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Zhao C, Biondic S, Vandal K, Björklund ÅK, Hagemann-Jensen M, Sommer TM, Canizo J, Clark S, Raymond P, Zenklusen DR, Rivron N, Reik W, Petropoulos S. Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids. Genome Res 2022; 32:gr.276665.122. [PMID: 35948369 PMCID: PMC9528977 DOI: 10.1101/gr.276665.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 08/04/2022] [Indexed: 11/25/2022]
Abstract
The preconceptual, intrauterine, and early life environments can have a profound and long-lasting impact on the developmental trajectories and health outcomes of the offspring. Given the relatively low success rates of assisted reproductive technologies (ART; ∼25%), additives and adjuvants, such as glucocorticoids, are used to improve the success rate. Considering the dynamic developmental events that occur during this window, these exposures may alter blastocyst formation at a molecular level, and as such, affect not only the viability of the embryo and the ability of the blastocyst to implant, but also the developmental trajectory of the first three cell lineages, ultimately influencing the physiology of the embryo. In this study, we present a comprehensive single-cell transcriptome, methylome, and small RNA atlas in the day 7 human embryo. We show that, despite no change in morphology and developmental features, preimplantation glucocorticoid exposure reprograms the molecular profile of the TE lineage, and these changes are associated with an altered metabolic and inflammatory response. Our data also suggest that glucocorticoids can precociously mature the TE sublineages, supported by the presence of extravillous trophoblast markers in the polar sublineage and presence of X Chromosome dosage compensation. Further, we have elucidated that epigenetic regulation-DNA methylation and microRNAs (miRNAs)-likely underlies the transcriptional changes observed. This study suggests that exposures to exogenous compounds during preimplantation may unintentionally reprogram the human embryo, possibly leading to suboptimal development and longer-term health outcomes.
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Affiliation(s)
- Cheng Zhao
- Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska Institutet, 14186 Stockholm, Sweden
| | - Savana Biondic
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, H2X 0A9 Montréal, Canada
- Département de Médecine, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Katherine Vandal
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, H2X 0A9 Montréal, Canada
- Département de Médecine, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Åsa K Björklund
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, SE-752 37 Uppsala, Sweden
| | | | - Theresa Maria Sommer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jesica Canizo
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, H2X 0A9 Montréal, Canada
- Département de Médecine, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Stephen Clark
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Pascal Raymond
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Daniel R Zenklusen
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, H3T 1J4 Montréal, Canada
| | - Nicolas Rivron
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom
- Center for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Sophie Petropoulos
- Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska Institutet, 14186 Stockholm, Sweden
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Axe Immunopathologie, H2X 0A9 Montréal, Canada
- Département de Médecine, Université de Montréal, H3T 1J4 Montréal, Canada
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Feng W, Ying Z, Ke F, Mei-Lin X. Apigenin suppresses TGF-β1-induced cardiac fibroblast differentiation and collagen synthesis through the downregulation of HIF-1α expression by miR-122-5p. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 83:153481. [PMID: 33607460 DOI: 10.1016/j.phymed.2021.153481] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 01/11/2021] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Apigenin can reduce cardiomyocyte hypertrophy by downregulating hypoxia inducible factor-1 alpha (HIF-1α) expression. However, its effects on cardiac fibroblasts (CFs) and its exact inhibitory molecular mechanisms on HIF-1α remain unclear. PURPOSE This study aims to examine the effects of apigenin on cell proliferation and differentiation, microRNA-122-5p (miR-122-5p) expression, and HIF-1α-mediated Smad signaling pathway in transforming growth factor beta 1 (TGF-β1)-stimulated CFs and cardiac fibrosis and to investigate the relationship between miR-122-5p and HIF-1α. METHODS The TGF-β1-stimulated CFs, the combination of TGF-β1-stimulated and miR-122-5p mimic-transfected CFs, the combination of TGF-β1-stimulated and miR-122-5p inhibitor-transfected CFs, and the isoproterenol-induced cardiac fibrotic mice were used and treated with or without apigenin. The recombinant lentiviruses overexpressing HIF-1α vector and miR-122-5p mimic were co-transfected to observe their interaction. Related mRNA and protein expressions and myocardial collagen were determined. The luciferase reporter gene that contains HIF-1α wild type or mutant type 3'-UTR was used, and the luciferase activity was determined to verify the direct link between miR-122-5p and HIF-1α. RESULTS In the TGF-β1-stimulated CFs, apigenin treatment increased the miR-122-5p and Smad7 expressions and decreased the HIF-1α, α-smooth muscle actin, collagen Ⅰ/Ⅲ, Smad2/3, and p-Smad2/3 expressions. Similar and inverse results were observed in the miR-122-5p mimic- and inhibitor-transfected CFs, respectively. Moreover, the miR-122-5p mimic could antagonize the effects of TGF-β1 in the TGF-β1 and miR-122-5p mimic-combined CFs, and the miR-122-5p inhibitor could enhance the effects of TGF-β1 in the TGF-β1 and miR-122-5p inhibitor-combined CFs. In the two aforementioned cell models, the addition of apigenin could further enhance the effects of miR-122-5p mimic and partially reverse the effects of miR-122-5p inhibitor. After treatment of HIF-1α-transfected CFs with miR-122-5p mimic, the HIF-1α expression decreased. Further study confirmed that HIF-1α was a direct target of miR-122-5p. Apigenin also decreased the myocardial collagen accumulation in cardiac fibrotic mice. CONCLUSION Apigenin could suppress the differentiation and collagen synthesis of TGF-β1-stimulated CFs and mouse cardiac fibrosis, and its mechanisms were related to the increment of miR-122-5p expression and subsequent downregulation of HIF-1α expression via direct interaction, which might finally result in the decrements of Smad2/3 and p-Smad2/3 expressions and increment of Smad7 expression.
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Affiliation(s)
- Wang Feng
- Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, Jiangsu Province, China; Department of Pharmacy, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou 215008, Jiangsu Province, China
| | - Zhao Ying
- Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, Jiangsu Province, China
| | - Fan Ke
- Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, Jiangsu Province, China
| | - Xie Mei-Lin
- Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, Jiangsu Province, China.
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Li Z, Lin W, Zheng J, Hong W, Zou J, Zhang T, Chen Y, Lu H. Identification of immune-related lncRNAs to improve the prognosis prediction for patients with papillary thyroid cancer. Biosci Rep 2021; 41:BSR20204086. [PMID: 33554245 PMCID: PMC7902395 DOI: 10.1042/bsr20204086] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE To identify immune-related long non-coding RNAs (lncRNAs) in papillary thyroid cancer (PTC). METHODS The Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were used to obtain the gene expression profile. Immune-related lncRNAs were screened from the Molecular Signatures Database v4.0 (MsigDB). We performed a survival analysis of critical lncRNAs. Further, the function of prognostic lncRNAs was inferred using the Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) to clarify the possible mechanisms underlying their predictive ability. The assessment was performed in clinical samples and PTC cells. RESULTS We obtained 4 immune-related lncRNAs, 15 microRNAs (miRNAs), and 375 mRNAs as the key mediators in the pathophysiological processes of PTC from the GEO database. Further, Lasso regression analysis identified seven prognostic markers (LINC02550, SLC26A4-AS1, ACVR2B-AS1, AC005479.2, LINC02454, and AL136366.1), most of which were related to tumor development. The KEGG pathway enrichment analysis showed different, changed genes mainly enriched in the cancer-related pathways, PI3K-Akt signaling pathway, and focal adhesion. Only SLC26A4-AS1 had an intersection in the results of the two databases. CONCLUSION LncRNA SLC26A4-AS1, which is the most associated with prognosis, may play an oncogenic role in the development of PTC.
