsan-gu, Seoul, 04401, Republic of Korea
| | - Jong-Soo Choi
- Department of Physiology, College of Medicine, Yeungnam University, Daegu, 42415, Republic of Korea
| | - Kyung-Oh Doh
- Department of Physiology, College of Medicine, Yeungnam University, Daegu, 42415, Republic of Korea.
| | - Soon Hyo Kwon
- Division of Nephrology, Soonchunhyang University Seoul Hospital, 59 Daesagwan-ro, Youngsan-gu, Seoul, 04401, Republic of Korea.
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Liu Q, Liu J, Lin B, Zhang Y, Ma M, Yang M, Qin X. Novel Biomarkers in Membranous Nephropathy. Front Immunol 2022; 13:845767. [PMID: 35529848 PMCID: PMC9074781 DOI: 10.3389/fimmu.2022.845767] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/25/2022] [Indexed: 01/13/2023] Open
Abstract
Membranous nephropathy (MN) is the main cause of adult nephrotic syndrome (NS). The pathogenesis of MN is complex and involves subepithelial immune complex deposition. Approximately one-third of patients with MN develop end-stage renal disease (ESRD). Timely diagnosis and reasonable intervention are the keys to improving prognosis. In recent years, with the development of high-throughput technologies, such as mass spectrometry (MS), microarray, and sequencing technologies, the discovery of biomarkers for MN has become an important area of research. In this review, we summarize the significant progress in biomarker identification. For example, a variety of podocyte target antigens and their autoantibodies have been reported. Phospholipase A2 receptor (PLA2R) is the most well-established target antigen in MN. PLA2R and its autoantibodies have clinical significance, with both diagnostic and therapeutic value for MN. In addition, a variety of new biomarkers, including proteins, metabolites, noncoding RNAs (ncRNAs), and immune cells, have recently been found. These MN-related biomarkers have great significance in the diagnosis, progression, prognosis, and treatment response of MN.
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Affiliation(s)
- Qiuying Liu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Laboratory Medicine, Beijing Haidian Hospital, Beijing Haidian Section of Peking University Third Hospital, Beijing, China
| | - Jianhua Liu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Baoxu Lin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yue Zhang
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Meichen Ma
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Mei Yang
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaosong Qin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Xiaosong Qin,
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Renal mitochondrial injury in the pathogenesis of CKD: mtDNA and mitomiRs. Clin Sci (Lond) 2022; 136:345-360. [PMID: 35260892 PMCID: PMC10018514 DOI: 10.1042/cs20210512] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 02/14/2022] [Accepted: 02/24/2022] [Indexed: 12/31/2022]
Abstract
Chronic kidney disease (CKD) is a public health concern that affects over 200 million people worldwide and is associated with a tremendous economic burden. Therefore, deciphering the mechanisms underpinning CKD is crucial to decelerate its progression towards end-stage renal disease (ESRD). Renal tubular cells are populated with a high number of mitochondria, which produce cellular energy and modulate several important cellular processes, including generation of reactive oxygen species (ROS), calcium homeostasis, proliferation, and apoptosis. Over the past few years, increasing evidence has implicated renal mitochondrial damage in the pathogenesis of common etiologies of CKD, such as diabetes, hypertension, metabolic syndrome (MetS), chronic renal ischemia, and polycystic kidney disease (PKD). However, most compelling evidence is based on preclinical studies because renal biopsies are not routinely performed in many patients with CKD. Previous studies have shown that urinary mitochondrial DNA (mtDNA) copy numbers may serve as non-invasive biomarkers of renal mitochondrial dysfunction. Emerging data also suggest that CKD is associated with altered expression of mitochondria-related microRNAs (mitomiRs), which localize in mitochondria and regulate the expression of mtDNA and nucleus-encoded mitochondrial genes. This review summarizes relevant evidence regarding the involvement of renal mitochondrial injury and dysfunction in frequent forms of CKD. We further provide an overview of non-invasive biomarkers and potential mechanisms of renal mitochondrial damage, especially focusing on mtDNA and mitomiRs.
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Zhou X, Dai H, Jiang H, Rui H, Liu W, Dong Z, Zhang N, Zhao Q, Feng Z, Hu Y, Hou F, Zheng Y, Liu B. MicroRNAs: Potential mediators between particulate matter 2.5 and Th17/Treg immune disorder in primary membranous nephropathy. Front Pharmacol 2022; 13:968256. [PMID: 36210816 PMCID: PMC9532747 DOI: 10.3389/fphar.2022.968256] [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: 06/13/2022] [Accepted: 08/29/2022] [Indexed: 11/19/2022] Open
Abstract
Primary membranous nephropathy (PMN), is an autoimmune glomerular disease and the main reason of nephrotic syndrome in adults. Studies have confirmed that the incidence of PMN increases yearly and is related to fine air pollutants particulate matter 2.5 (PM2.5) exposure. These imply that PM2.5 may be associated with exposure to PMN-specific autoantigens, such as the M-type receptor for secretory phospholipase A2 (PLA2R1). Emerging evidence indicates that Th17/Treg turns to imbalance under PM2.5 exposure, but the molecular mechanism of this process in PMN has not been elucidated. As an important indicator of immune activity in multiple diseases, Th17/Treg immune balance is sensitive to antigens and cellular microenvironment changes. These immune pathways play an essential role in the disease progression of PMN. Also, microRNAs (miRNAs) are susceptible to external environmental stimulation and play link role between the environment and immunity. The contribution of PM2.5 to PMN may induce Th17/Treg imbalance through miRNAs and then produce epigenetic affection. We summarize the pathways by which PM2.5 interferes with Th17/Treg immune balance and attempt to explore the intermediary roles of miRNAs, with a particular focus on the changes in PMN. Meanwhile, the mechanism of PM2.5 promoting PLA2R1 exposure is discussed. This review aims to clarify the potential mechanism of PM2.5 on the pathogenesis and progression of PMN and provide new insights for the prevention and treatment of the disease.
