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Fragoso MF, Fernandez GJ, Vanderveer L, Cooper HS, Slifker M, Clapper ML. Dysregulation of miR-1-3p: An Early Event in Colitis-Associated Dysplasia. Int J Mol Sci 2022; 23:13024. [PMID: 36361810 PMCID: PMC9657954 DOI: 10.3390/ijms232113024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2023] Open
Abstract
Detection of colorectal dysplasia during surveillance colonoscopy remains the best method of determining risk for colitis-associated colorectal cancer (CAC). miRNAs (miRs) show great promise as tissue-specific biomarkers of neoplasia. The goal of this study was to explore the miR expression profile of precancerous dysplastic lesions in the AOM/DSS mouse model and identify early molecular changes associated with CAC. Epithelial cells were laser-microdissected from the colonic mucosa (inflamed versus dysplastic) of mice with AOM/DSS-induced colitis. A miR signature that can distinguish inflamed non-neoplastic mucosa from dysplasia was identified. Bioinformatic analyses led to the discovery of associated miR gene targets and enriched pathways and supported the construction of a network interaction map. miR-1a-3p was one of the miRs with the highest number of predicted targets, including Cdk6. Interestingly, miR-1a-3p and Cdk6 were down- and up-regulated in dysplastic lesions, respectively. Transfection of HCT116 and RKO cells with miR-1a-3p mimics induced apoptosis and cell cycle arrest in G1, suggesting its biological function. A slight reduction in the level of CDK6 transcripts was also observed in cells transfected with miR-1. These data provide novel insight into the early molecular alterations that accompany the development of CAC and identify a miR signature that represents a promising biomarker for the early detection of colitis-associated dysplasia.
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Affiliation(s)
- Mariana F. Fragoso
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Geysson J. Fernandez
- Group Biología y Control de Enfermedades Infecciosas, Universidad de Antioquia–UdeA, Medellín 050010, Colombia
| | - Lisa Vanderveer
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Harry S. Cooper
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Michael Slifker
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Margie L. Clapper
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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Combinatorial targeting of microRNA-26b and microRNA-101 exerts a synergistic inhibition on cyclooxygenase-2 in brain metastatic triple-negative breast cancer cells. Breast Cancer Res Treat 2021; 187:695-713. [PMID: 34041621 DOI: 10.1007/s10549-021-06255-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/04/2021] [Indexed: 12/16/2022]
Abstract
PURPOSE Extravasation of triple-negative (TN) metastatic breast cancer (BC) cells through the brain endothelium (BE) is a critical step in brain metastasis (BM). During extravasation, metastatic cells induce alteration in the inter-endothelial junctions and transmigrate through the endothelial barrier. Transmigration of metastatic cells is mediated by the upregulation of cyclooxygenase-2 (COX-2) that induces matrix metalloproteinase-1 (MMP-1) capable of degrading inter-endothelial junctional proteins. Despite their important role in BM, the molecular mechanisms upregulating COX-2 and MMP-1 in TNBC cells remain poorly understood. In this study, we unraveled a synergistic effect of a pair of micro-RNAs (miR-26b-5p and miR-101-3p) on COX-2 expression and the brain transmigration ability of BC cells. METHODS Using a gain-and-loss of function approach, we modulated levels of miR-26b-5p and miR-101-3p in two TNBC cell lines (the parental MDA-MB-231 and its brain metastatic variant MDA-MB-231-BrM2), and examined the resultant effect on COX-2/MMP-1 expression and the transmigration of cancer cells through the BE. RESULTS We observed that the dual inhibition of miR-26b-5p and miR-101-3p in BC cells results in higher increase of COX-2/MMP-1 expression and a higher trans-endothelial migration compared to either micro-RNA alone. The dual restoration of both micro-RNAs exerted a synergistic inhibition on COX-2/MMP-1 by targeting COX-2 and potentiated the suppression of trans-endothelial migration compared to single micro-RNA. CONCLUSION These findings provide new insights on a synergism between miR-26-5p and miR-101-3p in regulating COX-2 in metastatic TNBC cells and shed light on miR-26-5p and miR-101-3p as prognostic and therapeutic targets that can be exploited to predict or prevent BM.
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Zhang J, Pham VVH, Liu L, Xu T, Truong B, Li J, Rao N, Le TD. Identifying miRNA synergism using multiple-intervention causal inference. BMC Bioinformatics 2019; 20:613. [PMID: 31881825 PMCID: PMC6933624 DOI: 10.1186/s12859-019-3215-5] [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: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Studying multiple microRNAs (miRNAs) synergism in gene regulation could help to understand the regulatory mechanisms of complicated human diseases caused by miRNAs. Several existing methods have been presented to infer miRNA synergism. Most of the current methods assume that miRNAs with shared targets at the sequence level are working synergistically. However, it is unclear if miRNAs with shared targets are working in concert to regulate the targets or they individually regulate the targets at different time points or different biological processes. A standard method to test the synergistic activities is to knock-down multiple miRNAs at the same time and measure the changes in the target genes. However, this approach may not be practical as we would have too many sets of miRNAs to test. RESULTS n this paper, we present a novel framework called miRsyn for inferring miRNA synergism by using a causal inference method that mimics the multiple-intervention experiments, e.g. knocking-down multiple miRNAs, with observational data. Our results show that several miRNA-miRNA pairs that have shared targets at the sequence level are not working synergistically at the expression level. Moreover, the identified miRNA synergistic network is small-world and biologically meaningful, and a number of miRNA synergistic modules are significantly enriched in breast cancer. Our further analyses also reveal that most of synergistic miRNA-miRNA pairs show the same expression patterns. The comparison results indicate that the proposed multiple-intervention causal inference method performs better than the single-intervention causal inference method in identifying miRNA synergistic network. CONCLUSIONS Taken together, the results imply that miRsyn is a promising framework for identifying miRNA synergism, and it could enhance the understanding of miRNA synergism in breast cancer.