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Affiliation(s)
- Zhiyang Li
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Weixun Lin
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Jiehua Zheng
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Weida Hong
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Juan Zou
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Taofeng Zhang
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Yexi Chen
- Department of Thyroid, Breast and Hernia Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Hai Lu
- The Second Affiliated Hospital of GuangZhou University of Chinese Medicine, Guangzhou, Guangdong Province 510282, P.R. China
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province 510282, P.R. China
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Wu X, Liu J, Zhu C, Ma M, Chen X, Liu Y, Xia N, Dong Q. Identification of Potential Biomarkers of Prognosis-Related Long Non-Coding RNA (lncRNA) in Pediatric Rhabdoid Tumor of the Kidney Based on ceRNA Networks. Med Sci Monit 2020; 26:e927725. [PMID: 33328429 PMCID: PMC7754694 DOI: 10.12659/msm.927725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Long non-coding RNA (lncRNA) can act as competing endogenous RNA (ceRNA) during tumor development. However, no study has elucidated the ceRNA network in pediatric rhabdoid tumor of the kidney (RTK) and its prognostic-related lncRNAs. The goal of the present study was to identify potential biomarkers of prognostic-related lncRNAs. MATERIAL AND METHODS RNA sequencing and clinical data were procured from the TARGET database. The "EdgeR" package was used to obtain differentially expressed lncRNA (DElncRNA), differentially expressed messenger RNAs (DEmRNA), and differentially expressed microRNAs (DEmiRNA). Cytoscape software was used to construct a ceRNA network. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were conducted on the ceRNA network-related DEmRNA. The Kaplan-Meier method was used for predicting survival with ceRNA network-related DElncRNA. Univariate and multivariate Cox analyses were used to identify prognosis-related lncRNAs in the ceRNA network, and an RTK prognostic signature was constructed. RESULTS We identified 1109 DElncRNAs, 215 DEmiRNAs, and 3436 DEmRNAs; and 107 DElncRNAs, 21 DEmiRNAs, and 74 DEmRNAs were included in the ceRNA regulatory network. GO enrichment analysis and KEGG pathway enrichment indicated that the DEmRNAs were mainly related to the regulation of phospholipase C activity and the MAPK signaling pathway. Survival analysis showed that 9 of 107 DElncRNAs were correlated with prognosis (P<0.05). Univariate and multivariate Cox analysis identified 4 DElncRNAs (HNF1A-AS1, TPTEP1, SNHG6, and ZNF503-AS2) to establish a predictive model and can be used as independent prognostic biomarkers. CONCLUSIONS We constructed a ceRNA network that reveals potential lncRNA biomarkers for pediatric RTK.
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Affiliation(s)
- Xiongwei Wu
- Department of Pediatric Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Jie Liu
- Department of Pediatric Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Chengzhan Zhu
- Shandong Key Laboratory of Digital Medicine and Computer Assisted Surgery, Qingdao, Shandong, China (mainland)
| | - Mingdi Ma
- Department of Pediatric Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Xin Chen
- Department of Pediatric Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Yusheng Liu
- Department of Pediatric Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Nan Xia
- Shandong Key Laboratory of Digital Medicine and Computer Assisted Surgery, Qingdao, Shandong, China (mainland)
| | - Qian Dong
- Department of Pediatric Surgery, Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland).,Shandong Key Laboratory of Digital Medicine and Computer Assisted Surgery, Qingdao, Shandong, China (mainland)
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miRNA-Based Feature Classifier Is Associated with Tumor Mutational Burden in Head and Neck Squamous Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1686480. [PMID: 33490233 PMCID: PMC7787755 DOI: 10.1155/2020/1686480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/07/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023]
Abstract
Tumor mutation burden (TMB) is considered to be an independent genetic biomarker that can predict the tumor patient's response to immune checkpoint inhibitors (ICIs). Meanwhile, microRNA (miRNA) plays a key role in regulating the anticancer immune response. However, the correlation between miRNA expression patterns and TMB is not elucidated in HNSCC. In the HNSCC cohort of the TCGA dataset, miRNAs that were differentially expressed in high TMB and low TMB samples were screened. The least absolute contraction and selection operator (LASSO) method is used to construct a miRNA-based feature classifier to predict the TMB level in the training set. The test set is used to verify the classifier. The correlation between the miRNA-based classifier index and the expression of three immune checkpoints (PD1, PDL1, and CTLA4) was explored. We further perform functional enrichment analysis on the miRNA contained in the miRNA-based feature classifier. Twenty-five differentially expressed miRNAs are used to build miRNA-based feature classifiers to predict TMB levels. The accuracy of the 25-miRNA-based signature classifier is 0.822 in the training set, 0.702 in the test set, and 0.774 in the total set. The miRNA-based feature classifier index showed a low correlation with PD1 and PDL1, but no correlation with CTLA4. The enrichment analysis of these 25 miRNAs shows that they are involved in many immune-related biological processes and cancer-related pathways. The miRNA expression patterns are related to tumor mutation burden, and miRNA-based feature classifiers can be used as biomarkers to predict TMB levels in HNSCC.
