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Wu KL, Chou CY, Chang HY, Wu CH, Li AL, Chen CL, Tsai JC, Chen YF, Chen CT, Tseng CC, Chen JB, Wang IK, Hsu YJ, Lin SH, Huang CC, Ma N. Peritoneal effluent MicroRNA profile for detection of encapsulating peritoneal sclerosis. Clin Chim Acta 2022; 536:45-55. [PMID: 36130656 DOI: 10.1016/j.cca.2022.09.007] [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: 08/12/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Encapsulating peritoneal sclerosis (EPS) is a catastrophic complication of peritoneal dialysis (PD) with high mortality. Our aim is to develop a novel noninvasive microRNA (miRNA) test for EPS. METHODS We collected 142 PD effluents (EPS: 62 and non-EPS:80). MiRNA profiles of PD effluents were examined by a high-throughput real-time polymerase chain reaction (PCR) array to first screen. Candidate miRNAs were verified by single real-time PCR. The model for EPS prediction was evaluated by multiple logistic regression and machine learning. RESULTS Seven candidate miRNAs were identified from the screening of PCR-array of 377 miRNAs. The top five area under the curve (AUC) values with 5 miRNA-ratios were selected using 127 samples (EPS: 56 vs non-EPS: 71) to produce a receiver operating characteristic curve. After considering clinical characteristics and 5 miRNA-ratios, the accuracies of the machine learning model of Random Forest and multiple logistic regression were boosted to AUC 0.97 and 0.99, respectively. Furthermore, the pathway analysis of miRNA associated targeting genes and miRNA-compound interaction network revealed that these five miRNAs played the roles in TGF-β signaling pathway. CONCLUSION The model-based miRNA expressions in PD effluents may help determine the probability of EPS and provide further therapeutic opinion for EPS.
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Affiliation(s)
- Kun-Lin Wu
- Department of Biomedical Sciences and Engineering, Institute of Systems Biology and Bioinformatics, National Central University, Taoyuan, Taiwan; Division of Nephrology, Department of Internal Medicine, Taoyuan Armed Forces General Hospital, Taoyuan, Taiwan; Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Che-Yi Chou
- Division of Nephrology, Department of Internal Medicine, Asia University Hospital, Taichung, Taiwan
| | - Hui-Yin Chang
- Department of Biomedical Sciences and Engineering, Institute of Systems Biology and Bioinformatics, National Central University, Taoyuan, Taiwan
| | - Chih-Hsun Wu
- Artificial Intelligence and E-Learning Center, National Chengchi University, Taiwan
| | - An-Lun Li
- Department of Biomedical Sciences and Engineering, Institute of Systems Biology and Bioinformatics, National Central University, Taoyuan, Taiwan
| | - Chien-Lung Chen
- Division of Nephrology, Department of Medicine, Landseed International Hospital, Taoyuan, Taiwan
| | - Jen-Chieh Tsai
- Department of Biomedical Sciences and Engineering, Institute of Systems Biology and Bioinformatics, National Central University, Taoyuan, Taiwan; Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan; Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan
| | - Yi-Fan Chen
- Interdisciplinary Program of Engineering, National Central University, Taoyuan, Taiwan
| | - Chiung-Tong Chen
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan; Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan
| | - Chin-Chung Tseng
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital Dou-Liou Branch, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jin-Bor Chen
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and College of Medicine, Chang Gung University, Kaohsiung, Taiwan
| | - I-Kuan Wang
- Division of Nephrology and the Kidney Institute, China Medical University and Hospitals, Taichung, Taiwan
| | - Yu-Juei Hsu
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Shih-Hua Lin
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chiu-Ching Huang
- Division of Nephrology and the Kidney Institute, China Medical University and Hospitals, Taichung, Taiwan.
| | - Nianhan Ma
- Department of Biomedical Sciences and Engineering, Institute of Systems Biology and Bioinformatics, National Central University, Taoyuan, Taiwan.