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Affiliation(s)
- Junpeng Zhang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China.,School of Engineering, Dali University, Dali, 671003, Yunnan, China
| | - Vu Viet Hoang Pham
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Lin Liu
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Taosheng Xu
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Buu Truong
- Pham Ngoc Thach University of Medicine, Ho Chi Minh, Vietnam
| | - Jiuyong Li
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Nini Rao
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China.
| | - Thuc Duy Le
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia.
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Wang J, Nie Z, Zhao H, Gao K, Cao Y. MiRNA-125a-5p attenuates blood-spinal cord barrier permeability under hypoxia in vitro. Biotechnol Lett 2019; 42:25-34. [PMID: 31696327 DOI: 10.1007/s10529-019-02753-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/27/2019] [Indexed: 02/06/2023]
Abstract
Disruption of the blood-spinal cord barrier (BSCB) results in secondary injury and apoptosis of neurons, leading to permanent neurological dysfunction after spinal cord injury. In this study, we evaluate the role of miRNA-125a-5p in the BSCB under hypoxia. The miRNA-125a-5p mimics group showed lower horseradish peroxidase (HRP) permeability and endothelial cell death rates compared with the transfection control group. By contrast, the miRNA-125a-5p inhibitor group demonstrated higher HRP permeability and endothelial cell death rates than the transfection control group. The expressions of ZO-1, occludin, VE-cadherin and their mRNA significantly increased in miRNA-125a-5p-overexpressing cells. By contrast, a remarkable reduction in ZO-1, occludin, and VE-cadherin expression and their mRNA were observed in miRNA-125a-5p-inhibited cells. MiRNA-125a-5p appears to reduce the permeability of the BSCB by up regulating the expression of ZO-1, occludin, and VE-cadherin and their mRNA, and against hypoxia-induced apoptosis of spinal cord microvascular endothelial cells. Taken together, our results clearly indicate that miRNA-125a-5p plays an important role in protecting the functions of the BSCB under hypoxia.
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Affiliation(s)
- Jian Wang
- Department of Orthopedics, Jining No. 1 People's Hospital, Jining, 272000, China
| | - Zhikui Nie
- Department of Orthopedics, Jining No. 1 People's Hospital, Jining, 272000, China
| | - Huanhua Zhao
- Department of Emergency, Jining No. 1 People's Hospital, Jining, 272000, China
| | - Kai Gao
- Department of Orthopedics, Jining No. 1 People's Hospital, Jining, 272000, China
| | - Yang Cao
- Department of Orthopedics, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121000, China.
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Wu J, Huang J, Kuang S, Chen J, Li X, Chen B, Wang J, Cheng D, Shuai X. Synergistic MicroRNA Therapy in Liver Fibrotic Rat Using MRI-Visible Nanocarrier Targeting Hepatic Stellate Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1801809. [PMID: 30886803 PMCID: PMC6402399 DOI: 10.1002/advs.201801809] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/10/2018] [Indexed: 05/02/2023]
Abstract
Liver fibrosis, as one of the leading causes of liver-related morbidity and mortality, has no Food and Drug Administration (FDA)-approved antifibrotic therapy yet. Although microRNA-29b (miRNA-29b) and microRNA-122 (miRNA-122) have great potential in treating liver fibrosis via regulating profibrotic genes in hepatic stellate cells (HSCs), it is still a challenge to achieve a HSC-targeted and meanwhile noninvasively trackable delivery of miRNAs in vivo. Herein, a pH-sensitive and vitamin A (VA)-conjugated copolymer VA-polyethylene glycol-polyethyleneimine-poly(N-(N',N'-diisopropylaminoethyl)-co-benzylamino) aspartamide (T-PBP) is synthesized and assembled into superparamagnetic iron oxide (SPIO)-decorated cationic micelle for miRNA delivery. The T-PBP micelle efficiently transports the miRNA-29b and miRNA-122 to HSC in a magnetic resonance imaging-visible manner, resulting in a synergistic antifibrosis effect via downregulating the expression of fibrosis-related genes, including collagen type I alpha 1, α-smooth muscle actin, and tissue inhibitor of metalloproteinase 1. Consequently, the HSC-targeted combination therapy with miRNA-29b and miRNA-122 demonstrates a prominent antifibrotic efficacy in terms of improving liver function and relieving hepatic fibrosis.
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Affiliation(s)
- Jun Wu
- The Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630China
| | - Jinsheng Huang
- PCFM Lab of Ministry of EducationSchool of Materials Science and EngineeringSun Yat‐sen UniversityGuangzhou510275China
| | - Sichi Kuang
- The Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630China
| | - Jingbiao Chen
- The Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630China
| | - Xiaoxia Li
- PCFM Lab of Ministry of EducationSchool of Materials Science and EngineeringSun Yat‐sen UniversityGuangzhou510275China
| | - Bin Chen
- Department of Orthopaedics and TraumatologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Jin Wang
- The Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630China
| | - Du Cheng
- PCFM Lab of Ministry of EducationSchool of Materials Science and EngineeringSun Yat‐sen UniversityGuangzhou510275China
| | - Xintao Shuai
- The Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630China
- PCFM Lab of Ministry of EducationSchool of Materials Science and EngineeringSun Yat‐sen UniversityGuangzhou510275China
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6
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Xu J, Shao T, Ding N, Li Y, Li X. miRNA-miRNA crosstalk: from genomics to phenomics. Brief Bioinform 2018; 18:1002-1011. [PMID: 27551063 DOI: 10.1093/bib/bbw073] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Indexed: 12/11/2022] Open
Abstract
The discovery of microRNA (miRNA)-miRNA crosstalk has greatly improved our understanding of complex gene regulatory networks in normal and disease-specific physiological conditions. Numerous approaches have been proposed for modeling miRNA-miRNA networks based on genomic sequences, miRNA-mRNA regulation, functional information and phenomics alone, or by integrating heterogeneous data. In addition, it is expected that miRNA-miRNA crosstalk can be reprogrammed in different tissues or specific diseases. Thus, transcriptome data have also been integrated to construct context-specific miRNA-miRNA networks. In this review, we summarize the state-of-the-art miRNA-miRNA network modeling methods, which range from genomics to phenomics, where we focus on the need to integrate heterogeneous types of omics data. Finally, we suggest future directions for studies of crosstalk of noncoding RNAs. This comprehensive summarization and discussion elucidated in this work provide constructive insights into miRNA-miRNA crosstalk.