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Xie Y, Liu X, Hu T, Wang W. miR-302e Suppresses Glioma Progression by Targeting VEGFA. Cancer Manag Res 2020; 12:10965-10974. [PMID: 33154675 PMCID: PMC7608593 DOI: 10.2147/cmar.s268222] [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: 06/30/2020] [Accepted: 09/09/2020] [Indexed: 12/15/2022] Open
Abstract
Background MiRNA can be involved in regulating tumor genesis and development by regulating the expression of specific genes and regulating corresponding signaling pathways. In this study, we explored the function and mechanisms of miR-302e in glioma progression. Methods Experimental methods include the following: real-time quantitative PCR, Western Blot Analysis, CCK8 assay and detection of apoptosis. Results MiR-302e was down-regulated in cancer tissues and cell lines, and the expression of miR-302e was negatively correlated with the tumor grade, which indicated poor prognosis in glioma patients. Followed functional analysis showed overexpression of miR-302e inhibited proliferation, migration and invasion but promoted apoptosis of glioma cells, while silencing miR-302e showed the opposite effects. Mechanistic studies have shown that VEGFA was a directed target of miR-302e. Forced expression of VEGFA removed the inhibiting impact of miR-302e on glioma development. In vivo tumorigenesis experiments showed that miR-302e suppressed glioma development by targeting VEGFA. Conclusion Present study emphasized miR-302e suppressed glioma development by targeting VEGFA, which might be a valuable target for glioma treatment.
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Affiliation(s)
- Yunpeng Xie
- Department of Neurosurgery, Chengde Medical College Affiliated Hospital, Chengde, Hebei Province, People's Republic of China
| | - Xin Liu
- Department of Oncology, Chengde Medical College Affiliated Hospital, Chengde, Hebei Province, People's Republic of China
| | - Tiemin Hu
- Department of Neurosurgery, Chengde Medical College Affiliated Hospital, Chengde, Hebei Province, People's Republic of China
| | - Weixing Wang
- Department of Neurosurgery, Chengde Medical College Affiliated Hospital, Chengde, Hebei Province, People's Republic of China
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Kamalidehghan B, Habibi M, Afjeh SS, Shoai M, Alidoost S, Almasi Ghale R, Eshghifar N, Pouresmaeili F. The Importance of Small Non-Coding RNAs in Human Reproduction: A Review Article. APPLICATION OF CLINICAL GENETICS 2020; 13:1-11. [PMID: 32021379 PMCID: PMC6956659 DOI: 10.2147/tacg.s207491] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 12/04/2019] [Indexed: 12/14/2022]
Abstract
Background MicroRNAs (miRNA) play a key role in the regulation of gene expression through the translational suppression and control of post-transcriptional modifications. Aim Previous studies demonstrated that miRNAs conduct the pathways involved in human reproduction including maintenance of primordial germ cells (PGCs), spermatogenesis, oocyte maturation, folliculogenesis and corpus luteum function. The association of miRNA expression with infertility, polycystic ovary syndrome (PCOS), premature ovarian failure (POF), and repeated implantation failure (RIF) was previously revealed. Furthermore, there are evidences of the importance of miRNAs in embryonic development and implantation. Piwi-interacting RNAs (piRNAs) and miRNAs play an important role in the post-transcriptional regulatory processes of germ cells. Indeed, the investigation of small RNAs including miRNAs and piRNAs increase our understanding of the mechanisms involved in fertility. In this review, the current knowledge of microRNAs in embryogenesis and fertility is discussed. Conclusion Further research is necessary to provide new insights into the application of small RNAs in the diagnosis and therapeutic approaches to infertility.
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Affiliation(s)
- Behnam Kamalidehghan
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Habibi
- Central Laboratory, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sara S Afjeh
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Shoai
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Saeideh Alidoost
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Rouzbeh Almasi Ghale
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Nahal Eshghifar
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran and Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farkhondeh Pouresmaeili
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Xu Y, Huang X, Ye W, Zhang Y, Li C, Bai P, Lin Z, Chen C. Comprehensive analysis of key genes associated with ceRNA networks in nasopharyngeal carcinoma based on bioinformatics analysis. Cancer Cell Int 2020; 20:408. [PMID: 32863767 PMCID: PMC7448472 DOI: 10.1186/s12935-020-01507-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/18/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is an epithelial malignancy with high morbidity rates in the east and southeast Asia. The molecular mechanisms of NPC remain largely unknown. We explored the pathogenesis, potential biomarkers, and prognostic indicators of NPC. METHODS We analyzed mRNAs, long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) in the whole transcriptome sequencing dataset of our hospital (five normal tissues vs. five NPC tissues) and six microarray datasets (62 normal tissues vs. 334 NPC tissues) downloaded from the Gene Expression Omnibus (GSE12452, GSE13597, GSE95166, GSE126683, and GSE70970, GSE43039). Differential expression analyses, gene ontology (GO) enrichment, kyoto encyclopedia of genes and genomes (KEGG) analysis, and gene set enrichment analysis (GSEA) were conducted. The lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) networks were constructed using the miRanda and TargetScan database, and a protein-protein interaction (PPI) network of differentially expressed genes (DEGs) was built using Search Tool for the Retrieval of Interacting Genes (STRING) software. Hub genes were identified using Molecular Complex Detection (MCODE), NetworkAnalyzer, and CytoHubba. RESULTS We identified 61 mRNAs, 14miRNAs, and 10 lncRNAs as shared DEGs related to NPC in seven datasets. Changes in NPC were enriched in the chromosomal region, sister chromatid segregation, and nuclear chromosome segregation. GSEA indicated that the mitogen-activated protein kinase (MAPK) pathway, phosphatidylinositol-3 OH kinase/protein kinase B (PI3K-Akt) pathway, apoptotic pathway, and tumor necrosis factor (TNF) were involved in the initiation and development of NPC. Finally, 20 hub genes were screened out via the PPI network. CONCLUSIONS Several DEGs and their biological processes, pathways, and interrelations were found in our current study by bioinformatics analyses. Our findings may offer insights into the biological mechanisms underlying NPC and identify potential therapeutic targets for NPC.