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2
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Wang Y, Li M, Pan C, Huang H, Hu X, Liu J. Hsa_circ_0007637 Facilitates Nasopharyngeal Carcinoma Progression by Sponging miR-636/TPD52 Axis. Cancer Manag Res 2022; 13:9439-9452. [PMID: 35002322 PMCID: PMC8722538 DOI: 10.2147/cmar.s328207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/06/2021] [Indexed: 12/11/2022] Open
Abstract
Purpose Hsa_circ_0007637 was discovered to be differentially expressed in nasopharyngeal carcinoma (NPC). However, the exact function and mechanism of Hsa_circ_0007637 on NPC have not been studied. This study firstly researched the function and mechanism of Hsa_circ_0007637 on NPC progression. Methods Hsa_circ_0007637, miR-636 and TPD52 expressions in 80 NPC patients were detected by quantitative real-time polymerase chain reaction. Hsa_circ_0007637 effect on NPC cell proliferation, apopticosis, invasion and migration was investigated by cell counting kit-8 assay, flow cytometry, transwell experiment and wound healing assay accordingly. Dual-luciferase reporter gene assay, RNA immunoprecipitation experiment and RNA fluorescence in situ hybridization experiment were performed to identify the binding between Hsa_circ_0007637 and miR-636. Dual-luciferase reporter gene assay and RNA pull down assay were conducted to verify the binding between miR-636 and TPD52. TPD52 protein expression in NPC cells was determined by Western blot. In vivo study was performed using nude mice. Immunohistochemistry was performed to assess TPD52 and Ki67 expression in tissues. Results Hsa_circ_0007637 was overexpressed in NPC tissues and cells. High Hsa_circ_0007637 expression predicted a poor outcome for NPC patients. Hsa_circ_0007637 knockdown decreased proliferation, invasion, migration and increased apoptosis of NPC cells (P < 0.01). Hsa_circ_0007637 could enhance TPD52 expression via sponging miR-636. miR-636 overexpression or TPD52 knockdown weakened the promoting effect of Hsa_circ_0007637 on NPC cells malignant phenotype (P < 0.01). Hsa_circ_0007637 knockdown suppressed NPC cells growth in vivo (P < 0.01). Conclusion Hsa_circ_0007637 facilitates NPC progression by sponging miR-636/TPD52 axis.
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Affiliation(s)
- Yihong Wang
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Manyi Li
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Chen Pan
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Haiping Huang
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Xiaoqing Hu
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Jisheng Liu
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
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3
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Li AL, Chou CY, Chen CL, Wu KL, Lin SC, Chen HC, Wang MC, Chang CC, Hsu BG, Wu MS, Ma N, Huang CC. The MicroRNA Prediction Models as Ancillary Diagnosis Biomarkers for Urothelial Carcinoma in Patients With Chronic Kidney Disease. Front Med (Lausanne) 2021; 8:726214. [PMID: 34660637 PMCID: PMC8517232 DOI: 10.3389/fmed.2021.726214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/07/2021] [Indexed: 12/24/2022] Open
Abstract
Urothelial carcinoma is a common urological cancer in chronic kidney disease patients. Cystoscopy and urine cytology are the clinical diagnostic tools for UC. However, cystoscopy is an invasive procedure, while urine cytology showed low sensitivity for low-grade urothelial tumors. High accuracy with non-invasive tools for UC is needed for CKD patients. Our study collected a total of 272 urine and 138 plasma samples to detect the miRNA expression levels for establishing UC signatures from CKD patients. Seventeen candidate miRNAs of biofluids were selected and confirmed by qRT-PCR. Our results showed that urinary miR-1274a and miR-30a-5p expression levels were significantly lower but miR-19a-5p expression levels were higher in UC when compared with CKD. In plasma samples, miR-155-5p, miR-19b-1-5p, miR-378, and miR-636 showed significantly lower expression in UC compared to those with CKD. The Kaplan-Meier curve showed that lower expression of miR-19a, miR-19b, miR-636 and miR-378, and higher expression of miR-708-5p were associated with poor prognosis in patients with bladder cancer. In addition, we produced classifiers for predicting UC by multiple logistic regression. The urine signature was developed with four miRNAs, and the AUC was 0.8211. Eight miRNA expression levels from both urine and plasma samples were examined, and the AUC was 0.8595. Two miRNA classifiers and the nomograms could improve the drawbacks of current UC biomarker screenings for patients with CKD.
