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Rinaldi L, Chiuso F, Senatore E, Borzacchiello D, Lignitto L, Iannucci R, Donne RD, Fuggi M, Reale C, Russo F, Russo NA, Giurato G, Rizzo F, Sellitto A, Santangelo M, De Biase D, Paciello O, D'Ambrosio C, Amente S, Garbi C, Dalla E, Scaloni A, Weisz A, Ambrosino C, Insabato L, Feliciello A. Downregulation of praja2 restrains endocytosis and boosts tyrosine kinase receptors in kidney cancer. Commun Biol 2024; 7:208. [PMID: 38379085 PMCID: PMC10879500 DOI: 10.1038/s42003-024-05823-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common kidney cancer in the adult population. Late diagnosis, resistance to therapeutics and recurrence of metastatic lesions account for the highest mortality rate among kidney cancer patients. Identifying novel biomarkers for early cancer detection and elucidating the mechanisms underlying ccRCC will provide clues to treat this aggressive malignant tumor. Here, we report that the ubiquitin ligase praja2 forms a complex with-and ubiquitylates the AP2 adapter complex, contributing to receptor endocytosis and clearance. In human RCC tissues and cells, downregulation of praja2 by oncogenic miRNAs (oncomiRs) and the proteasome markedly impairs endocytosis and clearance of the epidermal growth factor receptor (EGFR), and amplifies downstream mitogenic and proliferative signaling. Restoring praja2 levels in RCC cells downregulates EGFR, rewires cancer cell metabolism and ultimately inhibits tumor cell growth and metastasis. Accordingly, genetic ablation of praja2 in mice upregulates RTKs (i.e. EGFR and VEGFR) and induces epithelial and vascular alterations in the kidney tissue.In summary, our findings identify a regulatory loop between oncomiRs and the ubiquitin proteasome system that finely controls RTKs endocytosis and clearance, positively impacting mitogenic signaling and kidney cancer growth.
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Affiliation(s)
- Laura Rinaldi
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
| | - Francesco Chiuso
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
| | - Emanuela Senatore
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
| | - Domenica Borzacchiello
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
| | - Luca Lignitto
- Cancer Research Center of Marseille (CRCM), CNRS, Aix Marseille Univ, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Rosa Iannucci
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
| | - Rossella Delle Donne
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
| | - Mariano Fuggi
- Department of Advanced Biomedical Sciences, University Hospital Federico II, Naples, Italy
| | - Carla Reale
- Biogem, Biology and Molecular Genetics Institute, Ariano Irpino, Italy
| | - Filomena Russo
- Biogem, Biology and Molecular Genetics Institute, Ariano Irpino, Italy
| | | | - Giorgio Giurato
- Genome Research Center for Health, Baronissi (SA), Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry SMS, Baronissi (SA), Italy
| | - Francesca Rizzo
- Genome Research Center for Health, Baronissi (SA), Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry SMS, Baronissi (SA), Italy
| | - Assunta Sellitto
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry SMS, Baronissi (SA), Italy
| | - Michele Santangelo
- Department of Advanced Biomedical Sciences, University Hospital Federico II, Naples, Italy
| | - Davide De Biase
- Department of Pharmacy, University of Salerno, Salerno, Italy
| | - Orlando Paciello
- Department of Veterinary Medicine and Animal Production, Pathology Unit, University Federico II, Naples, Italy
| | - Chiara D'Ambrosio
- Proteomics, Metabolomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Portici (Naples), Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
| | - Corrado Garbi
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
| | - Emiliano Dalla
- Department of Medicine, University of Udine, Udine, Italy
| | - Andrea Scaloni
- Proteomics, Metabolomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Portici (Naples), Italy
| | - Alessandro Weisz
- Genome Research Center for Health, Baronissi (SA), Italy
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry SMS, Baronissi (SA), Italy
| | - Concetta Ambrosino
- Biogem, Biology and Molecular Genetics Institute, Ariano Irpino, Italy
- Department of Science and Technology University of Sannio, Sannio, Italy
| | - Luigi Insabato
- Department of Advanced Biomedical Sciences, University Hospital Federico II, Naples, Italy
| | - Antonio Feliciello
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy.