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Affiliation(s)
- Yuanji Xu
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014 Fujian People’s Republic of China
| | - Xinyi Huang
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014 Fujian People’s Republic of China
- Fujian Medical University, Fuzhou, Fujian People’s Republic of China
| | - Wangzhong Ye
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014 Fujian People’s Republic of China
- Fujian Medical University, Fuzhou, Fujian People’s Republic of China
| | - Yangfan Zhang
- Fujian Normal University, Fuzhou, Fujian People’s Republic of China
| | - Changkun Li
- Fujian Normal University, Fuzhou, Fujian People’s Republic of China
| | - Penggang Bai
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014 Fujian People’s Republic of China
| | - Zhizhong Lin
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014 Fujian People’s Republic of China
| | - Chuanben Chen
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, No. 420, Fuma Road, Fuzhou, 350014 Fujian People’s Republic of China
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Tang F, Lu Z, Wang J, Li Z, Wu W, Duan H, He Z. Competitive endogenous RNA (ceRNA) regulation network of lncRNAs, miRNAs, and mRNAs in Wilms tumour. BMC Med Genomics 2019; 12:194. [PMID: 31842887 PMCID: PMC6915924 DOI: 10.1186/s12920-019-0644-y] [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: 06/05/2019] [Accepted: 12/08/2019] [Indexed: 12/19/2022] Open
Abstract
Background Competitive endogenous RNAs (ceRNAs) have revealed a new mechanism of interaction between RNAs. However, an understanding of the ceRNA regulatory network in Wilms tumour (WT) remains limited. Methods The expression profiles of mRNAs, miRNAs and lncRNAs in Wilms tumour samples and normal samples were obtained from the Therapeutically Applicable Research to Generate Effective Treatment (TARGET) database. The EdgeR package was employed to identify differentially expressed lncRNAs, miRNAs and mRNAs. Functional enrichment analyses via the ClusterProfile R package were performed, and the lncRNA–miRNA–mRNA interaction ceRNA network was established in Cytoscape. Subsequently, the correlation between the ceRNA network and overall survival was analysed. Results A total of 2037 lncRNAs, 154 miRNAs and 3609 mRNAs were identified as differentially expressed RNAs in Wilms tumour. Of those, 205 lncRNAs, 26 miRNAs and 143 mRNAs were included in the ceRNA regulatory network. The results of Gene Ontology (GO) analysis revealed that the differentially expressed genes (DEGs) were mainly enriched in terms related to response to mechanical stimuli, transcription factor complexes, and transcription factor activity (related to RNA polymerase II proximal promoter sequence-specific DNA binding). The results of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the DEGs were mainly enriched in pathways related to the cell cycle. The survival analysis results showed that 16 out of the 205 lncRNAs, 1 out of 26 miRNAs and 5 out of 143 mRNAs were associated with overall survival in Wilms tumour patients (P < 0.05). Conclusions CeRNA networks play an important role in Wilms tumour. This finding might provide effective, novel insights for further understanding the mechanisms underlying Wilms tumour.
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Affiliation(s)
- Fucai Tang
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Zechao Lu
- First Clinical College of Guangzhou Medical University, Guangzhou, 510230, China
| | - Jiamin Wang
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Zhibiao Li
- Three Clinical College of Guangzhou Medical University, Guangzhou, 510230, China
| | - Weijia Wu
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Haifeng Duan
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Zhaohui He
- Department of Urology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China.