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Affiliation(s)
- Xiaoshan Zhou
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Haoran Dai
- Shunyi Branch, Beijing Hospital of Traditional Chinese Medicine, Beijing, China
| | - Hanxue Jiang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Hongliang Rui
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,Beijing Institute of Chinese Medicine, Beijing, China
| | - Wenbin Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Zhaocheng Dong
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Na Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Qihan Zhao
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Zhendong Feng
- Pinggu Hospital, Beijing Hospital of Traditional Chinese Medicine, Beijing, China
| | - Yuehong Hu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Fanyu Hou
- School of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Yang Zheng
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Baoli Liu
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,Shunyi Branch, Beijing Hospital of Traditional Chinese Medicine, Beijing, China
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Biomarker Identification in Membranous Nephropathy Using a Long Non-coding RNA-Mediated Competitive Endogenous RNA Network. Interdiscip Sci 2021; 13:615-623. [PMID: 34472046 DOI: 10.1007/s12539-021-00466-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 07/01/2021] [Accepted: 07/23/2021] [Indexed: 10/20/2022]
Abstract
PURPOSE This study was aimed to identify biomarker associated with membranous nephropathy (MN) progression by integration of expression profiles and competitive endogenous RNA (ceRNA) network analysis. METHODS The gene (GSE108113) and microRNAs (miRNAs) expression profiles (GSE64306) were downloaded to identify the differentially expressed mRNAs, miRNAs and long non-coding RNAs (lncRNAs) between MN and control groups. The functions and pathways enriched by the differentially expressed mRNAs were analyzed. The mRNA-lncRNA co-expression network was constructed followed by and the ceRNA network construction. RESULTS Total 264 upregulated and 196 downregulated differentially expressed mRNAs, 79 upregulated and 4 downregulated lncRNAs, as well as 115 upregulated and 93 downregulated miRNAs were obtained between MN and control groups. After analysis, the differential mRNAs were significantly involved in multiple immune-related processes, and cell proliferation, apoptosis and differentiation processes, as well as pathways of taste transduction and lysosome. Finally, a ceRNA network consisting of 4 mRNAs (EPB41L5, FAM43A, PRKG1 and TTC14), 3 lncRNAs (LINC00052, LINC00641 and N4BP2L2-IT2) and 5 miRNAs (hsa-miR-145-5p, hsa-miR-3605-5p, hsa-miR-148a-3p, hsa-miR-497-5p and hsa-miR-148b-3p) was constructed. CONCLUSION Our study indicated dysregulation of immune- and apoptosis-associated functions and taste transduction and lysosome pathways may play important roles in MN progression. Deregulated ceRNAs, such as LINC00052-hsa-miR-145-5p-EPB41L5, LINC00052-hsa-miR-148a-3p-FAM43A and LINC00641-hsa-497-5p-PRKG1, may be associated with MN development.
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Iranzad R, Motavalli R, Ghassabi A, Pourakbari R, Etemadi J, Yousefi M. Roles of microRNAs in renal disorders related to primary podocyte dysfunction. Life Sci 2021; 277:119463. [PMID: 33862110 DOI: 10.1016/j.lfs.2021.119463] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/19/2021] [Accepted: 03/27/2021] [Indexed: 12/20/2022]
Abstract
Through the regulation of gene expression, microRNAs (miRNAs) are capable of modulating vital biological processes, such as proliferation, differentiation, and apoptosis. Several mechanisms control the function of miRNAs, including translational inhibition and targeted miRNA degradation. Through utilizing high-throughput screening methods, such as small RNA sequencing and microarray, alterations in miRNA expression of kidneys have recently been observed both in rodent models and humans throughout the development of chronic kidney disease (CKD) and acute kidney injury (AKI). The levels of miRNAs in urine supernatant, sediment, and exosomal fraction could predict novel biomarker candidates in different diseases of kidneys, including IgA nephropathy, lupus nephritis, and diabetic nephropathy. The therapeutic potential of administrating anti-miRNAs and miRNAs has also been reported recently. The present study is aimed at reviewing the state-of-the-art research with regards to miRNAs involved in renal disorders related to primary podocyte dysfunction by laying particular emphasis on Focal Segmental Glomerulosclerosis (FSGS), Minimal Change Disease (MCD) and Membranous Nephropathy (MN).