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Affiliation(s)
- An-Lun Li
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Che-Yi Chou
- Division of Nephrology, Department of Internal Medicine, Asia University Hospital, Taichung, Taiwan
| | - Chien-Lung Chen
- Department of Nephrology, Landseed International Hospital, Taoyuan, Taiwan
| | - Kun-Lin Wu
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan.,Division of Nephrology, Department of Internal Medicine, Taoyuan Armed Forces General Hospital, Taoyuan, Taiwan
| | - Shih-Chieh Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hung-Chun Chen
- Division of Nephrology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Cheng Wang
- Division of Nephrology, Cheng Kung University Hospital, Tainan, Taiwan
| | - Chia-Chu Chang
- Division of Nephrology, Department of Internal Medicine, Kuang Tien General Hospital, Taichung, Taiwan.,Department of Nutrition, Hungkuang University, Taichung, Taiwan
| | - Bang-Gee Hsu
- Division of Nephrology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan
| | - Mai-Szu Wu
- Division of Nephrology, Taipei Medical University and Hospitals, Taipei, Taiwan
| | - Nianhan Ma
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Chiu-Ching Huang
- Division of Nephrology and The Kidney Institute, China Medical University and Hospitals, Taichung, Taiwan
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4
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Dong Z, Gu H, Guo Q, Liang S, Xue J, Yao F, Liu X, Li F, Liu H, Sun L, Zhao K. Profiling of Serum Exosome MiRNA Reveals the Potential of a MiRNA Panel as Diagnostic Biomarker for Alzheimer's Disease. Mol Neurobiol 2021; 58:3084-3094. [PMID: 33629272 DOI: 10.1007/s12035-021-02323-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 02/05/2021] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease in the older adults. Although much effort has been made in the analyses of diagnostic biomarkers, such as amyloid-β, tau, and neurofilament light chain, identifying peripheral blood-based biomarkers is in extremely urgent need for their minimal invasiveness and more convenience. Here we characterized the miRNA profile by RNA sequencing in human serum exosomes from AD patients and healthy controls (HC) to investigate its potential for AD diagnosis. Subsequently, Gene Ontology analysis and pathway analysis were performed for the targeted genes from the differentially expressed miRNAs. These basic functions were differentially enriched, including cell adhesion, regulation of transcription, and the ubiquitin system. Functional network analysis highlighted the pathways of proteoglycans in cancer, viral carcinogenesis, signaling pathways regulating pluripotency of stem cells, and cellular senescence in AD. A total of 24 miRNAs showed significantly differential expression between AD and HC with more than ± 2.0-fold change at p value < 0.05 and at least 50 reads for each sample. Logistic regression analysis established a model for AD prediction by serum exosomal miR-30b-5p, miR-22-3p, and miR-378a-3p. Sequencing results were validated using quantitative reverse transcription PCR. The data showed that miR-30b-5p, miR-22-3p, and miR-378a-3p were significantly deregulated in AD, with area under the curve (AUC) of 0.668, 0.637, and 0.718, respectively. The combination of the three miRs gained a better diagnostic capability with AUC of 0.880. This finding revealed a miR panel as potential biomarker in the peripheral blood to distinguish AD from HC.
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Affiliation(s)
- Zhiwu Dong
- Department of Laboratory Medicine, Jinshan Branch of Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, 147 Jiankang Road, Jinshan District, Shanghai, 201599, People's Republic of China.