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Shao T, Wang G, Chen H, Xie Y, Jin X, Bai J, Xu J, Li X, Huang J, Jin Y, Li Y. Survey of miRNA-miRNA cooperative regulation principles across cancer types. Brief Bioinform 2018; 20:1621-1638. [DOI: 10.1093/bib/bby038] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/05/2018] [Indexed: 02/06/2023] Open
Abstract
AbstractCooperative regulation among multiple microRNAs (miRNAs) is a complex type of posttranscriptional regulation in human; however, the global view of the system-level regulatory principles across cancers is still unclear. Here, we investigated miRNA-miRNA cooperative regulatory landscape across 18 cancer types and summarized the regulatory principles of miRNAs. The miRNA-miRNA cooperative pan-cancer network exhibited a scale-free and modular architecture. Cancer types with similar tissue origins had high similarity in cooperative network structure and expression of cooperative miRNA pairs. In addition, cooperative miRNAs showed divergent properties, including higher expression, greater expression variation and a stronger regulatory strength towards targets and were likely to regulate cancer hallmark-related functions. We found a marked rewiring of miRNA-miRNA cooperation between various cancers and revealed conserved and rewired network miRNA hubs. We further identified the common hubs, cancer-specific hubs and other hubs, which tend to target known anticancer drug targets. Finally, miRNA cooperative modules were found to be associated with patient survival in several cancer types. Our study highlights the potential of pan-cancer miRNA-miRNA cooperative regulation as a novel paradigm that may aid in the discovery of tumorigenesis mechanisms and development of anticancer drugs.
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Affiliation(s)
- Tingting Shao
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Guangjuan Wang
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Hong Chen
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Yunjin Xie
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Xiyun Jin
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Jing Bai
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Juan Xu
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Yan Jin
- Department of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Yongsheng Li
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
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8
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Wang D, Sun-Waterhouse D, Li F, Xin L, Li D. MicroRNAs as molecular targets of quercetin and its derivatives underlying their biological effects: A preclinical strategy. Crit Rev Food Sci Nutr 2018; 59:2189-2201. [DOI: 10.1080/10408398.2018.1441123] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Dan Wang
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Taian, P.R. China
- Shandong Institute of Pomology, Taian, P.R. China
| | - Dongxiao Sun-Waterhouse
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Taian, P.R. China
- School of Chemical Sciences, the University of Auckland, New Zealand
| | - Feng Li
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Taian, P.R. China
| | - Li Xin
- Shandong Institute of Pomology, Taian, P.R. China
| | - Dapeng Li
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Taian, P.R. China
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9
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Chen X, Zhao W, Yuan Y, Bai Y, Sun Y, Zhu W, Du Z. MicroRNAs tend to synergistically control expression of genes encoding extensively-expressed proteins in humans. PeerJ 2017; 5:e3682. [PMID: 28828274 PMCID: PMC5560240 DOI: 10.7717/peerj.3682] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 07/22/2017] [Indexed: 01/02/2023] Open
Abstract
Considering complicated microRNA (miRNA) biogenesis and action mechanisms, it was thought so high energy-consuming for a cell to afford simultaneous over-expression of many miRNAs. Thus it prompts that an alternative miRNA regulation pattern on protein-encoding genes must exist, which has characteristics of energy-saving and precise protein output. In this study, expression tendency of proteins encoded by miRNAs’ target genes was evaluated in human organ scale, followed by quantitative assessment of miRNA synergism. Expression tendency analysis suggests that universally expressed proteins (UEPs) tend to physically interact in clusters and participate in fundamental biological activities whereas disorderly expressed proteins (DEPs) are inclined to relatively independently execute organ-specific functions. Consistent with this, miRNAs that mainly target UEP-encoding mRNAs, such as miR-21, tend to collaboratively or even synergistically act with other miRNAs in fine-tuning protein output. Synergistic gene regulation may maximize miRNAs’ efficiency with less dependence on miRNAs’ abundance and overcome the deficiency that targeting plenty of genes by single miRNA makes miRNA-mediated regulation high-throughput but insufficient due to target gene dilution effect. Furthermore, our in vitro experiment verified that merely 25 nM transfection of miR-21 be sufficient to influence the overall state of various human cells. Thus miR-21 was identified as a hub in synergistic miRNA–miRNA interaction network. Our findings suggest that synergistic miRNA–miRNA interaction is an important endogenous miRNA regulation mode, which ensures adequate potency of miRNAs at low abundance, especially those implicated in fundamental biological regulation.