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Affiliation(s)
- Rahim Iranzad
- Tabriz University of Medical Sciences, Tabriz, Iran; Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Roza Motavalli
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Ghassabi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ramin Pourakbari
- Tabriz University of Medical Sciences, Tabriz, Iran; Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalal Etemadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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10
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Wu L, Zhang X, Luo L, Li X, Liu Y, Qin X. Altered expression of serum miR-106a, miR-19b, miR-17, and PTEN in patients with idiopathic membranous nephropathy. J Clin Lab Anal 2021; 35:e23737. [PMID: 33745222 PMCID: PMC8059741 DOI: 10.1002/jcla.23737] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND To find new diagnostic markers for idiopathic membranous nephropathy (IMN) and also conduct preliminary explorations into the possible pathogenesis of IMN by comparing the expression of microRNA-451a (miR-451a), miR-106a, miR-19b, miR-17, and phosphatase and tensin homolog (PTEN) protein in the serum of patients with IMN and healthy controls. METHODS The expression levels of miR-451a, miR-106a, miR-19b, and miR-17 in the serum of patients in the IMN group (n = 55, age: 50.2 ± 12.1 years) and the control group (n = 58, age 47.4 ± 13.1 years) were measured by quantitative real-time polymerase chain reaction (qRT-PCR), and the concentration of serum PTEN protein was determined by enzyme-linked immunosorbent assay (ELISA). RESULTS Compared with the control group, the expression of miR-106a, miR-19b, and miR-17 was decreased significantly in the IMN group, whereas PTEN protein concentration was increased significantly in the IMN group. The areas under the receiver operating characteristic curve (AUC) of serum miR-106a, miR-19b, miR-17, and PTEN were 0.66 (95% confidence interval [CI], 0.56-0.76), 0.81 (95% CI, 0.73-0.89), 0.69 (95% CI, 0.59-0.79), and 0.86 (95% CI, 0.79-0.93), respectively. The level of serum PTEN protein was negatively correlated with the expression of miR-106a and miR-19b. PTEN concentration was positively correlated with serum urea (Urea), creatinine (Crea), cystatin C (Cysc), 24 h urine total protein (24 h-UP) and negatively correlated with albumin (Alb) and estimated glomerular filtration rate (eGFR). CONCLUSIONS MiR-106a, miR-19b, miR-17, and PTEN are involved in the pathogenesis of IMN and may become new biomarkers for the diagnosis of IMN.
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Affiliation(s)
- Lina Wu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xinpeng Zhang
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China.,Department of Laboratory Medicine, The People's Hospital of Liupanshui City, Liupanshui, China
| | - Lin Luo
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaoying Li
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yong Liu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaosong Qin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
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11
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Sun Z, Xu Q, Ma Y, Yang S, Shi J. Circ_0000524/miR-500a-5p/CXCL16 axis promotes podocyte apoptosis in membranous nephropathy. Eur J Clin Invest 2021; 51:e13414. [PMID: 32974919 DOI: 10.1111/eci.13414] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Podocytes apoptosis is a hallmark of membranous nephropathy (MN). Circ_0000524 has been reported to be associated with patients with MN, whereas the effect of circ_0000524 on podocytes apoptosis and the underlying mechanisms in MN have not been elaborated. METHODS Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were performed to detect the expressions of circ_0000524, microRNA-500a-5p (miR-500a-5p), and C-X-C chemokine ligand 16 (CXCL16) in MN tissues and podocytes. Podocyte injury was induced by angiotensin II (AngII). Cell apoptosis was detected by flow cytometry. Caspase-3 or caspase-9 activity was evaluated using a caspase-3 or caspase-9 activity assay kit, respectively. Dual-luciferase reporter assay, RNA immunoprecipitation (RIP) and pull-down assay were used to address the relationship among circ_0000524,miR-500a-5p and CXCL16. RESULTS Upregulation of circ_0000524 and CXCL16 and low expression of miR-500a-5p were observed in MN tissues. AngII treatment induced the overexpression of circ_0000524 and CXCL16, a decrease of miR-500a-5p, and induced cell apoptosis in podocytes. Circ_0000524 negatively modulated the expression of miR-500a-5p. Circ_0000524 depletion inhibited podocyte apoptosis, which was rescued by loss of miR-500a-5p. miR-500a-5p contained the binding sites with CXCL16. Circ_0000524 knockdown hampered CXCL16 expression by upregulating miR-500a-5p expression. Additionally, miR-500a-5p upregulation suppressed AngII-induced podocyte apoptosis, which was rescued by enhanced expression of CXCL16. CONCLUSION Circ_0000524/miR-500a-5p/CXCL16 pathway regulated podocyte apoptosis in MN.
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Affiliation(s)
- Zhiqiang Sun
- Department of Nephrology, Huaihe Hospital of Henan University, Kaifeng, China
| | - Qingqing Xu
- Department of Nephrology, Huaihe Hospital of Henan University, Kaifeng, China
| | - Yali Ma
- Department of Nephrology, Huaihe Hospital of Henan University, Kaifeng, China
| | - Suxia Yang
- Department of Nephrology, Huaihe Hospital of Henan University, Kaifeng, China
| | - Jun Shi
- Department of Nephrology, Huaihe Hospital of Henan University, Kaifeng, China
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12
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Motavalli R, Etemadi J, Soltani-Zangbar MS, Ardalan MR, Kahroba H, Roshangar L, Nouri M, Aghebati-Maleki L, Khiavi FM, Abediazar S, Mehdizadeh A, Hojjat-Farsangi M, Mahmoodpoor A, Kafil HS, Zolfaghari M, Ahmadian Heris J, Yousefi M. Altered Th17/Treg ratio as a possible mechanism in pathogenesis of idiopathic membranous nephropathy. Cytokine 2021; 141:155452. [PMID: 33571932 DOI: 10.1016/j.cyto.2021.155452] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/26/2022]
Abstract
Idiopathic membranous nephropathy (IMN) as a single organ autoimmune disease is a main cause of nephrotic syndrome in adults which is determined through autoantibodies to podocytes proteins. Th17/regulatory T (Treg) balance has emerged as a prominent factor in the regulation of autoimmunity. In this study, we evaluated the balance of Th17 and Treg cells, expression level of related master transcription factors, cytokines and microRNAs in mononuclear cells of peripheral blood of 30 patients with IMN and 30 healthy individuals before treatment. No significant variation was observed in Th17 cell frequency, retinoic acid receptor-related orphan nuclear receptor γt (RORɣt), signal transducer and Activator of transcription 3(STAT3), IL-17, and IL-23, while IL-21, IL-4, and IL-10 had significant increase in mRNA expression and protein level of peripheral blood mononuclear cells in IMN cases. Reduction in the percentage of Treg cells was also accompanied with significantly decreased expression of Forkhead box P3(FOXP3) and Transforming growth factor beta(TGF-β) in IMN patients compared to the control group. Our study revealed that Th17 cells themselves might not be engaged in the pathogenesis of newly diagnosed patients with IMN; however, decreased T reg cells and increased ratio of Th17/Treg lymphocytes might display a role in the pathogenesis of IMN before treatment.