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He K, Zhou X, Zhao J, Du H, Guo J, Deng R, Wang J. Identification and Functional Mechanism Verification of Novel MicroRNAs Associated with the Fibrosis Progression in Chronic Kidney Disease. Biochem Genet 2024:10.1007/s10528-024-10688-7. [PMID: 38316653 DOI: 10.1007/s10528-024-10688-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024]
Abstract
Chronic kidney disease (CKD) is a serious threat to human health worldwide, and its incidence is increasing annually. A growing amount of information is emerging about the role of micoRNAs (miRNAs) in the regulation of renal fibrosis, which has aroused interest in the development of drugs that block pathogenic miRNAs or restore protective miRNAs levels. To clarify the role of miRNAs in CKD, we selected patients with significant renal fibrotic disease (diabetic nephropathy (DN) and focal segmental glomerulosclerosis (FSGS)) as the disease group, and patients with little or no renal fibrotic disease (minimal change disease (MCD) and renal carcinoma adjacent to normal kidney) as controls. Significantly differentially expressed miRNAs were obtained by human kidney tissue sequencing, subsequently verified in mice models of DN and FSGS, and subsequently inhibited or overexpressed in human renal tubular epithelial cells (HK-2) stimulated by high glucose (HG) and TGF-β1 in vitro. Therefore, the mechanism of its action in renal fibrosis was further elaborated. Finally, the downstream target genes of the corresponding miRNAs were verified by bioinformatics analysis, qRT-PCR, western blot and double luciferase report analysis. Two novel miRNAs, hsa-miR-1470-3p (miR-1470) and hsa-miR-4483-3p (miR-4483), were detected by renal tissue sequencing in the disease group with significant renal fibrosis (DN and FSGS) and the control group with little or no renal fibrosis (MCD and normal renal tissue adjacent to renal carcinoma). Subsequent human renal tissue qRT-PCR verified that the expression of miR-1470 was significantly increased, while the expression of miR-4483 was markedly decreased in the disease group (p < 0.05). Moreover, in vivo DN and FSGS mice models, the expression levels of miR-1470 and miR-4483 were consistent with the results of human kidney tissue. In vitro, miR-4483 was suppressed, whereas miR-1470 was induced by treatment with TGF-β1 or HG. Inhibition of miR-1470 or overexpression of miR-4483 promoted HG or TGF-β1-induced fibrosis in HK-2 cells. Further study revealed that MMP-13 and TIMP1 were the target genes ofmiR-1470 and miR-4483, respectively. Our study identifies newly dysregulated miRNA profiles related to fibrosis kidneys. miR-1470 and miR-4483 are demonstrated to participate in kidney fibrosis by regulation of MMP-13, TIMP1 respectively. Our results may represent a promising research direction for renal disorders and help identify new biomarkers and therapeutic targets for CKD.
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Affiliation(s)
- Kaiying He
- Lanzhou University, Lanzhou, Gansu, China
- Department of Nephrology, The Second Hospital & Clinical Medical School, Lanzhou University, No. 82 Cuiyingmen, Lanzhou, Gansu, China
| | - Xiaochun Zhou
- Department of Nephrology, The Second Hospital & Clinical Medical School, Lanzhou University, No. 82 Cuiyingmen, Lanzhou, Gansu, China
| | - Jing Zhao
- Lanzhou University, Lanzhou, Gansu, China
- Department of Nephrology, The Second Hospital & Clinical Medical School, Lanzhou University, No. 82 Cuiyingmen, Lanzhou, Gansu, China
| | - Hongxuan Du
- Lanzhou University, Lanzhou, Gansu, China
- Department of Nephrology, The Second Hospital & Clinical Medical School, Lanzhou University, No. 82 Cuiyingmen, Lanzhou, Gansu, China
| | - Juan Guo
- Xi'an Huyi District Hospital Of Traditional Chinese Medicine, Xi'an, Shaanxi, China
| | - Rongrong Deng
- Lanzhou University, Lanzhou, Gansu, China
- Department of Nephrology, The Second Hospital & Clinical Medical School, Lanzhou University, No. 82 Cuiyingmen, Lanzhou, Gansu, China
| | - Jianqin Wang
- Department of Nephrology, The Second Hospital & Clinical Medical School, Lanzhou University, No. 82 Cuiyingmen, Lanzhou, Gansu, China.
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Ji JL, Shi HM, Li ZL, Jin R, Qu GT, Zheng H, Wang E, Qiao YY, Li XY, Ding L, Ding DF, Ding LC, Gan WH, Wang B, Zhang AQ. Satellite cell-derived exosome-mediated delivery of microRNA-23a/27a/26a cluster ameliorates the renal tubulointerstitial fibrosis in mouse diabetic nephropathy. Acta Pharmacol Sin 2023; 44:2455-2468. [PMID: 37596398 PMCID: PMC10692096 DOI: 10.1038/s41401-023-01140-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/12/2023] [Indexed: 08/20/2023] Open
Abstract
Renal tubulointerstitial fibrosis (TIF) is considered as the final convergent pathway of diabetic nephropathy (DN) without effective therapies currently. MiRNAs play a key role in fibrotic diseases and become promising therapeutic targets for kidney diseases, while miRNA clusters, formed by the cluster arrangement of miRNAs on chromosomes, can regulate diverse biological functions alone or synergistically. In this study, we developed clustered miR-23a/27a/26a-loaded skeletal muscle satellite cells-derived exosomes (Exos) engineered with RVG peptide, and investigated their therapeutic efficacy in a murine model of DN. Firstly, we showed that miR-23a-3p, miR-26a-5p and miR-27a-3p were markedly decreased in serum samples of DN patients using miRNA sequencing. Meanwhile, we confirmed that miR-23a-3p, miR-26a-5p and miR-27a-3p were primarily located in proximal renal tubules and highly negatively correlated with TIF in db/db mice at 20 weeks of age. We then engineered RVG-miR-23a/27a/26a cluster loaded Exos derived from muscle satellite cells, which not only enhanced the stability of miR-23a/27a/26a cluster, but also efficiently delivered more miR-23a/27a/26a cluster homing to the injured kidney. More importantly, administration of RVG-miR-23a/27a/26a-Exos (100 μg, i.v., once a week for 8 weeks) significantly ameliorated tubular injury and TIF in db/db mice at 20 weeks of age. We revealed that miR-23a/27a/26a-Exos enhanced antifibrotic effects by repressing miRNA cluster-targeting Lpp simultaneously, as well as miR-27a-3p-targeting Zbtb20 and miR-26a-5p-targeting Klhl42, respectively. Knockdown of Lpp by injection of AAV-Lpp-RNAi effectively ameliorated the progression of TIF in DN mice. Taken together, we established a novel kidney-targeting Exo-based delivery system by manipulating the miRNA-23a/27a/26a cluster to ameliorate TIF in DN, thus providing a promising therapeutic strategy for DN.