| | - Hongjun Gu
- Shanghai Jinshan Zhongren Aged Care Hospital, Shanghai, 201501, China
| | - Qiang Guo
- Department of Ultrasound Medicine, Jinshan Branch of Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai, 201599, China
| | - Shuang Liang
- Department of Laboratory Medicine, Jinshan Branch of Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, 147 Jiankang Road, Jinshan District, Shanghai, 201599, People's Republic of China
| | - Jian Xue
- Shanghai Jinshan Zhongren Aged Care Hospital, Shanghai, 201501, China
| | - Feng Yao
- Shanghai Jinshan Zhongren Aged Care Hospital, Shanghai, 201501, China
| | - Xianglu Liu
- Department of Laboratory Medicine, Jinshan Branch of Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, 147 Jiankang Road, Jinshan District, Shanghai, 201599, People's Republic of China
| | - Feifei Li
- Department of Laboratory Medicine, Jinshan Branch of Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, 147 Jiankang Road, Jinshan District, Shanghai, 201599, People's Republic of China
| | - Huiling Liu
- Department of Laboratory Medicine, Jinshan Branch of Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, 147 Jiankang Road, Jinshan District, Shanghai, 201599, People's Republic of China
| | - Li Sun
- Department of Laboratory Medicine, Jinshan Branch of Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, 147 Jiankang Road, Jinshan District, Shanghai, 201599, People's Republic of China
| | - Kewen Zhao
- Department of Pathophysiology, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
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Stempor PA, Avni D, Leibowitz R, Sidi Y, Stępień M, Dzieciątkowski T, Dobosz P. Comprehensive Analysis of Correlations in the Expression of miRNA Genes and Immune Checkpoint Genes in Bladder Cancer Cells. Int J Mol Sci 2021; 22:2553. [PMID: 33806327 PMCID: PMC7961343 DOI: 10.3390/ijms22052553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
Personalised medicine is the future and hope for many patients, including those with cancers. Early detection, as well as rapid, well-selected treatment, are key factors leading to a good prognosis. MicroRNA mediated gene regulation is a promising area of development for new diagnostic and therapeutic methods, crucial for better prospects for patients. Bladder cancer is a frequent neoplasm, with high lethality and lacking modern, advanced therapeutic modalities, such as immunotherapy. MicroRNAs are involved in bladder cancer pathogenesis, proliferation, control and response to treatment, which we summarise in this perspective in response to lack of recent review publications in this field. We further performed a correlation-based analysis of microRNA and gene expression data in bladder cancer (BLCA) TCGA dataset. We identified 27 microRNAs hits with opposite expression profiles to genes involved in immune response in bladder cancer, and 24 microRNAs hits with similar expression profiles. We discuss previous studies linking the functions of these microRNAs to bladder cancer and assess if they are good candidates for personalised medicine therapeutics and diagnostics. The discussed functions include regulation of gene expression, interplay with transcription factors, response to treatment, apoptosis, cell proliferation and angiogenesis, initiation and development of cancer, genome instability and tumour-associated inflammatory reaction.
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Affiliation(s)
- Przemysław A. Stempor
- SmartImmune Ltd, Accelerate Cambridge, University of Cambridge Judge Business School, Cambridge CB4 1EE, UK;
| | - Dror Avni
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashome 52621, Israel;
| | - Raya Leibowitz
- Oncology Institute, Shamir Medical Center, Be’er Yaakov, Tel Hashome 52621, Israel;
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel;
| | - Yechezkel Sidi
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel;
| | - Maria Stępień
- Faculty of Medicine, Medical University of Lublin, 20-059 Lublin, Poland;
| | | | - Paula Dobosz
- Department of Hematology, Transplantationand Internal Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland
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6
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Ma J, Zhou C, Chen X. miR-636 inhibits EMT, cell proliferation and cell cycle of ovarian cancer by directly targeting transcription factor Gli2 involved in Hedgehog pathway. Cancer Cell Int 2021; 21:64. [PMID: 33472614 PMCID: PMC7819188 DOI: 10.1186/s12935-020-01725-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 12/19/2020] [Indexed: 02/08/2023] Open
Abstract