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Affiliation(s)
- Roza Motavalli
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalal Etemadi
- Kidney Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | | | - Mohamad-Reza Ardalan
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Kidney Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Houman Kahroba
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Roshangar
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Nouri
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Sima Abediazar
- Kidney Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Mehdizadeh
- Endocrine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hojjat-Farsangi
- Department of Oncology-Pathology, Immune and Gene Therapy Lab, Cancer Center Karolinska (CCK), Karolina University Hospital Solna and Karolinska Institute, Stockholm, Sweden
| | - Ata Mahmoodpoor
- Department of Anesthesiology and Critical Care Medicine, Faculty of Medicine, University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohamadali Zolfaghari
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javad Ahmadian Heris
- Department of Pediatrics, School of Medicine, Children Medical Research and Training Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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13
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MicroRNAs as Biomarkers for Nephrotic Syndrome. Int J Mol Sci 2020; 22:ijms22010088. [PMID: 33374848 PMCID: PMC7795691 DOI: 10.3390/ijms22010088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022] Open
Abstract
Nephrotic syndrome represents the clinical situation characterized by presence of massive proteinuria and low serum protein caused by a variety of diseases, including minimal change nephrotic syndrome (MCNS), focal segmental glomerulosclerosis (FSGS) and membranous glomerulonephropathy. Differentiating between diagnoses requires invasive renal biopsies in general. Even with the biopsy, we encounter difficulties to differentiate MCNS and FSGS in some cases. There is no other better option currently available for the diagnosis other than renal biopsy. MicroRNAs (miRNAs) are no-coding RNAs of approximately 20 nucleotides in length, which regulate target genes in the post-transcriptional processes and have essential roles in many diseases. MiRNAs in serum and urine have been shown as non-invasive biomarkers in multiple diseases, including renal diseases. In this article, we summarize the current knowledge of miRNAs as the promising biomarkers for nephrotic syndrome.
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14
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Hejazian SM, Rahbar Saadat Y, Bahmanpour Z, Hosseiniyan Khatibi SM, Ardalan M, Zununi Vahed S. Dicer and Drosha expression in patients with nephrotic syndrome. Biofactors 2020; 46:645-652. [PMID: 32412691 DOI: 10.1002/biof.1638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/02/2020] [Accepted: 04/17/2020] [Indexed: 12/19/2022]
Abstract
Podocytes play an essential role in the regulation of glomerular filtration and the appropriate function of the kidney. Podocytes injury is involved in the pathogenesis of nephrotic syndrome (NS), a common renal glomerulus dysfunction characterized by proteinuria. Some in vivo studies in Dicer/Drosha knockout mice indicate the importance of Dicer, Drosha, and microRNAs (miRNAs) in the pathogenesis of NS. In the present study, the expression levels of Dicer and Drosha along with miR-30 family, miR-186, miR-193, and miR-217 were evaluated in peripheral blood mononuclear cell samples of patients with NS (N = 60) using real-time PCR. Dicer expression level in NS patients was significantly upregulated when compared to healthy controls (p = .008). No significant change was observed in the Drosha expression level in the NS group. Upregulated levels of the studied microRNAs were observed in NS group in comparison to controls, the miR-30c-5p (p = .005) and miR-193-3p (p = .041) were statistically significant. In conclusion, dysregulation in expression level of Dicer and Drosha and consequently, alteration in miRNA levels are involved in the pathophysiology of NS.
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Affiliation(s)
- Seyyedeh Mina Hejazian
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yalda Rahbar Saadat
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Nutrition Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Bahmanpour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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15
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Guo Y, Ma J, Xiao L, Fang J, Li G, Zhang L, Xu L, Lai X, Pan G, Chen Z. Identification of key pathways and genes in different types of chronic kidney disease based on WGCNA. Mol Med Rep 2019; 20:2245-2257. [PMID: 31257514 PMCID: PMC6691232 DOI: 10.3892/mmr.2019.10443] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/15/2019] [Indexed: 02/07/2023] Open
Abstract
Chronic kidney disease (CKD) is a highly heterogeneous nephrosis that occurs when the structure and function of the kidney is damaged. Gene expression studies have been widely used to elucidate various biological processes; however, the gene expression profile of CKD is currently unclear. The present study aimed to identify diagnostic biomarkers and therapeutic targets using renal biopsy sample data from patients with CKD. Gene expression data from 30 patients with CKD and 21 living donors were analyzed by weighted gene co-expression network analysis (WGCNA), in order to identify gene networks and profiles for CKD, as well as its specific characteristics, and to potentially uncover diagnostic biomarkers and therapeutic targets for patients with CKD. In addition, functional enrichment analysis was performed on co-expressed genes to determine modules of interest. Four co-expression modules were constructed from the WGCNA. The number of genes in the constructed modules ranged from 269 genes in the Turquoise module to 60 genes in the Yellow module. All four co-expression modules were correlated with CKD clinical traits (P<0.05). For example, the Turquoise module, which mostly contained genes that were upregulated in CKD, was positively correlated with CKD clinical traits, whereas the Blue, Brown and Yellow modules were negatively correlated with clinical traits. Functional enrichment analysis revealed that the Turquoise module was mainly enriched in genes associated with the ‘defense response’, ‘mitotic cell cycle’ and ‘collagen catabolic process’ Gene Ontology (GO) terms, implying that genes involved in cell cycle arrest and fibrogenesis were upregulated in CKD. Conversely, the Yellow module was mainly enriched in genes associated with ‘glomerulus development’ and ‘kidney development’ GO terms, indicating that genes associated with renal development and damage repair were downregulated in CKD. The hub genes in the modules were acetyl-CoA carboxylase α, cyclin-dependent kinase 1, Wilm's tumour 1, NPHS2 stomatin family member, podocin, JunB proto-oncogene, AP-1 transcription factor subunit, activating transcription factor 3, forkhead box O1 and v-abl Abelson murine leukemia viral oncogene homolog 1, which were confirmed to be significantly differentially expressed in CKD biopsies. Combining the eight hub genes enabled a high capacity for discrimination between patients with CKD and healthy subjects, with an area under the receiver operating characteristic curve of 1.00. In conclusion, this study provided a framework for co-expression modules of renal biopsy samples from patients with CKD and living donors, and identified several potential diagnostic biomarkers and therapeutic targets for CKD.