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Zhao D, Ren C, Yao Y, Wang Q, Li F, Li Y, Jiang A, Wang G. Identifying prognostic biomarkers in endometrial carcinoma based on ceRNA network. J Cell Biochem 2019; 121:2437-2446. [PMID: 31692050 DOI: 10.1002/jcb.29466] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/08/2019] [Indexed: 12/18/2022]
Abstract
PURPOSE Endometrial carcinoma (EC), a common gynecological malignancy with high incidence, affects the mental and physical health of women. Mounting evidence shows that long noncoding RNAs (lncRNAs), messenger RNAs (mRNAs), and microRNAs (miRNAs) have instrumental roles in various biological processes associated with the pathogenesis of EC. In this research, we intend to further study the mechanism of EC and the potential predictive markers of EC. METHODS First, we obtained original data of EC RNA transcripts from The Cancer Genome Atlas database and performed differential analysis. Subsequently, according to the miRcode online software, relationship pairs of lncRNA-miRNA were constructed, and miRNA-mRNA pairs were established based on miRDB, TargetScan, and miRTarBase. Then, we constructed the competing endogenous RNA (ceRNA) network based on lncRNA-miRNA and miRNA-mRNA pairs. To further explain the function of the ceRNA network and explore the potential prognostic markers, functional enrichment analysis, and survival analysis were carried out. RESULTS The research showed that there were 744 differential expression lncRNAs (DElncRNAs), 164 differential expression miRNAs (DEmiRNAs), and 2447 differential expression mRNAs (DEmRNAs) between EC tissues and normal tissues. Subsequently, we built 103 DEmiRNA-DEmRNA interaction pairs and 369 DElncRNA-DEmiRNA pairs. Then, we established the ceRNA network of EC, including 62 DElncRNAs, 26 DEmiRNAs, and 70 DEmRNAs. Moreover, 10 of 62 lncRNAs, 19 of 70 mRNAs, and 4 of 26 miRNAs that closely related to the survival of EC with P < .05 were obtained. Notably, based on this network, it was found that LINC00261-hsa-mir-31 pair and LINC00261-hsa-mir-211 target pairs could be used as the potential prognostic markers of EC. CONCLUSION This research recommended an available basis for the molecular mechanism of EC and prognosis prediction, which could help guide the subsequent treatments and predict the prognosis for patients with EC.
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Affiliation(s)
- Dongli Zhao
- Clinical Medical Colleges, Weifang Medical University, Weifang, Shandong, China
| | - Chune Ren
- Department of Reproductive Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Yan Yao
- Clinical Medical Colleges, Weifang Medical University, Weifang, Shandong, China
| | - Qinjian Wang
- Clinical Medical Colleges, Weifang Medical University, Weifang, Shandong, China
| | - Fei Li
- Clinical Medical Colleges, Weifang Medical University, Weifang, Shandong, China
| | - Yang Li
- Clinical Medical Colleges, Weifang Medical University, Weifang, Shandong, China
| | - Aifang Jiang
- Department of Reproductive Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Guili Wang
- Department of Reproductive Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
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11
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Liu J, Li W, Zhang J, Ma Z, Wu X, Tang L. Identification of key genes and long non-coding RNA associated ceRNA networks in hepatocellular carcinoma. PeerJ 2019; 7:e8021. [PMID: 31695969 PMCID: PMC6827457 DOI: 10.7717/peerj.8021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/10/2019] [Indexed: 12/20/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Although multiple efforts have been made to understand the development of HCC, morbidity, and mortality rates remain high. In this study, we aimed to discover the mRNAs and long non-coding RNAs (lncRNAs) that contribute to the progression of HCC. We constructed a lncRNA-related competitive endogenous RNA (ceRNA) network to elucidate the molecular regulatory mechanism underlying HCC. Methods A microarray dataset (GSE54238) containing information about both mRNAs and lncRNAs was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and lncRNAs (DElncRNAs) in tumor tissues and non-cancerous tissues were identified using the limma package of the R software. The miRNAs that are targeted by DElncRNAs were predicted using miRcode, while the target mRNAs of miRNAs were retrieved from miRDB, miRTarBas, and TargetScan. Functional annotation and pathway enrichment of DEGs were performed using the EnrichNet website. We constructed a protein–protein interaction (PPI) network of DEGs using STRING, and identified the hub genes using Cytoscape. Survival analysis of the hub genes and DElncRNAs was performed using the gene expression profiling interactive analysis database. The expression of molecules with prognostic values was validated on the UALCAN database. The hepatic expression of hub genes was examined using the Human Protein Atlas. The hub genes and DElncRNAs with prognostic values as well as the predictive miRNAs were selected to construct the ceRNA networks. Results We found that 10 hub genes (KPNA2, MCM7, CKS2, KIF23, HMGB2, ZWINT, E2F1, MCM4, H2AFX, and EZH2) and four lncRNAs (FAM182B, SNHG6, SNHG1, and SNHG3) with prognostic values were overexpressed in the hepatic tumor samples. We also constructed a network containing 10 lncRNA–miRNA–mRNA pathways, which might be responsible for regulating the biological mechanisms underlying HCC. Conclusion We found that the 10 significantly overexpressed hub genes and four lncRNAs were negatively correlated with the prognosis of HCC. Further, we suggest that lncRNA SNHG1 and the SNHG3-related ceRNAs can be potential research targets for exploring the molecular mechanisms of HCC.