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Affiliation(s)
- Jia-Ling Ji
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Hui-Min Shi
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Zuo-Lin Li
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, 210009, China
| | - Ran Jin
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Gao-Ting Qu
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Hui Zheng
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - E Wang
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Yun-Yang Qiao
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Xing-Yue Li
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Ling Ding
- Department of Pediatrics, the Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, 210031, China
| | - Da-Fa Ding
- Department of Endocrinology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Liu-Cheng Ding
- Department of Urology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Wei-Hua Gan
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Bin Wang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, 210009, China.
| | - Ai-Qing Zhang
- Department of Pediatrics, the Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, 210031, China.
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Deng S, Li C, Cao J, Cui Z, Du J, Fu Z, Yang H, Chen P. Organ-on-a-chip meets artificial intelligence in drug evaluation. Theranostics 2023; 13:4526-4558. [PMID: 37649608 PMCID: PMC10465229 DOI: 10.7150/thno.87266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/02/2023] [Indexed: 09/01/2023] Open
Abstract
Drug evaluation has always been an important area of research in the pharmaceutical industry. However, animal welfare protection and other shortcomings of traditional drug development models pose obstacles and challenges to drug evaluation. Organ-on-a-chip (OoC) technology, which simulates human organs on a chip of the physiological environment and functionality, and with high fidelity reproduction organ-level of physiology or pathophysiology, exhibits great promise for innovating the drug development pipeline. Meanwhile, the advancement in artificial intelligence (AI) provides more improvements for the design and data processing of OoCs. Here, we review the current progress that has been made to generate OoC platforms, and how human single and multi-OoCs have been used in applications, including drug testing, disease modeling, and personalized medicine. Moreover, we discuss issues facing the field, such as large data processing and reproducibility, and point to the integration of OoCs and AI in data analysis and automation, which is of great benefit in future drug evaluation. Finally, we look forward to the opportunities and challenges faced by the coupling of OoCs and AI. In summary, advancements in OoCs development, and future combinations with AI, will eventually break the current state of drug evaluation.
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Affiliation(s)
- Shiwen Deng
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Caifeng Li
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Robot Intelligent Laboratory of Traditional Chinese Medicine, Experimental Research Center, China Academy of Chinese Medical Sciences & MEGAROBO, Beijing 100700, China
| | - Junxian Cao
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zhao Cui
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jiang Du
- Yunnan Biovalley Pharmaceutical Co., Ltd, Kunming 650503, China
| | - Zheng Fu
- Robot Intelligent Laboratory of Traditional Chinese Medicine, Experimental Research Center, China Academy of Chinese Medical Sciences & MEGAROBO, Beijing 100700, China
| | - Hongjun Yang
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Robot Intelligent Laboratory of Traditional Chinese Medicine, Experimental Research Center, China Academy of Chinese Medical Sciences & MEGAROBO, Beijing 100700, China
| | - Peng Chen
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Yunnan Biovalley Pharmaceutical Co., Ltd, Kunming 650503, China
- Robot Intelligent Laboratory of Traditional Chinese Medicine, Experimental Research Center, China Academy of Chinese Medical Sciences & MEGAROBO, Beijing 100700, China
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Zhuang W, Shi X, Gao S, Qin X. Restoring gluconeogenesis by TEF inhibited proliferation and promoted apoptosis and immune surveillance in kidney renal clear cell carcinoma. Cancer Metab 2023; 11:11. [PMID: 37553601 PMCID: PMC10410999 DOI: 10.1186/s40170-023-00312-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Kidney renal clear cell carcinoma (KIRC) is the major histological subtype of kidney tumor which covers approximately 80% of the cases. Although various therapies have been developed, the clinical outcome remains unsatisfactory. Metabolic dysregulation is a key feature of KIRC, which impacts progression and prognosis of the disease. Therefore, understanding of the metabolic changes in KIRC is of great significance in improving the treatment outcomes. METHODS The glycolysis/gluconeogenesis genes were analyzed in the KIRC transcriptome from the Cancer Genome Atlas (TCGA) by the different expression genes (DEGs) test and survival analysis. The gluconeogenesis-related miRNAs were identified by ImmuLncRNA. The expression levels of indicated genes and miRNAs were validated in KIRC tumor and adjunct tissues by QPCR. The effects of miR-4477b and PCK1 on cell proliferation and apoptosis were examined using the cell viability assay, cell apoptosis assay, and clone information. The interaction of miR-4477b with TEF was tested by the luciferase report gene assay. The different gluconeogenesis statuses of tumor cells and related signatures were investigated by single-cell RNA sequencing (scRNA-seq) analysis. RESULTS The 11 gluconeogenesis genes were found to be suppressed in KIRC (referring as PGNGs), and the less suppression of PGNGs indicated better survival outcomes. Among the 11 PGNGs, we validated four rate-limiting enzyme genes in clinical tumor patients. Moreover, restoring gluconeogenesis by overexpressing PCK1 or TEF through miR-4477b inhibition significantly inhibited tumor cell proliferation, colony formation, and induced cell apoptosis in vitro. Independent single-cell RNA sequencing (scRNA-seq) data analysis revealed that the tumor cells had high levels of PGNG expression (PGNG + tumor cells) represented a phenotype of early stage of neoplasia and prompted immune surveillance. CONCLUSIONS Our study suggests that the deficiency of gluconeogenesis is a key metabolic feature of KIRC, and restoring gluconeogenesis could effectively inhibit the proliferation and progression of KIRC cells.