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Affiliation(s)
- Yuhe Guo
- Department of Organ Transplantation, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Junjie Ma
- Department of Organ Transplantation, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Lanyan Xiao
- Department of Center Laboratory, The Third Affiliated Hospital, Sun Yat‑sen University, Guangzhou, Guangdong 510700, P.R. China
| | - Jiali Fang
- Department of Organ Transplantation, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Guanghui Li
- Department of Organ Transplantation, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Lei Zhang
- Department of Organ Transplantation, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Lu Xu
- Department of Organ Transplantation, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Xingqiang Lai
- Department of Organ Transplantation, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Guanghui Pan
- Department of Organ Transplantation, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
| | - Zheng Chen
- Department of Organ Transplantation, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510260, P.R. China
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16
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Zhou G, Zhang X, Wang W, Zhang W, Wang H, Xin G. Both Peripheral Blood and Urinary miR-195-5p, miR-192-3p, miR-328-5p and Their Target Genes PPM1A, RAB1A and BRSK1 May Be Potential Biomarkers for Membranous Nephropathy. Med Sci Monit 2019; 25:1903-1916. [PMID: 30865617 PMCID: PMC6427931 DOI: 10.12659/msm.913057] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background To identify noninvasive diagnostic biomarkers for membranous nephropathy (MN). Material/Methods The mRNA microarray datasets GSE73953 using peripheral blood mononuclear cells (PBMCs) of 8 membranous nephropathy patients and 2 control patients; and microRNAs (miRNA) microarray dataset GSE64306 using urine sediments of 4 membranous nephropathy patients and 6 control patients were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were respectively identified from PBMCs and urine sediments of membranous nephropathy patients, followed with functional enrichment analysis, protein-protein interaction (PPI) analysis, and miRNA-target gene analysis. Finally, the DEGs and the target genes of DEMs were overlapped to obtain crucial miRNA-mRNA interaction pairs for membranous nephropathy. Results A total of 1246 DEGs were identified from PBMCs samples, among them upregulated CCL5 was found to be involved in the chemokine signaling pathway, and BAX was found to be apoptosis related; while downregulated PPM1A and CDK1 were associated with the MAPK signaling pathway and the p53 signaling pathway, respectively. The hub role of CDK1 (degree=18) and CCL5 (degree=12) were confirmed after protein-protein interaction network analysis in which CKD1 could interact with RAB1A. A total of 28 DEMs were identified in urine sediments. The 276 target genes of DEMs were involved in cell cycle arrest (PPM1A) and intracellular signal transduction (BRSK1). Thirteen genes were shared between the DEGs in PMBCs and the target genes of DEMs in urine sediments, but only hsa-miR-192-3p-RAB1A, hsa-miR-195-5p-PPM1A, and hsa-miR-328-5p-BRSK1 were negatively related in their expression level. Conclusions Both peripheral blood and urinary miR-195-5p, miR-192-3p, miR-328-5p, and their target genes PPM1A, RAB1A, and BRSK1 may be potential biomarkers for membranous nephropathy by participating in inflammation and apoptosis.
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Affiliation(s)
- Guangyu Zhou
- Department of Nephrology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Xiaofei Zhang
- Department of Pediatrics, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Wanning Wang
- Department of Nephrology, The First Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Wenlong Zhang
- Department of Hematology and Oncology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Huaying Wang
- Department of Nephrology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Guangda Xin
- Department of Nephrology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China (mainland)
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17
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Barbagallo C, Passanisi R, Mirabella F, Cirnigliaro M, Costanzo A, Lauretta G, Barbagallo D, Bianchi C, Pagni F, Castorina S, Granata A, Di Pietro C, Ragusa M, Malatino LS, Purrello M. Upregulated microRNAs in membranous glomerulonephropathy are associated with significant downregulation of IL6 and MYC mRNAs. J Cell Physiol 2018; 234:12625-12636. [PMID: 30515781 DOI: 10.1002/jcp.27851] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022]
Abstract
Membranous glomerulonephropathy (MGN) is a glomerulopathy characterized by subepithelial deposits of immune complexes on the extracapillary side of the glomerular basement membrane. Insertion of C5b-9 (complement membrane-attack complex) into the membrane leads to functional impairment of the glomerular capillary wall. Knowledge of the molecular pathogenesis of MGN is actually scanty. MicroRNA (miRNA) profiling in MGN and unaffected tissues was performed by TaqMan Low-Density Arrays. Expression of miRNAs and miRNA targets was evaluated in Real-Time polymerase chain reaction (PCR). In vitro transient silencing of miRNAs was achieved through transfection with miRNA inhibitors. Ten miRNAs (let-7a-5p, let-7b-5p, let-7c-5p, let-7d-5p, miR-107, miR-129-3p, miR-423-5p, miR-516-3p, miR-532-3p, and miR-1275) were differentially expressed (DE) in MGN biopsies compared to unaffected controls. Interleukin 6 (IL6) and MYC messenger RNAs (mRNAs; targets of DE miRNAs) were significantly downregulated in biopsies from MGN patients, and upregulated in A498 cells following let-7a-5p or let-7c-5p transient silencing. Gene ontology analysis showed that DE miRNAs regulate pathways associated with MGN pathogenesis, including cell cycle, proliferation, and apoptosis. A significant correlation between DE miRNAs and mRNAs and clinical parameters (i.e., antiphospholipid antibodies, serum creatinine, estimated glomerular filtration, proteinuria, and serum cholesterol) has been detected. Based on our data, we propose that DE miRNAs and their downstream network may be involved in MGN pathogenesis and could be considered as potential diagnostic biomarkers of MGN.