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Affiliation(s)
- Xue Chen
- Department of Pharmacy, The Second Affiliated Hospital of Harbin Medical University (Institute of Clinical Pharmacy, The Heilongjiang Key Laboratory of Drug Research, Harbin Medical University), Harbin, China
| | - Wei Zhao
- Department of Pharmacy, The Second Affiliated Hospital of Harbin Medical University (Institute of Clinical Pharmacy, The Heilongjiang Key Laboratory of Drug Research, Harbin Medical University), Harbin, China
| | - Ye Yuan
- Department of Pharmacy, The Second Affiliated Hospital of Harbin Medical University (Institute of Clinical Pharmacy, The Heilongjiang Key Laboratory of Drug Research, Harbin Medical University), Harbin, China
| | - Yan Bai
- Department of Pharmacy, The Second Affiliated Hospital of Harbin Medical University (Institute of Clinical Pharmacy, The Heilongjiang Key Laboratory of Drug Research, Harbin Medical University), Harbin, China
| | - Yong Sun
- Department of Pharmacy, The Second Affiliated Hospital of Harbin Medical University (Institute of Clinical Pharmacy, The Heilongjiang Key Laboratory of Drug Research, Harbin Medical University), Harbin, China
| | - Wenliang Zhu
- Department of Pharmacy, The Second Affiliated Hospital of Harbin Medical University (Institute of Clinical Pharmacy, The Heilongjiang Key Laboratory of Drug Research, Harbin Medical University), Harbin, China
| | - Zhimin Du
- Department of Pharmacy, The Second Affiliated Hospital of Harbin Medical University (Institute of Clinical Pharmacy, The Heilongjiang Key Laboratory of Drug Research, Harbin Medical University), Harbin, China
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Ma X, Li L, Jia T, Chen M, Liu G, Li C, Li N, Yang D. miR-203a controls keratinocyte proliferation and differentiation via targeting the stemness-associated factor ΔNp63 and establishing a regulatory circuit with SNAI2. Biochem Biophys Res Commun 2017; 491:241-249. [PMID: 28754589 DOI: 10.1016/j.bbrc.2017.07.131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 07/24/2017] [Indexed: 01/31/2023]
Abstract
Keratinocyte differentiation plays a pivotal role in the function of epidermal barrier and can be triggered by extracellular calcium in vitro and in vivo, but the precise mechanism still need to be further investigated. On the other hand, it is known that microRNAs control multiple biological events including cellular proliferation and differentiation. The present study demonstrated that miR-203a expression was upregulated in calcium-induced HaCaT Cells in a dose-dependent manner, whereas the stemness-associated factors SNAI2 and ΔNp63 were downregulated. Furthermore, SNAI2 and ΔNp63 were identified as the targets of miR-203a by computational prediction and luciferase reporter assays. The protein levels of SNAI2 and ΔNp63 were suppressed by ectopic expression of miR-203a. Functionally, silencing of miR-203a or overexpression of SNAI2 and ΔNp63 attenuated cell cycle arrest induced by calcium without any changes in cellular apoptosis. Additionally, ectopic expression of SNAI2 inhibited miR-203a in calcium-induced HaCaT cells, by binding to the promoter region of miR-203a. In conclusion, our findings demonstrate that miR-203a plays an essential role in keratinocyte proliferation and differentiation caused by extracellular calcium by targeting the SNAI2 and ΔNp63 genes. Furthermore, SNAI2 was found to suppress the transcription of miR-203a. Our data highlights a coherent cross-talk between two transcription factors (SNAI2 and ΔNp63) and miR-203a in keratinocyte differentiation and epidermal development.
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Affiliation(s)
- Xu Ma
- Department of Plastic Surgery, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang Block, Harbin 150086, Heilongjiang, China
| | - Ling Li
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang Block, Harbin 150086, Heilongjiang, China
| | - Tao Jia
- Department of Hand and Microsurgery, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang Block, Harbin 150086, Heilongjiang, China
| | - Mingwei Chen
- Department of Anatomy, Harbin Medical University, 157 Baojian Road, Nangang Block, Harbin 150086, Heilongjiang, China
| | - Guofeng Liu
- Department of Plastic Surgery, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang Block, Harbin 150086, Heilongjiang, China
| | - Chunyang Li
- Department of Plastic Surgery, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang Block, Harbin 150086, Heilongjiang, China
| | - Ning Li
- Department of Plastic Surgery, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang Block, Harbin 150086, Heilongjiang, China
| | - Daping Yang
- Department of Plastic Surgery, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang Block, Harbin 150086, Heilongjiang, China.
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11
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D'Adamo S, Cetrullo S, Minguzzi M, Silvestri Y, Borzì RM, Flamigni F. MicroRNAs and Autophagy: Fine Players in the Control of Chondrocyte Homeostatic Activities in Osteoarthritis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:3720128. [PMID: 28713485 PMCID: PMC5497632 DOI: 10.1155/2017/3720128] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/12/2017] [Accepted: 05/22/2017] [Indexed: 12/17/2022]
Abstract
Osteoarthritis (OA) is a debilitating degenerative disease of the articular cartilage with a multifactorial etiology. Aging, the main risk factor for OA development, is associated with a systemic oxidative and inflammatory phenotype. Autophagy is a central housekeeping system that plays an antiaging role by supporting the clearance of senescence-associated alterations of macromolecules and organelles. Autophagy deficiency has been related to OA pathogenesis because of the accumulation of cellular defects in chondrocytes. Microribonucleic acids (microRNAs or miRs) are a well-established class of posttranscriptional modulators belonging to the family of noncoding RNAs that have been identified as key players in the regulation of cellular processes, such as autophagy, by targeting their own cognate mRNAs. Here, we present a state-of-the-art literature review on the role of miRs and autophagy in the scenario of OA pathogenesis. In addition, a comprehensive survey has been performed on the functional connections of the miR network and the autophagy pathway in OA by using "microRNA," "autophagy," and "osteoarthritis" as key words. Discussion of available evidence sheds light on some aspects that need further investigation in order to reach a more comprehensive view of the potential of this topic in OA.
