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Jiang C, Qin B, Liu G, Sun X, Shi H, Ding S, Liu Y, Zhu M, Chen X, Zhao C. MicroRNA-184 promotes differentiation of the retinal pigment epithelium by targeting the AKT2/mTOR signaling pathway. Oncotarget 2018; 7:52340-52353. [PMID: 27418134 PMCID: PMC5239556 DOI: 10.18632/oncotarget.10566] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/30/2016] [Indexed: 12/13/2022] Open
Abstract
Dedifferentiation of retinal pigment epithelium (RPE) cells is a crucial contributing factor to the pathology of retinal degenerative diseases, including age-related macular degeneration (AMD). Herein, we aim to reveal the roles of microRNAs (miRNAs) in RPE dedifferentiation and seek for potential therapeutic targets. Based on the microarray data, miR-184 was sorted out as the most up-regulated signature along with the differentiation from human induced pluripotent stem cells (hiPSC) to RPE cells, suggesting its potential promotive role in RPE differentiation. In vitro study indicated that miR-184 insufficiency suppressed RPE differentiation, typified by reduction of RPE markers, and promoted cell proliferation and migration. The role of miR-184 in maintaining regular RPE function was further proved in zebrafish studies. We also noticed that miR-184 expression was reduced in the macular RPE-choroid from a donor with RPE dysfunction compared to a healthy control. We next demonstrated that RAC-beta serine/threonine-protein kinase (AKT2) was a direct target for miR-184. MiR-184 promoted RPE differentiation via suppression of AKT2/mammalian target of rapamycin (mTOR) signaling pathway. We also found that AKT2 was up-regulated in macular RPE-choroid of the donor with RPE dysfunction and dry AMD patients. Taken together, our findings suggest that miR-184 insufficiency is involved in the pathogenesis of dry AMD. MiR-184 promotes RPE differentiation via inhibiting the AKT2/mTOR signaling pathway. MiR-184 based supplementary therapeutics and mTOR blocker, like rapamycin, are prospective options for AMD treatment.
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Affiliation(s)
- Chao Jiang
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Bing Qin
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Ophthalmology, The First People's Hospital of Suqian, Suqian, China
| | - Guohua Liu
- Department of Ophthalmology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xiantao Sun
- Department of Ophthalmology, Children's Hospital of Zhengzhou, Zhengzhou, China
| | - Houxia Shi
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Sijia Ding
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Yuan Liu
- Department of Ophthalmology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Meidong Zhu
- Save Sight Institute, Discipline of Clinical Ophthalmology and Eye Health (CO9), The University of Sydney, Sydney, Australia
| | - Xue Chen
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Chen Zhao
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University and State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat Sen University, Guangzhou, China
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Fu Q, Song X, Liu Z, Deng X, Luo R, Ge C, Li R, Li Z, Zhao M, Chen Y, Lin X, Zhang Q, Fang W. miRomics and Proteomics Reveal a miR-296-3p/PRKCA/FAK/Ras/c-Myc Feedback Loop Modulated by HDGF/DDX5/β-catenin Complex in Lung Adenocarcinoma. Clin Cancer Res 2017; 23:6336-6350. [PMID: 28751441 DOI: 10.1158/1078-0432.ccr-16-2813] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 04/19/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022]
Abstract
Purpose: This study was performed to identify the detailed mechanisms by which miR-296-3p functions as a tumor suppressor to prevent lung adenocarcinoma (LADC) cell growth, metastasis, and chemoresistance.Experimental Design: The miR-296-3p expression was examined by real-time PCR and in situ hybridization. MTT, EdU incorporation, Transwell assays, and MTT cytotoxicity were respectively performed for cell proliferation, metastasis, and chemoresistance; Western blotting was performed to analyze the pathways by miR-296-3p and HDGF/DDX5 complex. The miRNA microarray and luciferase reporter assays were respectively used for the HDGF-mediated miRNAs and target genes of miR-296-3p. The ChIP, EMSA assays, and coimmunoprecipitation combined with mass spectrometry and GST pull-down were respectively designed to analyze the DNA-protein complex and HDGF/DDX5/β-catenin complex.Results: We observed that miR-296-3p not only controls cell proliferation and metastasis, but also sensitizes LADC cells to cisplatin (DDP) in vitro and in vivo Mechanistic studies demonstrated that miR-296-3p directly targets PRKCA to suppress FAK-Ras-c-Myc signaling, thus stimulating its own expression in a feedback loop that blocks cell cycle and epithelial-mesenchymal transition (EMT) signal. Furthermore, we observed that suppression of HDGF-β-catenin-c-Myc signaling activates miR-296-3p, ultimately inhibiting the PRKCA-FAK-Ras pathway. Finally, we found that DDX5 directly interacts with HDGF and induces β-catenin-c-Myc, which suppresses miR-296-3p and further activates PRKCA-FAK-Ras, cell cycle, and EMT signaling. In clinical samples, reduced miR-296-3p is an unfavorable factor that inversely correlates with HDGF/DDX5, but not PRKCA.Conclusions: Our study provides a novel mechanism that the miR-296-3p-PRKCA-FAK-Ras-c-Myc feedback loop modulated by HDGF/DDX5/β-catenin complex attenuates cell growth, metastasis, and chemoresistance in LADC. Clin Cancer Res; 23(20); 6336-50. ©2017 AACR.