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Affiliation(s)
- Jun Liu
- Department of Clinical Laboratory, Yue Bei People's Hospital, Shaoguan, Guangdong, China.,Morning Star Academic Cooperation, Shanghai, China
| | - Wenli Li
- Reproductive Medicine Center, Yue Bei People's Hospital, Shaoguan, Guangdong, China
| | - Jian Zhang
- Department of Clinical Laboratory, Yue Bei People's Hospital, Shaoguan, Guangdong, China
| | - Zhanzhong Ma
- Department of Clinical Laboratory, Yue Bei People's Hospital, Shaoguan, Guangdong, China
| | - Xiaoyan Wu
- Community Healthcare Center, Shanghai, Shanghai, China
| | - Lirui Tang
- Morning Star Academic Cooperation, Shanghai, China.,Shanghai JiaoTong University School of Medicine, Shanghai Ninth People's Hospital, Shanghai, China
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12
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Costard LS, Neubert V, Venø MT, Su J, Kjems J, Connolly NM, Prehn JH, Schratt G, Henshall DC, Rosenow F, Bauer S. Electrical stimulation of the ventral hippocampal commissure delays experimental epilepsy and is associated with altered microRNA expression. Brain Stimul 2019; 12:1390-1401. [DOI: 10.1016/j.brs.2019.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/18/2019] [Accepted: 06/05/2019] [Indexed: 12/31/2022] Open
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13
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Yin X, Huang S, Xu A, Fan F, Chen L, Sun C, Hu Y. Identification of distinctive long noncoding RNA competitive interactions and a six-methylated-gene prognostic signature in acute myeloid leukemia with -5/del(5q) or -7/del(7q). J Cell Biochem 2019; 121:1563-1574. [PMID: 31535409 DOI: 10.1002/jcb.29391] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 08/28/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Acute myeloid leukemia (AML) with -5/del(5q) or -7/del(7q) has special clinical and biological characteristics, but its molecular mechanisms and risk stratification remain unknown. METHODS The RNA sequencing and DNA methylation of 23 patients with -5/del(5q) or -7/del(7q) and 128 patients with other subtypes of acute myeloid leukemia were obtained from The Cancer Genome Atlas (TCGA). The regulatory mechanisms of competitive endogenous RNA (ceRNA) network and DNA methylation on gene expression were explored. To find robust and specific risk stratification for this AML subtype, a prognostic model was established and evaluated through four independent data sets. RESULTS We identified 966 differentially expressed long noncoding RNA, 2274 differentially expressed genes, and 47 differentially expressed microRNAs, and constructed a ceRNA network. After the integrated analysis of differentially methylated and expressed genes, 19 genes showed the opposite trend between the methylation variation and gene expression. An six-methylated-gene prognostic signature which highly correlated with overall survival was established, and the performance was validated by leave-one-out cross validation method and permutation test. Furthermore, the excellent prognostic value of this model was supported by an independent cohort, while specificity of this model was validated by three independent data sets, suggesting it as a predictive classifier with high efficiency for distinguishing those with -5/del(5q) or -7/del(7q) from other AML subtypes. CONCLUSIONS The ceRNA network may provide new ideas for the diagnosis and treatment for patients with -5/del(5q) or -7/del(7q).The six-methylated-gene prognostic signature was a robust, specific, and clinically practical risk stratification for the outcome of patients with AML having -5/del(5q) or -7/del(7q).