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Affiliation(s)
- Stefania D'Adamo
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - Silvia Cetrullo
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - Manuela Minguzzi
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
- Laboratorio di Immunoreumatologia e Rigenerazione Tissutale, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Ylenia Silvestri
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - Rosa Maria Borzì
- Laboratorio di Immunoreumatologia e Rigenerazione Tissutale, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Flavio Flamigni
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
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12
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Zhao Y, Cui X, Zhu W, Chen X, Shen C, Liu Z, Yang G, Liu Y, Zhao S. Synergistic regulatory effects of microRNAs on brain glioma cells. Mol Med Rep 2017; 16:1409-1416. [PMID: 29067452 DOI: 10.3892/mmr.2017.6709] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 03/20/2017] [Indexed: 11/06/2022] Open
Abstract
Glioma is among the most common types of cancer of the central nervous system and is difficult to cure. Due to the lack of glioma-specific treatments, patients with glioma exhibit high mortality rates. MicroRNAs (miRNAs) participate in the pathogenesis of glioma, and upregulation of specific miRNAs promotes cell proliferation, whereas apoptosis‑inducing miRNAs are markedly downregulated in the context of glioma. Therefore, miRNAs may be important contributors to the pathogenesis of glioma. In the present study, nine miRNAs were investigated as miRNA‑miRNA pairs, and the measured cell viabilities were consistent with the results of synergy predictions. Extensive synergy occurred among upregulated miRNAs in U87 cells, whereas downregulated miRNAs rarely exhibited synergism. Treatment with an miRNA‑miRNA pair exhibiting strong synergy increased the inhibitory effects of these miRNAs on tumor cells, and the combined inhibitory effects were increased compared with the sum of the individual inhibitory effects of each miRNA. Using cell viability assays, TUNEL staining, and flow cytometry, the present study demonstrates that cotransfection with miR‑20a and miR‑21inhibitors resulted in the highest synergistic effect on the promotion of apoptosis in U87 cells. The results of the present study provide important insights into the potential use of miRNAs in the treatment of glioma.
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Affiliation(s)
- Yilei Zhao
- Department of Pharmacy, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Xiaomeng Cui
- Institute of Measurement-Control Technology and Communications Engineering, Harbin University of Science and Technology, Harbin, Heilongjiang 150010, P.R. China
| | - Wenliang Zhu
- Institute of Clinical Pharmacology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Xin Chen
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Chen Shen
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Zhendong Liu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Guang Yang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Yaohua Liu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Shiguang Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
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13
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Zhang J, Duy Le T, Liu L, He J, Li J. Identifying miRNA synergistic regulatory networks in heterogeneous human data via network motifs. MOLECULAR BIOSYSTEMS 2016; 12:454-63. [PMID: 26660849 DOI: 10.1039/c5mb00562k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Understanding the synergism of multiple microRNAs (miRNAs) in gene regulation can provide important insights into the mechanisms of complex human diseases caused by miRNA regulation. Therefore, it is important to identify miRNA synergism and study miRNA characteristics in miRNA synergistic regulatory networks. A number of methods have been proposed to identify miRNA synergism. However, most of the methods only use downstream target genes of miRNAs to infer miRNA synergism when miRNAs can also be regulated by upstream transcription factors (TFs) at the transcriptional level. Additionally, most methods are based on statistical associations identified from data without considering the causal nature of gene regulation. In this paper, we present a causality based framework, called mirSRN (miRNA synergistic regulatory network), to infer miRNA synergism in human molecular systems by considering both downstream miRNA targets and upstream TF regulation. We apply the proposed framework to two real world datasets and discover that almost all the top 10 miRNAs with the largest node degree in the mirSRNs are associated with different human diseases, including cancer, and that the mirSRNs are approximately scale-free and small-world networks. We also find that most miRNAs in the networks are frequently synergistic with other miRNAs, and miRNAs related to the same disease are likely to be synergistic and in a cluster linked to a biological function. Synergistic miRNA pairs show higher co-expression level, and may have potential functional relationships indicating collaboration between the miRNAs. Functional validation of the identified synergistic miRNAs demonstrates that these miRNAs cause different kinds of diseases. These results deepen our understanding of the biological meaning of miRNA synergism.
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Affiliation(s)
- Junpeng Zhang
- School of Engineering, Dali University, Dali, Yunnan 671003, P. R. China.
| | - Thuc Duy Le
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA 5095, Australia.
| | - Lin Liu
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA 5095, Australia.
| | - Jianfeng He
- Institute of Biomedical Engineering, Kunming University of Science and Technology, Kunming, Yunnan 650500, P. R. China
| | - Jiuyong Li
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA 5095, Australia.
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14
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Raut SK, Singh GB, Rastogi B, Saikia UN, Mittal A, Dogra N, Singh S, Prasad R, Khullar M. miR-30c and miR-181a synergistically modulate p53–p21 pathway in diabetes induced cardiac hypertrophy. Mol Cell Biochem 2016; 417:191-203. [DOI: 10.1007/s11010-016-2729-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/20/2016] [Indexed: 12/27/2022]
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15
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Huang W, Tian SS, Hang PZ, Sun C, Guo J, Du ZM. Combination of microRNA-21 and microRNA-146a Attenuates Cardiac Dysfunction and Apoptosis During Acute Myocardial Infarction in Mice. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e296. [PMID: 26978580 PMCID: PMC5014454 DOI: 10.1038/mtna.2016.12] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 01/28/2016] [Indexed: 11/28/2022]
Abstract
Recent studies have revealed the cytoprotective roles of microRNAs (miRNAs) miR-21 and miR-146a against ischemic cardiac injuries. While these studies investigated each of these miRNAs as an independent individual factor, our previous study has suggested the possible interaction between these two miRNAs. The present study was designed to investigate this possibility by evaluating the effects of miR-21 and miR-146a combination on cardiac ischemic injuries and the underlying mechanisms. MiR-21 and miR-146a synergistically decreased apoptosis under ischemia/hypoxic conditions in cardiomyocytes compared with either miR-21 or miR-146a alone. Mice coinjected with agomiR-21 and agomiR-146a had decreased infarct size, increased ejection fraction (EF), and fractional shortening (FS). These effects were greater than those induced by either of the two agomiRs. Furthermore, greater decreases in p38 mitogen-associated protein kinase phosphorylation (p-p38 MAPK) were observed with miR-21: miR-146a combination as compared to application of either of the miRNAs. These data suggest that combination of miR-21 and miR-146a has a greater protective effect against cardiac ischemia/hypoxia-induced apoptosis as compared to these miRNAs applied individually. This synergistic action is mediated by enhanced potency of inhibition of cardiomyocyte apoptosis by the miR-21—PTEN/AKT—p-p38—caspase-3 and miR-146a—TRAF6—p-p38—caspase-3 signal pathways.