Background Hedgehog (Hh) signaling pathway, which is essential for cell proliferation and differentiation, is noted to be aberrantly activated in tumor from increasing studies in recent years. MicroRNAs (miRNAs) as an important non-coding RNA in cells have been proven to possess a regulatory role specific to the Hh signaling pathway. Here, in vitro and in vivo cellular/molecular experiments were adopted to clarify the regulatory mechanism linking miR-636 to the Hh signaling pathway in ovarian cancer (OVC). Methods Protein–protein interaction analysis was performed to identify the hub gene in the Hh pathway. TargetScan database was used to predict the potential upstream regulators for Gli2. qRT-PCR was performed to test the expression of miR-636, while Western blot was conducted to detect the expression of proteins related to the Hh pathway and epithelial-mesenchymal transition (EMT). For cell functional experiments, HO-8910PM OVC cell line was used. MTT assay and wound healing assay were used to measure the effect of miR-636 on cell proliferation and migration. Flow cytometry was carried out to examine the effect of miR-636 on cell cycle, and Western blot was used to identify the change in expression of Hh and EMT-related proteins. Dual-luciferase reporter gene assay was implemented to detect the targeting relationship between miR-636 and Gli2. Xenotransplantation models were established for in vivo examination. Results Gli2 was identified as the hub gene of the Hh pathway and it was validated to be regulated by miR-636 based on the data from TargetScan and GEO databases. In vitro experiments discovered that miR-636 was significantly lowly expressed in OVC cell lines, and overexpressing miR-636 significantly inhibited HO-8910PM cell proliferation, migration and induced cell cycle arrest in G0/G1 phase, while the inhibition of miR-636 caused opposite results. Dual-luciferase reporter gene assay revealed that Gli2 was the target gene of miR-636 in OVC. Besides, overexpressed miR-636 decreased protein expression of Gli2, and affected the expression of proteins related to the Hh signaling pathway and EMT. Rescue experiments verified that overexpression of Gli2 reversed the inhibitory effect of miR-636 on HO-8910PM cell proliferation and migration, and attenuated the blocking effect of miR-636 on cell cycle. The xenotransplantation experiment suggested that miR-636 inhibited cell growth of OVC by decreasing Gli2 expression. Besides, overexpressing Gli2 potentiated the EMT process of OVC cells via decreasing E-cadherin protein expression and increasing Vimentin protein expression, and it reversed the inhibitory effect of miR-636 on OVC cell proliferation in vivo. Conclusion miR-636 mediates the activation of the Hh pathway via binding to Gli2, thus inhibiting EMT, suppressing cell proliferation and migration of OVC. Trial registration: The experimental protocol was established, according to the ethical guidelines of the Helsinki Declaration and was approved by the Human Ethics Committee of The Second Affiliated hospital of Zhejiang University School of Medicine (IR2019001235). Written informed consent was obtained from individual or guardian participants.
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Affiliation(s)
- Jiong Ma
- Department of Gynecology, The Second Affiliated Hospital of Zhejiang University School of Medicine, No.88 Jiefang Road, Hangzhou, 310009, China
| | - Chunxia Zhou
- Department of Gynecology, The Second Affiliated Hospital of Zhejiang University School of Medicine, No.88 Jiefang Road, Hangzhou, 310009, China
| | - Xuejun Chen
- Department of Gynecology, The Second Affiliated Hospital of Zhejiang University School of Medicine, No.88 Jiefang Road, Hangzhou, 310009, China.
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Li G, Yang H, Cheng Y, Zhao X, Li X, Jiang R. Identification of a three-miRNA signature as a novel prognostic model for papillary renal cell carcinoma. Cancer Cell Int 2020; 20:317. [PMID: 32694939 PMCID: PMC7367267 DOI: 10.1186/s12935-020-01398-2] [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: 05/27/2020] [Accepted: 07/01/2020] [Indexed: 01/18/2023] Open
Abstract
Background Papillary renal cell carcinoma (pRCC) accounting for near 20% of renal cell carcinoma is the second most common histological subtype. MiRNAs have been demonstrated to played significant roles on predicting prognosis of patients with tumors. An appropriate and comprehensive miRNAs analysis based on a great deal of pRCC samples from The Cancer Genome Atlas (TCGA) will provide perspective in this field. Methods We integrated the expression of mRNAs, miRNAs and the relevant clinical data of 321 pRCC patients recorded in the TCGA database. The survival-related differential expressed miRNAs (sDEmiRs) were estimated by COX regression analysis. The high-risk group and the low-risk group were separated by the median risk score of the risk score model (RSM) based on three screened sDEmiRs. The target genes, underlying molecular mechanisms of these sDEmiRs were explored by computational biology. The expression levels of the three sDEmiRs and their correlations with clinicopathological parameters were further validated by qPCR. Results Based on univariate COX analysis (P < 0.001), eighteen differential expressed miRNAs (DEmiRs) were remarkably related with the overall survival (OS) of pRCC patients. Three sDEmiRs with the most significant prognostic values (miR-34a-5p, miR-410-3p and miR-6720-3p) were employed to establish the RSM which was certified as an independent prognosis factor and closely correlated with OS. In the verification of clinical samples, the overexpression of miR-410-3p and miR-6720-3p were detected to be associated with the advanced T-stages, while miR-34a-5p showed the reversed results. Conclusion The study developed a RSM based on the identified sDEmiRs with significant prognosis prediction values for pRCC patients. The results pave the avenue for establishing and optimizing a reliable and referable risk assessing model and provide novel insight into the researches of biomarkers and clinical treatment strategies.