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Affiliation(s)
- Qiaofen Fu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
- Cancer Research Institute of Southern Medical University, Guangzhou, Guangdong, P.R. China
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, P.R. China
| | - Xin Song
- Cancer Research Institute of Southern Medical University, Guangzhou, Guangdong, P.R. China
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, P.R. China
| | - Zhen Liu
- Cancer Research Institute of Southern Medical University, Guangzhou, Guangdong, P.R. China
- Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, P.R. China
| | - Xiaojie Deng
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
- Cancer Research Institute of Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Rongcheng Luo
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Chunlei Ge
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, P.R. China
| | - Ruilei Li
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, P.R. China
| | - Zhen Li
- Department of Cancer Biotherapy Center, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, Yunnan, P.R. China
| | - Mengyang Zhao
- Cancer Research Institute of Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Yiyu Chen
- Cancer Research Institute of Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Xian Lin
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Qianbing Zhang
- Cancer Research Institute of Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Weiyi Fang
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China.
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Raddatz BB, Spitzbarth I, Matheis KA, Kalkuhl A, Deschl U, Baumgärtner W, Ulrich R. Microarray-Based Gene Expression Analysis for Veterinary Pathologists: A Review. Vet Pathol 2017. [PMID: 28641485 DOI: 10.1177/0300985817709887] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
High-throughput, genome-wide transcriptome analysis is now commonly used in all fields of life science research and is on the cusp of medical and veterinary diagnostic application. Transcriptomic methods such as microarrays and next-generation sequencing generate enormous amounts of data. The pathogenetic expertise acquired from understanding of general pathology provides veterinary pathologists with a profound background, which is essential in translating transcriptomic data into meaningful biological knowledge, thereby leading to a better understanding of underlying disease mechanisms. The scientific literature concerning high-throughput data-mining techniques usually addresses mathematicians or computer scientists as the target audience. In contrast, the present review provides the reader with a clear and systematic basis from a veterinary pathologist's perspective. Therefore, the aims are (1) to introduce the reader to the necessary methodological background; (2) to introduce the sequential steps commonly performed in a microarray analysis including quality control, annotation, normalization, selection of differentially expressed genes, clustering, gene ontology and pathway analysis, analysis of manually selected genes, and biomarker discovery; and (3) to provide references to publically available and user-friendly software suites. In summary, the data analysis methods presented within this review will enable veterinary pathologists to analyze high-throughput transcriptome data obtained from their own experiments, supplemental data that accompany scientific publications, or public repositories in order to obtain a more in-depth insight into underlying disease mechanisms.