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Affiliation(s)
- Wenyuan Zhuang
- Department of Urology, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213003, China
| | - Xiaokai Shi
- Department of Urology, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213003, China
| | - Shenglin Gao
- Department of Urology, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213003, China.
- Gonghe County Hospital of Traditional Chinese Medicine, Hainan Prefecture, Qinghai Province, China.
| | - Xihu Qin
- Department of General Surgery, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213003, China.
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Zhu J, Xiang X, Hu X, Li C, Song Z, Dong Z. miR-147 Represses NDUFA4, Inducing Mitochondrial Dysfunction and Tubular Damage in Cold Storage Kidney Transplantation. J Am Soc Nephrol 2023; 34:1381-1397. [PMID: 37211637 PMCID: PMC10400108 DOI: 10.1681/asn.0000000000000154] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/25/2023] [Indexed: 05/23/2023] Open
Abstract
SIGNIFICANCE STATEMENT Cold storage-associated transplantation (CST) injury occurs in renal transplant from deceased donors, the main organ source. The pathogenesis of CST injury remains poorly understood, and effective therapies are not available. This study has demonstrated an important role of microRNAs in CST injury and revealed the changes in microRNA expression profiles. Specifically, microRNA-147 (miR-147) is consistently elevated during CST injury in mice and in dysfunctional renal grafts in humans. Mechanistically, NDUFA4 (a key component of mitochondrial respiration complex) is identified as a direct target of miR-147. By repressing NDUFA4, miR-147 induces mitochondrial damage and renal tubular cell death. Blockade of miR-147 and overexpression of NDUFA4 reduce CST injury and improve graft function, unveiling miR-147 and NDUFA4 as new therapeutic targets in kidney transplantation. BACKGROUND Kidney injury due to cold storage-associated transplantation (CST) is a major factor determining the outcome of renal transplant, for which the role and regulation of microRNAs remain largely unclear. METHODS The kidneys of proximal tubule Dicer (an enzyme for microRNA biogenesis) knockout mice and their wild-type littermates were subjected to CST to determine the function of microRNAs. Small RNA sequencing then profiled microRNA expression in mouse kidneys after CST. Anti-microRNA-147 (miR-147) and miR-147 mimic were used to examine the role of miR-147 in CST injury in mouse and renal tubular cell models. RESULTS Knockout of Dicer from proximal tubules attenuated CST kidney injury in mice. RNA sequencing identified multiple microRNAs with differential expression in CST kidneys, among which miR-147 was induced consistently in mouse kidney transplants and in dysfunctional human kidney grafts. Anti-miR-147 protected against CST injury in mice and ameliorated mitochondrial dysfunction after ATP depletion injury in renal tubular cells in intro . Mechanistically, miR-147 was shown to target NDUFA4, a key component of the mitochondrial respiration complex. Silencing NDUFA4 aggravated renal tubular cell death, whereas overexpression of NDUFA4 prevented miR-147-induced cell death and mitochondrial dysfunction. Moreover, overexpression of NDUFA4 alleviated CST injury in mice. CONCLUSIONS microRNAs, as a class of molecules, are pathogenic in CST injury and graft dysfunction. Specifically, miR-147 induced during CST represses NDUFA4, leading to mitochondrial damage and renal tubular cell death. These results unveil miR-147 and NDUFA4 as new therapeutic targets in kidney transplantation.
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Affiliation(s)
- Jiefu Zhu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan, China
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University and Charlie Norwood VA Medical Center, Augusta, Georgia
| | - Xiaohong Xiang
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University and Charlie Norwood VA Medical Center, Augusta, Georgia
- Department of Critical Care Medicine, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Xiaoru Hu
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University and Charlie Norwood VA Medical Center, Augusta, Georgia
- Department of Nephrology, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Chenglong Li
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University and Charlie Norwood VA Medical Center, Augusta, Georgia
| | - Zhixia Song
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University and Charlie Norwood VA Medical Center, Augusta, Georgia
- Department of Nephrology, Yichang Central People's Hospital, The First Clinical Medical College of Three Gorges University, Yichang, China
| | - Zheng Dong
- Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University and Charlie Norwood VA Medical Center, Augusta, Georgia
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Avčin SL, Črepinšek K, Jenko Bizjan B, Šket R, Kovač J, Vrhovšek B, Blazina J, Blatnik O, Kordič R, Kitanovski L, Jazbec J, Debeljak M, Tesovnik T. Integrative Transcriptomic Profiling of the Wilms Tumor. Cancers (Basel) 2023; 15:3846. [PMID: 37568662 PMCID: PMC10416970 DOI: 10.3390/cancers15153846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Our study aimed to identify relevant transcriptomic biomarkers for the Wilms tumor, the most common pediatric kidney cancer, independent of the histological type and stage. Using next-generation sequencing, we analyzed the miRNA profiles of 74 kidney samples, which were divided into two independent groups: fresh frozen tissue and formalin-fixed paraffin-embedded tissue samples. Subsequent mRNA expression profiling and pathway analysis were performed to establish the interplay and potential involvement of miRNAs and mRNA in the Wilms tumor. Comparative analysis, irrespective of post-dissection tissue processing, revealed 41 differentially expressed miRNAs, with 27 miRNAs having decreased expression and 14 miRNAs having increased expression in the Wilms tumor tissue compared to healthy kidney tissue. Among global mRNA transcriptomic profile differences, cross-sectional analysis suggested a limited list of genes potentially regulated by differentially expressed miRNAs in the Wilms tumor. This study identified the comprehensive miRNA and mRNA profile of the Wilms tumor using next-generation sequencing and bioinformatics approach, providing better insights into the pathogenesis of the Wilms tumor. The identified Wilms tumor miRNAs have potential as biomarkers for the diagnosis and treatment of the Wilms tumor, regardless of histological subtype and disease stage.