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Affiliation(s)
- Wei Huang
- Institute of Clinical Pharmacology of the Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Shan-Shan Tian
- Institute of Clinical Pharmacology of the Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Peng-Zhou Hang
- Institute of Clinical Pharmacology of the Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Chuan Sun
- Institute of Clinical Pharmacology of the Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jing Guo
- Institute of Clinical Pharmacology of the Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Zhi-Min Du
- Institute of Clinical Pharmacology of the Second Affiliated Hospital, Harbin Medical University, Harbin, China.,The University Key Laboratory of Drug Research, Heilongjiang Province, Harbin, China
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16
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Xuan L, Qu L, Zhou H, Wang P, Yu H, Wu T, Wang X, Li Q, Tian L, Liu M, Sun Y. Circular RNA: a novel biomarker for progressive laryngeal cancer. Am J Transl Res 2016; 13:4315-20. [PMID: 27158380 DOI: 10.3892/mmr.2016.5048] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 03/03/2016] [Indexed: 12/14/2022]
Abstract
Circular RNAs (circRNAs), a class of endogenous RNAs, are characterized by covalently closed continuous loop without 5' to 3' polarity and polyadenylated tail. Recent studies indicated that circRNAs might play an important role in cancer. However, the function of circRNA in laryngeal squamous cell cancer tissues (LSCC) is still unknown. In this study, we investigated the expression of circRNAs in 4 paired LSCC tissues and adjacent non-tumor tissues by microarray analysis. Results showed significant upregulation (n = 302) of or downregulation (n = 396) of 698 circRNAs in LSCC tissues. We further detected hsa_circRNA_100855 as the most upregulated circRNA and hsa_circRNA_104912 as the most downregulated circRNA using qRT-PCR methods. Results showed that hsa_circRNA_100855 level was significantly higher in LSCC than in the corresponding adjacent non-neoplastic tissues. Patients with T3-4 stage, neck nodal metastasis or advanced clinical stage had higher hsa_circRNA_100855 expression. The hsa_circRNA_104912 level was significantly lower in LSCC than in corresponding adjacent non-neoplastic tissues. Patients with T3-4 stage, neck nodal metastasis, poor differentiation or advanced clinical stage had a lower hsa_circRNA_104912 expression. Overall, our data suggest that circRNAs play an important role in the tumorigenesis of LSCC and may serve as novel and stable biomarkers for the diagnosis and progress of LSCC.
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Affiliation(s)
- Lijia Xuan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital, Harbin Medical University Harbin, China
| | - Lingmei Qu
- Department of Otorhinolaryngology, Head and Neck Surgery, The Fifth Affiliated Hospital, Harbin Medical University Daqing, China
| | - Han Zhou
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital, Harbin Medical University Harbin, China
| | - Peng Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital, Harbin Medical University Harbin, China
| | - Haoyang Yu
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital, Harbin Medical University Harbin, China
| | - Tianyi Wu
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital, Harbin Medical University Harbin, China
| | - Xin Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital, Harbin Medical University Harbin, China
| | - Qiuying Li
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital, Harbin Medical University Harbin, China
| | - Linli Tian
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital, Harbin Medical University Harbin, China
| | - Ming Liu
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital, Harbin Medical University Harbin, China
| | - Yanan Sun
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital, Harbin Medical University Harbin, China
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17
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Li X, Zhen Z, Tang G, Zheng C, Yang G. MiR-29a and MiR-140 Protect Chondrocytes against the Anti-Proliferation and Cell Matrix Signaling Changes by IL-1β. Mol Cells 2016; 39:103-10. [PMID: 26608362 PMCID: PMC4757797 DOI: 10.14348/molcells.2016.2179] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 10/10/2015] [Accepted: 10/12/2015] [Indexed: 12/21/2022] Open
Abstract
As a degenerative joint disease, osteoarthritis (OA) constitutes a major cause of disability that seriously affects the quality of life of a large population of people worldwide. However, effective treatment that can successfully reverse OA progression is lacking until now. The present study aimed to determine whether two small non-coding RNAs miR-29a and miR-140, which are significantly down-regulated in OA, can be applied together as potential therapeutic targets for OA treatment. MiRNA synergy score was used to screen the miRNA pairs that potentially synergistically regulate OA. An in vitro model of OA was established by treating murine chondrocytes with IL-1β. Transfection of miR-29a and miR-140 via plasmids was investigated on chondrocyte proliferation and expression of nine genes such as ADAMTS4, ADAMTS5, ACAN, COL2A1, COL10A1, MMP1, MMP3, MMP13 and TIMP metal-lopeptidase inhibitor 1 (TIMP1). Western blotting was used to determine the protein expression level of MMP13 and TIMP1, and ELISA was used to detect the content of type II collagen. Combined use of miR-29a and miR-140 successfully reversed the destructive effect of IL-1β on chondrocyte proliferation, and notably affected the MMP13 and TIMP1 gene expression that regulates extracellular matrix. Although co-transfection of miR-29a and miR-140 did not show a synergistic effect on MMP13 protein expression and type II collagen release, but both of them can significantly suppress the protein abundance of MMP13 and restore the type II collagen release in IL-1β treated chondrocytes. Compared with single miRNA transfection, cotransfection of both miRNAs exceedingly abrogated the suppressed the protein production of TIMP1 caused by IL-1β, thereby suggesting potent synergistic action. These results provided novel insights into the important function of miRNAs' collaboration in OA pathological development. The reduced MMP13, and enhanced TIMP1 protein production and type II collagen release also implies that miR-29a and miR-140 combination treatment may be a possible treatment for OA.