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Affiliation(s)
- Cristina Barbagallo
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Roberta Passanisi
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy.,Department of Thoracic Surgery, Centro Clinico e Diagnostico Morgagni, Catania, Italy
| | - Federica Mirabella
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Matilde Cirnigliaro
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Arianna Costanzo
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Giovanni Lauretta
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Davide Barbagallo
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Cristina Bianchi
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Section of Pathology, University of Milano-Bicocca, Monza, Italy
| | - Sergio Castorina
- Department of Thoracic Surgery, Centro Clinico e Diagnostico Morgagni, Catania, Italy.,Department of Medical and Surgical Sciences and Advanced Technologies, University of Catania, Catania, Italy
| | - Antonio Granata
- Unit of Nephrology, Ospedale S. Giovanni di Dio, Agrigento, Italy
| | - Cinzia Di Pietro
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Marco Ragusa
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy.,Oasi Research Institute - IRCCS, Troina, Italy
| | - Lorenzo S Malatino
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Michele Purrello
- Section of Biology and Genetics Giovanni Sichel, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
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18
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Liu D, Liu F, Wang X, Qiao Y, Pan S, Yang Y, Hu Y, Zhang Y, Tian F, Liu Z. MiR-130a-5p prevents angiotensin II-induced podocyte apoptosis by modulating M-type phospholipase A2 receptor. Cell Cycle 2018; 17:2484-2495. [PMID: 30394845 DOI: 10.1080/15384101.2018.1542901] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Podocyte apoptosis is considered as the important element that promotes the development and progress of membranous nephropathy (MN). Unfortunately, the underlying mechanism of podocytes apoptosis in MN remains elusive. We compared the renal expressions of miR-130a-5p and M-type phospholipase A2 receptor (PLA2R) between MN patients (n = 30) and 30 controls by qRT-PCR and western blot, respectively. The podocyte damage model in vitro was established by angiotensin II (Ang II, 100 nmol/L) exposure for 24 h. Interaction between miR-130a-5p and PLA2R was determined using dual-luciferase reporter gene assay. MN mice were induced by intravenous injection of cBSA. In this study, miR-130a-5p expression was significantly decreased both in the renal biopsy specimens from MN patients and podocyte cell line AB8/13 following stimulation of Ang II. Overexpressed miR-130a-5p in AB8/13 cells significantly attenuated the Ang II induced-apoptosis in vitro. In contrast, down-regulated miR-130a-5p induced podocyte apoptosis. PLA2R was identified as the target of miR-130a-5p in AB8/13 cells. And up-regulated or down-regulated PLA2R could obviously attenuate the effect of miR-130a-5p overexpression or knockdown on the apoptosis of AB8/13 cells. Furthermore, it was also observed that overexpressed miR-130a-5p by miR-130a-5p agomir could obviously alleviate renal injury in MN mice. In conclusion, decreased miR-130a-5p was contributed to the pathological mechanism of MN through increasing PLA2R expression, which induced podocyte apoptosis.
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Affiliation(s)
- Dongwei Liu
- a Department of Nephrology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou China.,b Research Institute of Nephrology , Zhengzhou University , Zhengzhou China.,c Key laboratory of precision diagnosis and treatment for chronic kidney disease in Henan province , Zhengzhou China.,d Core unit of national clinical medical research center of kidney disease , Zhengzhou China
| | - Fengxun Liu
- b Research Institute of Nephrology , Zhengzhou University , Zhengzhou China.,c Key laboratory of precision diagnosis and treatment for chronic kidney disease in Henan province , Zhengzhou China.,d Core unit of national clinical medical research center of kidney disease , Zhengzhou China
| | - Xutong Wang
- b Research Institute of Nephrology , Zhengzhou University , Zhengzhou China.,c Key laboratory of precision diagnosis and treatment for chronic kidney disease in Henan province , Zhengzhou China.,d Core unit of national clinical medical research center of kidney disease , Zhengzhou China
| | - Yingjin Qiao
- a Department of Nephrology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou China.,b Research Institute of Nephrology , Zhengzhou University , Zhengzhou China.,c Key laboratory of precision diagnosis and treatment for chronic kidney disease in Henan province , Zhengzhou China.,d Core unit of national clinical medical research center of kidney disease , Zhengzhou China
| | - Shaokang Pan
- a Department of Nephrology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou China.,b Research Institute of Nephrology , Zhengzhou University , Zhengzhou China.,c Key laboratory of precision diagnosis and treatment for chronic kidney disease in Henan province , Zhengzhou China.,d Core unit of national clinical medical research center of kidney disease , Zhengzhou China
| | - Yang Yang
- a Department of Nephrology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou China.,b Research Institute of Nephrology , Zhengzhou University , Zhengzhou China.,c Key laboratory of precision diagnosis and treatment for chronic kidney disease in Henan province , Zhengzhou China.,d Core unit of national clinical medical research center of kidney disease , Zhengzhou China
| | - Yifang Hu
- b Research Institute of Nephrology , Zhengzhou University , Zhengzhou China.,c Key laboratory of precision diagnosis and treatment for chronic kidney disease in Henan province , Zhengzhou China.,d Core unit of national clinical medical research center of kidney disease , Zhengzhou China
| | - Yilin Zhang
- b Research Institute of Nephrology , Zhengzhou University , Zhengzhou China.,c Key laboratory of precision diagnosis and treatment for chronic kidney disease in Henan province , Zhengzhou China.,d Core unit of national clinical medical research center of kidney disease , Zhengzhou China