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Affiliation(s)
- Simona Lucija Avčin
- Department of Haematology and Oncology, University Children’s Hospital, University Medical Centre Ljubljana (UMC), 1000 Ljubljana, Slovenia; (S.L.A.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Klementina Črepinšek
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Special Laboratory Diagnostic, University Children’s Hospital, University Medical Centre Ljubljana (UMC), 1000 Ljubljana, Slovenia
| | - Barbara Jenko Bizjan
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Special Laboratory Diagnostic, University Children’s Hospital, University Medical Centre Ljubljana (UMC), 1000 Ljubljana, Slovenia
| | - Robert Šket
- Institute of Special Laboratory Diagnostic, University Children’s Hospital, University Medical Centre Ljubljana (UMC), 1000 Ljubljana, Slovenia
| | - Jernej Kovač
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Special Laboratory Diagnostic, University Children’s Hospital, University Medical Centre Ljubljana (UMC), 1000 Ljubljana, Slovenia
| | - Blaž Vrhovšek
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Special Laboratory Diagnostic, University Children’s Hospital, University Medical Centre Ljubljana (UMC), 1000 Ljubljana, Slovenia
| | - Jerca Blazina
- Department of Pathology, Institute of Oncology Ljubljana, 1000 Ljubljana, Slovenia
| | - Olga Blatnik
- Department of Pathology, Institute of Oncology Ljubljana, 1000 Ljubljana, Slovenia
| | - Robert Kordič
- Department of Pediatric Surgery, University Children’s Hospital, University Medical Centre Ljubljana (UMC), 1000 Ljubljana, Slovenia
| | - Lidija Kitanovski
- Department of Haematology and Oncology, University Children’s Hospital, University Medical Centre Ljubljana (UMC), 1000 Ljubljana, Slovenia; (S.L.A.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Janez Jazbec
- Department of Haematology and Oncology, University Children’s Hospital, University Medical Centre Ljubljana (UMC), 1000 Ljubljana, Slovenia; (S.L.A.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Maruša Debeljak
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Special Laboratory Diagnostic, University Children’s Hospital, University Medical Centre Ljubljana (UMC), 1000 Ljubljana, Slovenia
| | - Tine Tesovnik
- Institute of Special Laboratory Diagnostic, University Children’s Hospital, University Medical Centre Ljubljana (UMC), 1000 Ljubljana, Slovenia
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8
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Zheng H, Liu J, Pan X, Cui X. Biomarkers for patients with Wilms tumor: a review. Front Oncol 2023; 13:1137346. [PMID: 37554168 PMCID: PMC10405734 DOI: 10.3389/fonc.2023.1137346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/27/2023] [Indexed: 08/10/2023] Open
Abstract
Wilms tumor, originating from aberrant fetal nephrogenesis, is the most common renal malignancy in childhood. The overall survival of children is approximately 90%. Although existing risk-stratification systems are helpful in identifying patients with poor prognosis, the recurrence rate of Wilms tumors remains as high as 15%. To resolve this clinical problem, diverse studies on the occurrence and progression of the disease have been conducted, and the results are encouraging. A series of molecular biomarkers have been identified with further studies on the mechanism of tumorigenesis. Some of these show prognostic value and have been introduced into clinical practice. Identification of these biomarkers can supplement the existing risk-stratification systems. In the future, more biomarkers will be discovered, and more studies are required to validate their roles in improving the detection rate of occurrence or recurrence of Wilms tumor and to enhance clinical outcomes.
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Affiliation(s)
| | | | - Xiuwu Pan
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xingang Cui
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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9
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Csók Á, Micsik T, Magyar Z, Tornóczky T, Kuthi L, Nishi Y, Szirák K, Csóka M, Ottóffy G, Soltész B, Balogh I, Buglyó G. Alterations of miRNA Expression in Diffuse Hyperplastic Perilobar Nephroblastomatosis: Mapping the Way to Understanding Wilms' Tumor Development and Differential Diagnosis. Int J Mol Sci 2023; 24:ijms24108793. [PMID: 37240139 DOI: 10.3390/ijms24108793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Wilms' tumor (WT) is the most common renal malignancy in children. In diffuse hyperplastic perilobar nephroblastomatosis (DHPLN), nephrogenic rests result in a bulky enlargement of the kidney, a condition considered as a premalignant state before WT. Despite relevant clinical differences between WT and DHPLN, they are often challenging to distinguish based on histology. Molecular markers would improve differential diagnosis, but none are available at present. In our study, we investigated the potential of microRNAs (miRNAs) as such biomarkers, also aiming to shed light on the chronological order of expression changes. Formalin-fixed, paraffin-embedded (FFPE) samples from four DHPLN cases and adjacent healthy tissues were tested using a PCR array containing primers for 84 miRNAs implicated in genitourinary cancer. Expression in DHPLN was compared to WT data available in dbDEMC. Let-7, miR-135, miR-146a-5p, miR-182-5p, miR-183-5p, miR-20b-3p, miR-29b-3p, miR-195-5p and miR-17-5p showed potential to be used as biomarkers to distinguish WT and DHPLN in cases when traditional differential diagnosis is inconclusive. Our study also revealed miRNAs which may play a role in the initial steps of the pathogenesis (at a precancerous stage) and ones which become deregulated later in WT. More experiments are needed to confirm our observations and find new candidate markers.