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Affiliation(s)
- Barbara B Raddatz
- 1 Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.,2 Center of Systems Neuroscience, Hannover, Germany
| | - Ingo Spitzbarth
- 1 Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.,2 Center of Systems Neuroscience, Hannover, Germany
| | - Katja A Matheis
- 3 Department of Nonclinical Drug Safety, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach (Riß), Germany
| | - Arno Kalkuhl
- 3 Department of Nonclinical Drug Safety, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach (Riß), Germany
| | - Ulrich Deschl
- 3 Department of Nonclinical Drug Safety, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach (Riß), Germany
| | - Wolfgang Baumgärtner
- 1 Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.,2 Center of Systems Neuroscience, Hannover, Germany
| | - Reiner Ulrich
- 1 Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.,2 Center of Systems Neuroscience, Hannover, Germany.,4 Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institute, Greifswald, Germany
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miR-3188 regulates nasopharyngeal carcinoma proliferation and chemosensitivity through a FOXO1-modulated positive feedback loop with mTOR-p-PI3K/AKT-c-JUN. Nat Commun 2016; 7:11309. [PMID: 27095304 PMCID: PMC4842991 DOI: 10.1038/ncomms11309] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/11/2016] [Indexed: 12/15/2022] Open
Abstract
The biological role of miR-3188 has not yet been reported in the context of cancer. In this study, we observe that miR-3188 not only reduces cell-cycle transition and proliferation, but also significantly prolongs the survival time of tumour-bearing mice as well as sensitizes cells to 5-FU. Mechanistic analyses indicate that miR-3188 directly targets mTOR to inactivate p-PI3K/p-AKT/c-JUN and induces its own expression. This feedback loop further suppresses cell-cycle signalling through the p-PI3K/p-AKT/p-mTOR pathway. Interestingly, we also observe that miR-3188 direct targeting of mTOR is mediated by FOXO1 suppression of p-PI3K/p-AKT/c-JUN signalling. In clinical samples, reduced miR-3188 is an unfavourable factor and negatively correlates with mTOR and c-JUN levels but positively correlates with FOXO1 expression. Our studies demonstrate that as a tumour suppressor, miR-3188 directly targets mTOR to stimulate its own expression and participates in FOXO1-mediated repression of cell growth, tumorigenesis and NPC chemotherapy resistance. Although miR-related mechanisms have been implicated in nasopharyngeal carcinoma (NPC), a precise role for miR-3188 has not been reported in this context. Here, Zhao et al. show that FOXO1-induced miR-3188 acts as a tumour suppressor in NPC by regulating the axis mTOR/PI3K/Akt/c-Jun.
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Ahmed FE. Liquid chromatography–mass spectrometry: a tool for proteome analysis and biomarker discovery and validation. ACTA ACUST UNITED AC 2009; 3:429-44. [DOI: 10.1517/17530050902832855] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Wheelan SJ, Martínez Murillo F, Boeke JD. The incredible shrinking world of DNA microarrays. MOLECULAR BIOSYSTEMS 2008; 4:726-32. [PMID: 18563246 PMCID: PMC2535915 DOI: 10.1039/b706237k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The efficacy of microarrays in examining gene expression, gene and genome structure, protein-DNA interactions, whole-genome similarities and differences, microRNA expression, methylation (and more) is no longer in question. It is a fast-developing, cutting edge technology that has grown up along with massive sequence databases and is likely to become part of everyday patient care. Many advances have recently expanded the power and utility of microarrays; among them is our development of a new array tiling technique that dramatically increases the scope of coverage of an oligonucleotide tiling array without substantially increasing its cost.
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Affiliation(s)
- Sarah J Wheelan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Yauk CL, Berndt ML. Review of the literature examining the correlation among DNA microarray technologies. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2007; 48:380-94. [PMID: 17370338 PMCID: PMC2682332 DOI: 10.1002/em.20290] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
DNA microarray technologies are used in a variety of biological disciplines. The diversity of platforms and analytical methods employed has raised concerns over the reliability, reproducibility and correlation of data produced across the different approaches. Initial investigations (years 2000-2003) found discrepancies in the gene expression measures produced by different microarray technologies. Increasing knowledge and control of the factors that result in poor correlation among the technologies has led to much higher levels of correlation among more recent publications (years 2004 to present). Here, we review the studies examining the correlation among microarray technologies. We find that with improvements in the technology (optimization and standardization of methods, including data analysis) and annotation, analysis across platforms yields highly correlated and reproducible results. We suggest several key factors that should be controlled in comparing across technologies, and are good microarray practice in general.
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Affiliation(s)
- Carole L Yauk
- Environmental and Occupational Toxicology Division, Safe Environments Programme, Health Canada, Ottawa, Ontario, Canada K1A 0K9.
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