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Affiliation(s)
- Ge Li
- Department of Urology, The Affiliated Hospital of Southwest Medical University, No. 25 Taiping Road, Jiangyang District, Luzhou, 646000 China
| | - Haifan Yang
- Department of Urology, The Affiliated Hospital of Southwest Medical University, No. 25 Taiping Road, Jiangyang District, Luzhou, 646000 China
| | - Yong Cheng
- Department of Urology, The Affiliated Hospital of Southwest Medical University, No. 25 Taiping Road, Jiangyang District, Luzhou, 646000 China
| | - Xin Zhao
- Department of Urology, The Affiliated Hospital of Southwest Medical University, No. 25 Taiping Road, Jiangyang District, Luzhou, 646000 China
| | - Xu Li
- Department of Urology, The Affiliated Hospital of Southwest Medical University, No. 25 Taiping Road, Jiangyang District, Luzhou, 646000 China
| | - Rui Jiang
- Department of Urology, The Affiliated Hospital of Southwest Medical University, No. 25 Taiping Road, Jiangyang District, Luzhou, 646000 China
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Bardin P, Foussignière T, Rousselet N, Rebeyrol C, Porter JC, Corvol H, Tabary O. miR-636: A Newly-Identified Actor for the Regulation of Pulmonary Inflammation in Cystic Fibrosis. Front Immunol 2019; 10:2643. [PMID: 31803183 PMCID: PMC6874100 DOI: 10.3389/fimmu.2019.02643] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/24/2019] [Indexed: 12/21/2022] Open
Abstract
Cystic fibrosis (CF) results from deficient CF transmembrane conductance regulator (CFTR) protein activity leading to defective epithelial ion transport. Pulmonary degradation due to excessive inflammation is the main cause of morbidity and mortality in CF patients. By analysing miRNAs (small RNAseq) in human primary air-liquid interface cell cultures, we measured the overexpression of miR-636 in CF patients compared to non-CF controls. We validated these results in explant biopsies and determined that the mechanism underlying miR-636 overexpression is linked to inflammation. To identify specific targets, we used bioinformatics analysis to predict whether miR-636 targets the 3′-UTR mRNA regions of IL1R1 and RANK (two pro-inflammatory cytokine receptors), IKBKB (a major protein in the NF-κB pathway), and FAM13A (a modifier gene of CF lung phenotype implicated in epithelial remodelling). Using bronchial epithelial cells from CF patients to conduct a functional analysis, we showed a direct interaction between miR-636 and IL1R1, RANK, and IKBKB, but not with FAM13A. These interactions led to a decrease in IL1R1 and IKKβ protein expression levels, while we observed an increase in RANK protein expression levels following the overexpression of miR-636. Moreover, NF-κB activity and IL-8 and IL-6 secretions decreased following the transfection of miR-636 mimics in CF cells. Similar but opposite effects were found after transfection with an antagomiR-636 in the same cells. Furthermore, we demonstrated that miR-636 was not regulated by Pseudomonas aeruginosa in our model. We went on to show that miR-636 is raised in the blood neutrophils, but not in the plasma, of CF patients and may have potential as a novel biomarker. Collectively, our findings reveal a novel actor for the regulation of inflammation in CF, miR-636, which is able to reduce constitutive NF-κB pathway activation when it is overexpressed.
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Affiliation(s)
- Pauline Bardin
- Faculté des Sciences, Sorbonne Université, Paris, France.,Inserm, Centre de Recherche Saint-Antoine, Paris, France
| | | | | | - Carine Rebeyrol
- UCL Respiratory, University College London, Hospitals NHS Foundation Trust, London, United Kingdom
| | - Joanna C Porter
- UCL Respiratory, University College London, Hospitals NHS Foundation Trust, London, United Kingdom
| | - Harriet Corvol
- Faculté des Sciences, Sorbonne Université, Paris, France.,Inserm, Centre de Recherche Saint-Antoine, Paris, France.,Département de Pédiatrie Respiratoire, Hôpital Trousseau, AP-HP, Paris, France
| | - Olivier Tabary
- Faculté des Sciences, Sorbonne Université, Paris, France.,Inserm, Centre de Recherche Saint-Antoine, Paris, France
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