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Affiliation(s)
- Ádám Csók
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Tamás Micsik
- Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary
| | - Zsófia Magyar
- Department of Obstetrics and Gynaecology, Baross Street Division, Semmelweis University, 1088 Budapest, Hungary
| | - Tamás Tornóczky
- Department of Pathology, University of Pécs Medical School and Clinical Center, 7624 Pécs, Hungary
| | - Levente Kuthi
- Department of Pathology, Faculty of Medicine, Albert Szent-Györgyi Medical School, University of Szeged, 6725 Szeged, Hungary
| | - Yumika Nishi
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Krisztina Szirák
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Monika Csóka
- Department of Paediatrics, Semmelweis University, 1094 Budapest, Hungary
| | - Gábor Ottóffy
- Department of Pediatrics, University of Pécs Medical School and Clinical Center, 7623 Pécs, Hungary
| | - Beáta Soltész
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - István Balogh
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
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10
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Doghish AS, Elballal MS, Elazazy O, Elesawy AE, Shahin RK, Midan HM, Sallam AAM, Elbadry AM, Mohamed AK, Ishak NW, Hassan KA, Ayoub AM, Shalaby RE, Elrebehy MA. miRNAs as potential game-changers in bone diseases: Future medicinal and clinical uses. Pathol Res Pract 2023; 245:154440. [PMID: 37031531 DOI: 10.1016/j.prp.2023.154440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/30/2023] [Accepted: 04/02/2023] [Indexed: 04/08/2023]
Abstract
MicroRNAs (miRNAs), short, highly conserved non-coding RNA, influence gene expression by sequential mechanisms such as mRNA breakdown or translational repression. Many biological processes depend on these regulating substances, thus changes in their expression have an impact on the maintenance of cellular homeostasis and result in the emergence of a variety of diseases. Relevant studies have shown in recent years that miRNAs are involved in many stages of bone development and growth. Additionally, abnormal production of miRNA in bone tissues has been closely associated with the development of numerous bone disorders, such as osteonecrosis, bone cancer, and bone metastases. Many pathological processes, including bone loss, metastasis, the proliferation of osteosarcoma cells, and differentiation of osteoblasts and osteoclasts, are under the control of miRNAs. By bringing together the most up-to-date information on the clinical relevance of miRNAs in such diseases, this study hopes to further the study of the biological features of miRNAs in bone disorders and explore their potential as a therapeutic target.
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11
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Zhang Y, Lv X, Chen F, Fan Q, Liu Y, Wan Z, Nibaruta J, Lv J, Han X, Wu L, Wang H, Leng Y. Role of microRNAs in programmed cell death in renal diseases: A review. Medicine (Baltimore) 2023; 102:e33453. [PMID: 37058073 PMCID: PMC10101263 DOI: 10.1097/md.0000000000033453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/15/2023] [Indexed: 04/15/2023] Open
Abstract
MicroRNAs (miRNAs) regulate gene expression involving kidney morphogenesis and cell proliferation, apoptosis, differentiation, migration, invasion, immune evasion, and extracellular matrix remodeling. Programmed cell death (PCD) is mediated and regulated by specific genes and a wealth of miRNAs, which participate in various pathological processes. Dysregulation of miRNAs can disrupt renal development and induce the onset and progression of various renal diseases. An in-depth understanding of how miRNAs regulate renal development and diseases is indispensable to comprehending how they can be used in new diagnostic and therapeutic approaches. However, the mechanisms are still insufficiently investigated. Hence, we review the current roles of miRNA-related signaling pathways and recent advances in PCD research and aim to display the potential crosstalk between miRNAs and PCD. The prospects of miRNAs as novel biomarkers and therapeutic targets are also described, which might provide some novel ideas for further studies.