| | - Fei Tian
- b Research Institute of Nephrology , Zhengzhou University , Zhengzhou China.,c Key laboratory of precision diagnosis and treatment for chronic kidney disease in Henan province , Zhengzhou China.,d Core unit of national clinical medical research center of kidney disease , Zhengzhou China
| | - Zhangsuo Liu
- a Department of Nephrology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou China.,b Research Institute of Nephrology , Zhengzhou University , Zhengzhou China.,c Key laboratory of precision diagnosis and treatment for chronic kidney disease in Henan province , Zhengzhou China.,d Core unit of national clinical medical research center of kidney disease , Zhengzhou China
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Chen W, Tang D, Dai Y, Diao H. Establishment of microRNA, transcript and protein regulatory networks in Alport syndrome induced pluripotent stem cells. Mol Med Rep 2018; 19:238-250. [PMID: 30483741 PMCID: PMC6297794 DOI: 10.3892/mmr.2018.9672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/12/2018] [Indexed: 12/14/2022] Open
Abstract
Alport syndrome (AS) is an inherited progressive disease caused by mutations in genes encoding for the α3, α4 and α5 chains, which are an essential component of type IV collagen and are required for formation of the glomerular basement membrane. However, the underlying etiology of AS remains largely unknown, and the aim of the present study was to examine the genetic mechanisms in AS. Induced pluripotent stem cells (iPSCs) were generated from renal tubular cells. The Illumina HiSeq™ 2000 system and iTRAQ‑coupled 2D liquid chromatography‑tandem mass spectrometry were used to generate the sequences of microRNAs (miRNAs), transcripts and proteins from AS‑iPSCs. Integration of miRNA, transcript and protein expression data was used to construct regulatory networks and identify specific miRNA targets amongst the transcripts and proteins. Relative quantitative proteomics using iTRAQ technology revealed 383 differentially abundant proteins, and high‑throughput sequencing identified 155 differentially expressed miRNAs and 1,168 differentially expressed transcripts. Potential miRNA targets were predicted using miRanda, TargetScan and Pictar. All target proteins and transcripts were subjected to network analysis with miRNAs. Gene ontology analysis of the miRNAs and their targets revealed functional information on the iPSCs, including biological process and cell signaling. Kyoto Encyclopedia of Genes and Genomes pathways analysis revealed that the transcripts and proteins were primarily enriched in metabolic and cell adhesion molecule pathways. In addition, the network maps identified hsa‑miRNA (miR)‑4775 as a prominent miRNA that was associated with a number of targets. Similarly, the prominent ELV‑like protein 1‑A and epidermal growth factor receptor (EGFR)‑associated transcripts were identified. Reverse transcription‑quantitative polymerase chain reaction analysis was used to confirm the upregulation of hsa‑miR‑4775 and EGFR. The integrated approach used in the present study provided a comprehensive molecular characterization of AS. The results may also further understanding of the genetic pathogenesis of AS and facilitate the identification of candidate biomarkers for AS.
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Affiliation(s)
- Wenbiao Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Donge Tang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, P.R. China
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, P.R. China
| | - Hongyan Diao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
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Chen HQ, Zhao J, Li Y, He LX, Huang YJ, Shu WQ, Cao J, Liu WB, Liu JY. Gene expression network regulated by DNA methylation and microRNA during microcystin-leucine arginine induced malignant transformation in human hepatocyte L02 cells. Toxicol Lett 2018. [PMID: 29518473 DOI: 10.1016/j.toxlet.2018.03.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Microcystin (MC) is a cyclic heptapeptide compound which could lead to the development of hepatocellular carcinoma. However, the underlying epigenetic regulation mechanism is largely unknown. In this study, microcystin-LR (L: lysine, R: arginine, MC-LR) was used to induce the malignant transformation of human hepatocyte L02 cell line. The profile of gene expression, microRNA (miRNA) and DNA methylation were detected through high-throughput sequencing. Compared with control group, the expression of 826 genes and 187 miRNAs changed significantly in MC-LR treated group. DNA methylation sequencing analysis showed that 2592 CpG sites differentially methylated in promoter or the coding DNA sequence (CDS) of genes, while DNA methyltransferase 3 alpha (DNMT3a) and DNA methyltransferase 3 beta (DNMT3b) were dramatically up-regulated. Functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that significantly changed mRNAs and microRNAs were mainly involved in the formation of cancer, proliferation, invasion, migration and metabolism. MiRNA-mRNA network and mRNA-mRNA network analysis showed that hsa-miR-320a, hsa-miR-331-3p, hsa-miR-26a-5p, hsa-miR-196a-5p, hsa-miR-221-3p, coiled-coil domain containing 180 (CCDC180), melanoma antigen gene family member D1 (MAGED1), membrane spanning 4-domains A7 (MS4A7), hephaestin like 1 (HEPHL1), BH3 (Bcl-2 homology 3)-like motif containing, cell death inducer (BLID), matrix metallopeptidase 13 (MMP13), guanylate binding protein 5 (GBP5), adipogenesis regulatory factor (ADIRF), formin homology 2 domain containing 1 (FHDC1), protein kinase CAMP-dependent type II regulatory subunit beta (PRKAR2B), nodium leak channel, non-selective (NALCN), myosin light chain kinase 3 (MYLK3), epidermal growth factor receptor (EGFR) and zinc finger protein 704 (ZNF704) were key miRNAs and genes in the malignant transformation induced by MC-LR in L02 cells. Moreover, we found that expression of MYLK3, EGFR and ZNF704 were regulated by DNA methylation and miRNAs, and these genes affected the cell cycle and cell division. Our study suggested that characteristic gene alterations regulated by DNA methylation and miRNA could play an important role in environmental MC-LR induced hepatic carcinogenesis.