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Affiliation(s)
- Xianghui Li
- Department of Pharmacy, the Second Affiliated Hospital of Harbin Medical University, Harbin,
China
| | - Zhilei Zhen
- Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin,
China
| | - Guodong Tang
- Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin,
China
| | - Chong Zheng
- Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin,
China
| | - Guofu Yang
- Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin,
China
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18
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Yuan D, Cui X, Wang Y, Zhao Y, Li H, Hu S, Chu X, Li Y, Li Q, Liu Q, Zhu W. Enrichment Analysis Identifies Functional MicroRNA-Disease Associations in Humans. PLoS One 2015; 10:e0136285. [PMID: 26296081 PMCID: PMC4546424 DOI: 10.1371/journal.pone.0136285] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 08/02/2015] [Indexed: 11/18/2022] Open
Abstract
Substantial evidence has shown that microRNAs (miRNAs) may be causally linked to the occurrence and progression of human diseases. Herein, we conducted an enrichment analysis to identify potential functional miRNA-disease associations (MDAs) in humans by integrating currently known biological data: miRNA-target interactions (MTIs), protein-protein interactions, and gene-disease associations. Two contributing factors to functional miRNA-disease associations were quantitatively considered: the direct effects of miRNA that target disease-related genes, and indirect effects triggered by protein-protein interactions. Ninety-nine miRNAs were scanned for possible functional association with 2223 MeSH-defined human diseases. Each miRNA was experimentally validated to target ≥ 10 mRNA genes. Putative MDAs were identified when at least one MTI was confidently validated for a disease. Overall, 19648 putative MDAs were found, of which 10.0% was experimentally validated. Further results suggest that filtering for miRNAs that target a greater number of disease-related genes (n ≥ 8) can significantly enrich for true MDAs from the set of putative associations (enrichment rate = 60.7%, adjusted hypergeometric p = 2.41×10-91). Considering the indirect effects of miRNAs further elevated the enrichment rate to 72.6%. By using this method, a novel MDA between miR-24 and ovarian cancer was found. Compared with scramble miRNA overexpression of miR-24 was validated to remarkably induce ovarian cancer cells apoptosis. Our study provides novel insight into factors contributing to functional MDAs by integrating large quantities of previously generated biological data, and establishes a feasible method to identify plausible associations with high confidence.
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Affiliation(s)
- Dandan Yuan
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaomeng Cui
- School of Measurement and Control Technology & Communications Engineering, Harbin University of Science and Technology, Harbin, China
| | - Yang Wang
- Department of Pharmacy, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yilei Zhao
- Department of Pharmacy, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Huiying Li
- Department of Obstetrics and Gynecology, Hongqi Hospital of Mudanjiang Medical University, Mudanjiang, China
| | - Suangjiu Hu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaodan Chu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yan Li
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qiang Li
- Department of General Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qian Liu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
- * E-mail: (QL); (WZ)
| | - Wenliang Zhu
- Institute of Clinical Pharmacology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
- * E-mail: (QL); (WZ)
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19
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Poole E, Kuan WL, Barker R, Sinclair J. The human cytomegalovirus non-coding Beta2.7 RNA as a novel therapeutic for Parkinson's disease--Translational research with no translation. Virus Res 2015; 212:64-9. [PMID: 26003955 DOI: 10.1016/j.virusres.2015.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 05/01/2015] [Accepted: 05/08/2015] [Indexed: 10/23/2022]
Abstract
Human cytomegalovirus (HCMV) encodes abundant numbers of microRNAs (miRNAs) and other non-coding RNAs (ncRNAs) whose functions are presently under intense investigation. In this chapter, we discuss the function of one of the more well characterised virus-encoded ncRNAs, derived from the viral major early gene (Beta2.7). This RNA plays an anti-apoptotic role during infection by directly interacting with mitochondrial complex I to help maintain high levels of ATP production and by preventing the stress induced re-localisation of retinoid/interferon-induced mortality-19 protein, GRIM-19. We then go on to describe how an 800 nucleotide sub-domain of the Beta2.7 transcript, p137, has been exploited in the development of a novel therapeutic for the treatment of Parkinson's disease.
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Affiliation(s)
- Emma Poole
- Department of Medicine, Addenbrooke's Hospital, Hills Road, England CB2 0QQ UK.
| | - Wei Li Kuan
- Department of Neurology, Addenbrooke's Hospital, Hills Road, England CB2 0QQ, UK
| | - Roger Barker
- Department of Neurology, Addenbrooke's Hospital, Hills Road, England CB2 0QQ, UK
| | - John Sinclair
- Department of Medicine, Addenbrooke's Hospital, Hills Road, England CB2 0QQ UK.
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20
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Dimitrakopoulou K, Vrahatis AG, Bezerianos A. Integromics network meta-analysis on cardiac aging offers robust multi-layer modular signatures and reveals micronome synergism. BMC Genomics 2015; 16:147. [PMID: 25887273 PMCID: PMC4367845 DOI: 10.1186/s12864-015-1256-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/19/2015] [Indexed: 02/02/2023] Open
Abstract
Background The avalanche of integromics and panomics approaches shifted the deciphering of aging mechanisms from single molecular entities to communities of them. In this orientation, we explore the cardiac aging mechanisms – risk factor for multiple cardiovascular diseases - by capturing the micronome synergism and detecting longevity signatures in the form of communities (modules). For this, we developed a meta-analysis scheme that integrates transcriptome expression data from multiple cardiac-specific independent studies in mouse and human along with proteome and micronome interaction data in the form of multiple independent weighted networks. Modularization of each weighted network produced modules, which in turn were further analyzed so as to define consensus modules across datasets that change substantially during lifespan. Also, we established a metric that determines - from the modular perspective - the synergism of microRNA-microRNA interactions as defined by significantly functionally associated targets. Results The meta-analysis provided 40 consensus integromics modules across mouse datasets and revealed microRNA relations with substantial collective action during aging. Three modules were reproducible, based on homology, when mapped against human-derived modules. The respective homologs mainly represent NADH dehydrogenases, ATP synthases, cytochrome oxidases, Ras GTPases and ribosomal proteins. Among various observations, we corroborate to the involvement of miR-34a (included in consensus modules) as proposed recently; yet we report that has no synergistic effect. Moving forward, we determined its age-related neighborhood in which HCN3, a known heart pacemaker channel, was included. Also, miR-125a-5p/-351, miR-200c/-429, miR-106b/-17, miR-363/-92b, miR-181b/-181d, miR-19a/-19b, let-7d/-7f, miR-18a/-18b, miR-128/-27b and miR-106a/-291a-3p pairs exhibited significant synergy and their association to aging and/or cardiovascular diseases is supported in many cases by a disease database and previous studies. On the contrary, we suggest that miR-22 has not substantial impact on heart longevity as proposed recently. Conclusions We revised several proteins and microRNAs recently implicated in cardiac aging and proposed for the first time modules as signatures. The integromics meta-analysis approach can serve as an efficient subvening signature tool for more-oriented better-designed experiments. It can also promote the combinational multi-target microRNA therapy of age-related cardiovascular diseases along the continuum from prevention to detection, diagnosis, treatment and outcome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1256-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Aristidis G Vrahatis
- Department of Medical Physics, School of Medicine, University of Patras, Patras, 26500, Greece. .,Department of Computer Engineering and Informatics, University of Patras, Patras, 26500, Greece.