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Affiliation(s)
- Yan Zhang
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
- The First Clinical Medical College of Lanzhou University, Lanzhou, GanSu Province, China
| | - Xinghua Lv
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Feng Chen
- The First Clinical Medical College of Lanzhou University, Lanzhou, GanSu Province, China
| | - Qian Fan
- Tianjin Eye Hospital, Tianjin Key Lab of Ophthalmology and Visual Science, Tianjin Eye Institute, Nankai University Affiliated Eye Hospital, Tianjin, China
- Nankai Eye Institute, Nankai University, Tianjin, China
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Yongqiang Liu
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
- The First Clinical Medical College of Lanzhou University, Lanzhou, GanSu Province, China
| | - Zhanhai Wan
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
- The First Clinical Medical College of Lanzhou University, Lanzhou, GanSu Province, China
| | - Janvier Nibaruta
- The First Clinical Medical College of Lanzhou University, Lanzhou, GanSu Province, China
| | - Jipeng Lv
- The First Clinical Medical College of Lanzhou University, Lanzhou, GanSu Province, China
| | - Xuena Han
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
- The First Clinical Medical College of Lanzhou University, Lanzhou, GanSu Province, China
| | - Lin Wu
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Hao Wang
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yufang Leng
- Department of Anesthesiology, First Hospital of Lanzhou University, Lanzhou, Gansu, China
- The First Clinical Medical College of Lanzhou University, Lanzhou, GanSu Province, China
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12
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Baig MS, Deepanshu, Prakash P, Alam P, Krishnan A. In silico analysis reveals hypoxia-induced miR-210-3p specifically targets SARS-CoV-2 RNA. J Biomol Struct Dyn 2023; 41:12305-12327. [PMID: 36752331 DOI: 10.1080/07391102.2023.2175255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/01/2023] [Indexed: 02/09/2023]
Abstract
Human coronaviruses (HCoVs) until the emergence of SARS in 2003 were associated with mild cold and upper respiratory tract infections. The ongoing pandemic caused by SARS-CoV-2 has enhanced the potential for infection and transmission as compared to other known members of this family. MicroRNAs (miRNA) are 21-25 nucleotides long non-coding RNA that bind to 3' UTR of genes and regulate almost every aspect of cellular function. Several human miRNAs have been known to target viral genomes, mostly to downregulate their expression and sometimes to upregulate also. In some cases, host miRNAs could be sequestered by the viral genome to create a condition for favourable virus existence. The ongoing SARS CoV-2 pandemic is unique based on its transmissibility and severity and we hypothesised that there could be a unique mechanism for its pathogenesis. In this study, we exploited in silico approach to identify human respiratory system-specific miRNAs targeting the viral genome of three highly pathogenic HCoVs (SARS-CoV-2 Wuhan strain, SARS-CoV, and MERS-CoV) and three low pathogenic HCoVs (OC43, NL63, and HKU1). We identified ten common microRNAs that target all HCoVs studied here. In addition, we identified unique miRNAs which targeted specifically one particular HCoV. miR-210-3p was the single unique lung-specific miRNA, which was found to target the NSP3, NSP4, and NSP13 genes of SARS-CoV-2. Further miR-210-NSP3, miR-210-NSP4, and miR-210-NSP13 SARS-CoV-2 duplexes were docked with the hAGO2 protein (PDB ID 4F3T) which showed Z-score values of -1.9, -1.7, and -1.6, respectively. The role of miR-210-3p as master hypoxia regulator and inflammation regulation may be important for SARS-CoV-2 pathogenesis. Overall, this analysis advocates that miR-210-3p be investigated experimentally in SARS-CoV-2 infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Deepanshu
- Department of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Prem Prakash
- Department of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Pravej Alam
- Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Anuja Krishnan
- Department of Molecular Medicine, Jamia Hamdard, New Delhi, India
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13
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Ribatti D, Ligresti G, Nicosia RF. Kidney endothelial cell heterogeneity, angiocrine activity and paracrine regulatory mechanisms. Vascul Pharmacol 2023; 148:107139. [PMID: 36539108 PMCID: PMC10828957 DOI: 10.1016/j.vph.2022.107139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/07/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
The blood microvascular endothelium consists of a heterogeneous population of cells with regionally distinct morphologies and transcriptional signatures in different tissues and organs. In addition to providing an anti-thrombogenic surface for blood flow, endothelial cells perform a multitude of additional regulatory tasks involving organogenesis, metabolism, angiogenesis, inflammation, repair and organ homeostasis. To communicate with surrounding cells and accomplish their many functions, endothelial cells secrete angiocrine factors including growth factors, chemokines, cytokines, extracellular matrix components, and proteolytic enzymes. Nonendothelial parenchymal and stromal cells in turn regulate endothelial growth, differentiation and survival during embryonal development and in the adult by paracrine mechanisms. Driven by advances in molecular biology, animal genetics, single cell transcriptomics and microscopic imaging, knowledge of organotypic vasculatures has expanded rapidly in recent years. The kidney vasculature, in particular, has been the focus of intensive investigation and represents a primary example of how endothelial heterogeneity and crosstalk with nonendothelial cells contribute to the development and function of a vital organ. In this paper, we review the morphology, function, and development of the kidney vasculature, with an emphasis on blood microvascular endothelial heterogeneity, and provide examples of endothelial and nonendothelial-derived factors that are critically involved in kidney development, growth, response to injury, and homeostasis.
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Affiliation(s)
- Domenico Ribatti
- Dipartimento di Scienze Mediche di Base, Neuroscienze e Organi di Senso (SMBNOS), Universita' degli Studi Aldo Moro, Policlinico, Piazza G. Cesare, 11, - Bari, Italy.