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Affiliation(s)
- Hong-Qiang Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Ji Zhao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China; College of Public Health and Management, Ningxia Medical University, Yinchuan 750004, PR China
| | - Yan Li
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China; The Calmette International Hospital, Kunming 650224, PR China
| | - Li-Xiong He
- Department of Environmental Hygiene, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Yu-Jing Huang
- Department of Environmental Hygiene, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Wei-Qun Shu
- Department of Environmental Hygiene, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Wen-Bin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China.
| | - Jin-Yi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China.
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miR-217 Is a Useful Diagnostic Biomarker and Regulates Human Podocyte Cells Apoptosis via Targeting TNFSF11 in Membranous Nephropathy. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2168767. [PMID: 29214160 PMCID: PMC5682891 DOI: 10.1155/2017/2168767] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/24/2017] [Accepted: 10/01/2017] [Indexed: 12/13/2022]
Abstract
Background MicroRNAs have recently been verified as useful diagnostic biomarkers in various diseases. In this study, we investigated whether miR-217 is a useful diagnostic biomarker and the possible pathological mechanism of miR-217 in this disease. Methods Patients with focal segmental glomerulosclerosis (FSGS), membranous nephropathy (MN), and diabetic nephropathy (DN) and control patients were enrolled in this study. The miR-217 inhibitor and mimics were transfected into human podocyte cells to investigate the pathological mechanism of miR-217 in this disease. Relevant indicators were detected and tested. Results Compared with control patients, miR-217 was significantly downregulated and TNFSF11 was significantly upregulated in MN. Then, miR-217 had obvious separation between patients with MN and control patients, with an AUC of 0.941, a cutoff value of <750.0 copies/ul, and sensitivity and specificity of 88.9% and 75.9%. In addition, the TNFSF11 was confirmed to be the target gene of miR-217. Finally, in in vitro experiments, the upregulation of miR-217 could decrease the expression of TNFSF11 and not induce human podocyte cells apoptosis; however, the downregulation of miR-217 could bring about an opposite change. Conclusions miR-217 is a useful diagnostic biomarker and is involved in human podocyte cells apoptosis via targeting TNFSF11 in membranous nephropathy.
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Kalantari S, Nafar M. A comprehensive narrative review of diagnostic biomarkers in human primary membranous nephropathy. Biomark Med 2017; 11:781-797. [DOI: 10.2217/bmm-2017-0081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Membranous nephropathy (MN) is relatively major cause of nephrotic syndrome in adults which is recognized as an organ-specific autoimmune disease. The etiology of most cases is idiopathic, whereas the secondary MN is caused by systemic autoimmune diseases, infections, medications and malignancies. The idiopathic disease is developed by the formation of sub-epithelial immune complex deposits most likely due to binding the circulating auto-antibodies to intrinsic antigen on podocytes. The major auto antibody is the anti-phospholipase A2 receptor (anti-PLA2R), however, it is not enough sensitive. Several attempts for diagnostic biomarker identification by modern analytical technologies have been devoted recently. This article reviews the biomarker candidates for primary type of MN that are detected by different approaches on human subjects.
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Affiliation(s)
- Shiva Kalantari
- Chronic Kidney Disease Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Nafar
- Urology Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Kamyshova ES, Bobkova IN. MicroRNAs in chronic glomerulonephritis: Promising biomarkers for diagnosis and prognosis estimation. TERAPEVT ARKH 2017; 89:89-96. [DOI: 10.17116/terarkh201789689-96] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Landolt L, Strauss P, Marti HP, Eikrem Ø. Next Generation Sequencing: A Tool for This Generation of Nephrologists. EUROPEAN MEDICAL JOURNAL 2016. [DOI: 10.33590/emj/10314001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The emergence of next generation sequencing (NGS) techniques has made the sequencing of whole genomes, transcriptomes, and epigenomes faster and more readily available than previous methods such as Sanger sequencing, which was developed in the 1970s. It is now 10 years since NGS began to revolutionise biological and medical research. Sequencing of RNA provides insights into up or downregulated gene expression patterns and therefore into molecular disease mechanisms. This can lead to the detection of new biomarkers that can be used as diagnostic tools in risk stratification, or even as new therapeutic targets. In nephrology, NGS plays a role in both basic and experimental research, but also in the clinical setting, whereby the diagnosis of innate genetic diseases such as ciliopathies or genetically moderated acquired diseases such as glomerulopathies has improved. NGS enables precise diagnosis and classification of common diseases of the kidneys and urinary tract, aids in both prognostic and predictive decision-making, and in the avoidance of unnecessary therapies. It also plays a role in the risk stratification of disease recurrence after transplantation. NGS is a robust method; however, the performance of NGS is dependent on the method of tissue storage, the extraction of DNA or RNA, and on the sequencing platform itself, as well as on the bioinformatic analyses performed, integration of clinical data, and comprehensive interpretation of the results. The aim of this article is to review and emphasise the importance of NGS as a tool for this generation of nephrologists.
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Affiliation(s)
- Lea Landolt
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Philipp Strauss
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Øystein Eikrem
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
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