| | - Anastasios Bezerianos
- Department of Medical Physics, School of Medicine, University of Patras, Patras, 26500, Greece. .,Singapore Institute for Neurotechnology (SINAPSE), Center of Life Sciences, National University of Singapore, Singapore, 117456, Singapore.
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21
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Bhajun R, Guyon L, Pitaval A, Sulpice E, Combe S, Obeid P, Haguet V, Ghorbel I, Lajaunie C, Gidrol X. A statistically inferred microRNA network identifies breast cancer target miR-940 as an actin cytoskeleton regulator. Sci Rep 2015; 5:8336. [PMID: 25673565 PMCID: PMC5389139 DOI: 10.1038/srep08336] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/14/2015] [Indexed: 01/21/2023] Open
Abstract
MiRNAs are key regulators of gene expression. By binding to many genes, they create a complex network of gene co-regulation. Here, using a network-based approach, we identified miRNA hub groups by their close connections and common targets. In one cluster containing three miRNAs, miR-612, miR-661 and miR-940, the annotated functions of the co-regulated genes suggested a role in small GTPase signalling. Although the three members of this cluster targeted the same subset of predicted genes, we showed that their overexpression impacted cell fates differently. miR-661 demonstrated enhanced phosphorylation of myosin II and an increase in cell invasion, indicating a possible oncogenic miRNA. On the contrary, miR-612 and miR-940 inhibit phosphorylation of myosin II and cell invasion. Finally, expression profiling in human breast tissues showed that miR-940 was consistently downregulated in breast cancer tissues
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Affiliation(s)
- Ricky Bhajun
- 1] Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France [2] CEA, iRTSV-BGE, F-38000 Grenoble, France [3] INSERM, BGE, F-38000 Grenoble, France
| | - Laurent Guyon
- 1] Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France [2] CEA, iRTSV-BGE, F-38000 Grenoble, France [3] INSERM, BGE, F-38000 Grenoble, France
| | - Amandine Pitaval
- 1] Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France [2] CEA, iRTSV-BGE, F-38000 Grenoble, France [3] INSERM, BGE, F-38000 Grenoble, France
| | - Eric Sulpice
- 1] Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France [2] CEA, iRTSV-BGE, F-38000 Grenoble, France [3] INSERM, BGE, F-38000 Grenoble, France
| | - Stéphanie Combe
- 1] Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France [2] CEA, iRTSV-BGE, F-38000 Grenoble, France [3] INSERM, BGE, F-38000 Grenoble, France
| | - Patricia Obeid
- 1] Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France [2] CEA, iRTSV-BGE, F-38000 Grenoble, France [3] INSERM, BGE, F-38000 Grenoble, France
| | - Vincent Haguet
- 1] Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France [2] CEA, iRTSV-BGE, F-38000 Grenoble, France [3] INSERM, BGE, F-38000 Grenoble, France
| | - Itebeddine Ghorbel
- 1] Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France [2] CEA, iRTSV-BGE, F-38000 Grenoble, France [3] INSERM, BGE, F-38000 Grenoble, France
| | - Christian Lajaunie
- 1] Center for Computational Biology - CBIO, Mines ParisTech, F-77300 Fontainebleau, France [2] Institut Curie, F-75248 Paris, France [3] INSERM, U900, F-75248 Paris, France
| | - Xavier Gidrol
- 1] Univ. Grenoble Alpes, iRTSV-BGE, F-38000 Grenoble, France [2] CEA, iRTSV-BGE, F-38000 Grenoble, France [3] INSERM, BGE, F-38000 Grenoble, France
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22
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Small molecules, big effects: the role of microRNAs in regulation of cardiomyocyte death. Cell Death Dis 2014; 5:e1325. [PMID: 25032848 PMCID: PMC4123081 DOI: 10.1038/cddis.2014.287] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/28/2014] [Accepted: 06/03/2014] [Indexed: 01/14/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in posttranscriptional regulation of gene expression, and exerting regulatory roles in plethora of biological processes. In recent years, miRNAs have received increased attention for their crucial role in health and disease, including in cardiovascular disease. This review summarizes the role of miRNAs in regulation of cardiac cell death/cell survival pathways, including apoptosis, autophagy and necrosis. It is envisaged that these miRNAs may explain the mechanisms behind the pathogenesis of many cardiac diseases, and, most importantly, may provide new avenues for therapeutic intervention that will limit cardiomyocyte cell death before it irreversibly affects cardiac function. Through an in-depth literature analysis coupled with integrative bioinformatics (pathway and synergy analysis), we dissect here the landscape of complex relationships between the apoptosis-regulating miRNAs in the context of cardiomyocyte cell death (including regulation of autophagy–apoptosis cross talk), and examine the gaps in our current understanding that will guide future investigations.
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