| | - Giovanni Ligresti
- Department of Medicine, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, United States of America
| | - Roberto F Nicosia
- Department of Laboratory Medicine and Pathology, University of Washington, Box 356100, 1959 NE Pacific St, Seattle, WA 98195, United States of America
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14
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Yang Q, Wang X, Li H, Yin X, Liu H, Hu W, Qing Y, Ding L, Yang L, Li Z, Sun H. Integrative analysis of renal microRNA and mRNA to identify hub genes and pivotal pathways associated with cyclosporine-induced acute kidney injury in mice. Hum Exp Toxicol 2023; 42:9603271231215499. [PMID: 37950702 DOI: 10.1177/09603271231215499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2023]
Abstract
Cyclosporine (CsA) is an immunosuppressive agent that often causes acute kidney injury (AKI) in children. The specific mechanisms underlying CsA-induced AKI are currently unknown. This study used an integrated network analysis of microRNA (miRNA) and mRNA expression profiles, biochemical and pathological analyses to further investigate these potential mechanisms of CsA-induced AKI. Small RNA sequence analysis identified 25 differentially expressed miRNAs, RNA sequencing analysis identified 4,109 differentially expressed mRNAs. We obtained a total of 4,367 target genes from the 25 differentially expressed miRNAs based on three algorithms, including the Mirdb, Mirtarbase, and TargetScan. 971 target genes overlapped between the 4,367 target genes and 4,109 differentially expressed mRNAs were identified for further bioinformatics analysis. Finally, 30 hub genes and two main modules were recognized. Functional enrichment analysis of 30 hub genes indicated that inflammation and epithelial-mesenchymal transition (EMT) related genes were mainly concentrated together. Pathway analysis revealed that the PI3K-Akt signaling pathway plays an integral role in CsA-induced AKI. Network analysis identified 3 important miRNAs, mmu-miR-17b-5p, mmu-miR-19b-3p, and mmu-mir-423-5p that may further promote the development of inflammatory responses and EMT by mediating a complex network of factors. Our research provides a clearer understanding the molecular mechanism of this specific drug-induced AKI by CsA use, which is useful for discovering potential targets for gene therapies, and drug development in CsA-induced AKI.
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Affiliation(s)
- Qiaoling Yang
- Department of Pharmacy, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xunjiang Wang
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hongjing Li
- Department of Pharmacy, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Pediatrics, Hunan Children's Hospital, Changsha, China
| | - Xuedong Yin
- Department of Pharmacy, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hongxia Liu
- Department of Pharmacy, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenjuan Hu
- Department of Pharmacy, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Qing
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Lili Ding
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Li Yang
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhiling Li
- Department of Pharmacy, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huajun Sun
- Department of Pharmacy, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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15
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Huang L, Shi Y, Hu J, Ding J, Guo Z, Yu B. Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of Egr1, Rxra and Max in kidney stone disease. Urolithiasis 2022; 51:13. [PMID: 36484839 DOI: 10.1007/s00240-022-01384-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022]
Abstract
Nephrolithiasis is one of the most common and frequent urologic diseases worldwide. The molecular mechanism of kidney stone formation is complex and remains to be illustrated. Transcript factors (TFs) that influenced the expression pattern of multiple genes, as well as microRNAs, important posttranscriptional modulators, play vital roles in this disease progression. Datasets of nephrolithiasis mice and kidney stone patients were acquired from Gene Expression Omnibus repository. TFs were predicted from differentially expressed genes by RcisTarget. The target genes of differential-expressed microRNAs were predicted by miRWalk. MicroRNA-mRNA network and PPI network were constructed. Functional enrichment analysis was performed via Metascape and Cytoscape identified hub genes. The assay of quantitative real-time PCR (q-PCR) and immunochemistry and the datasets of oxalate diet-induced nephrolithiasis mice kidneys and kidney stone patients' samples were utilized to validate the bioinformatic results. We identified three potential key TFs (Egr1, Rxra, Max), which can be modulated by miR-181a-5p, miR-7b-3p and miR-22-3p, respectively. The TFs and their regulated hub genes influenced the progression of nephrolithiasis via altering the expression of genes enriched in the functions of fibrosis, cell proliferation and molecular transportation and metabolism. The expression changes of transcription factors were consistent in q-PCR and immunochemistry results. For regulated hub genes, they showed consistent expression changes in oxalate diet-induced nephrolithiasis mice model and human kidneys with stones. The identified and verified three TFs, which may be modulated by microRNAs in nephrolithiasis disease progression, mainly influence biological processes responding to fibrosis, proliferation and molecular transportation and metabolism. The transcript influence showed consistency in multiple nephrolithiasis mice models and kidney stone patients.
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Affiliation(s)
- Linxi Huang
- Department of Nephrology, Changhai Hospital, Naval Medical University (Second Military Medical University), 168 Changhai Road, Shanghai, 200433, People's Republic of China
- Department of Cell Biology, Naval Medical University (Second Military Medical University), 800 Xiangyin Road, Shanghai, 200433, People's Republic of China
| | - Yuxuan Shi
- Department of Nephrology, Changhai Hospital, Naval Medical University (Second Military Medical University), 168 Changhai Road, Shanghai, 200433, People's Republic of China
| | - Junjie Hu
- Department of Cell Biology, Naval Medical University (Second Military Medical University), 800 Xiangyin Road, Shanghai, 200433, People's Republic of China
| | - Jiarong Ding
- Department of Nephrology, Changhai Hospital, Naval Medical University (Second Military Medical University), 168 Changhai Road, Shanghai, 200433, People's Republic of China
| | - Zhiyong Guo
- Department of Nephrology, Changhai Hospital, Naval Medical University (Second Military Medical University), 168 Changhai Road, Shanghai, 200433, People's Republic of China.
| | - Bing Yu
- Department of Cell Biology, Naval Medical University (Second Military Medical University), 800 Xiangyin Road, Shanghai, 200433, People's Republic of China.
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