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Affiliation(s)
- Xuejiao Yin
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sui Huang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aoshuang Xu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fengjuan Fan
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Chen
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunyan Sun
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
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Gong Y, Zou B, Chen J, Ding L, Li P, Chen J, Chen J, Zhang B, Li J. Potential Five-MicroRNA Signature Model for the Prediction of Prognosis in Patients with Wilms Tumor. Med Sci Monit 2019; 25:5435-5444. [PMID: 31328722 PMCID: PMC6668497 DOI: 10.12659/msm.916230] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Wilms tumor (WT) is the most common type of pediatric renal malignancy, and is associated with poor prognosis. The aim of the present study was to identify microRNA (miRNA) signatures which might predict prognosis and categorize WTs into high- and low-risk subgroups. Material/Methods The miRNA expression profiles of WT patients and normal samples were obtained from the Therapeutically Applicable Research to Generate Effective Treatment database. Differentially expressed miRNAs between WT patients and normal samples were identified using the EdgeR package. Subsequently, correlations between differentially expressed miRNAs and the prognosis of overall survival were analyzed. Enrichment analyses for the targeted mRNAs were conducted via the Database for Annotation, Visualization, and Integration Discovery. Results A total of 154 miRNAs were identified as differentially expressed in WT. Of those, 18 miRNAs were associated with overall survival (P<0.05). A prognostic signature of 5 differentially expressed miRNAs (i.e., has-mir-149, has-mir-7112, has-mir-940, has-mir-1248, and has-mir-490) was constructed to classify the patients into high- and low-risk subgroups. The targeted mRNAs of these prognostic miRNAs were primarily enriched in Gene Ontology terms (i.e., protein autophosphorylation, protein dephosphorylation, and stress-activated MAPK cascade) and the Kyoto Encyclopedia of Genes and Genomes signaling pathways (i.e., MAPK, AMPK, and PI3K-Akt). Conclusions The 5-miRNA signature model might be useful in determining the prognosis of WT patients. As a promising prediction tool, this prognosis signature might serve as a potential biomarker for WT patients.
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Affiliation(s)
- Yihang Gong
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Baojia Zou
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Jianxu Chen
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Lei Ding
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Peiping Li
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Jiafan Chen
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Jiandi Chen
- Department of Endocrinology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Baimeng Zhang
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
| | - Jian Li
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China (mainland)
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Yuan Y, Li N, Zeng L, Shen Z, Jiang C. Pathogenesis investigation of miR-199-5p in oral submucous fibrosis based on bioinformatics analysis. Oral Dis 2018; 25:456-465. [PMID: 30485610 DOI: 10.1111/odi.13008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/08/2018] [Accepted: 11/22/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Fibrosis diseases are one of the leading causes of suffering and death. However, no systematic investigation has been carried out on fibrosis-related genes. MATERIALS AND METHODS By querying PubMed using keywords "fibrosis" and "gene" or "protein," we identified fibrosis-related genes in the last decade. Bioinformatics analysis was performed by MAS 3.0 software. Key miRNA was selected to assess its relationship with oral submucous fibrosis (OSF) and fibroblast functions. RESULTS A total of 1,310 genes related to fibrosis were identified. TGF-β1, CTGF, MMP9, HSP47, and S1P were found to be associated with mainly fibrotic organs. In total, 244 cellular components terms, 595 molecular function terms, 1,816 cellular component terms, and 136 KEGG pathway annotations were predicted. miR-199-5p was selected as the key miRNA, which has higher level in OSF. Upregulated miR-199-5p was significantly related to OSF duration and OSF histological grade (p = 0.028 and 0.012, respectively). Overexpressive miR-199-5p reduced proliferation and induced apoptosis in buccal fibroblasts. Additionally, expression levels of collagen I (COL I) and III (COL III) were promoted by overexpressive miR-199-5p in buccal fibroblasts. CONCLUSION These results indicate that fibrosis-related genes are related to a series of complex mechanisms. The characteristics of miR-199-5p may supply important clues for developing therapeutic strategy for OSF.
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Affiliation(s)
- Yongxiang Yuan
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Ning Li
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Lijuan Zeng
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhengzhong Shen
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Canhua Jiang
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Changsha, China
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16
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Gao C, Li H, Zhuang J, Zhang H, Wang K, Yang J, Liu C, Liu L, Zhou C, Sun C. The construction and analysis of ceRNA networks in invasive breast cancer: a study based on The Cancer Genome Atlas. Cancer Manag Res 2018; 11:1-11. [PMID: 30588106 PMCID: PMC6301306 DOI: 10.2147/cmar.s182521] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Studies have shown that long noncoding RNAs (lncRNAs) make up the major proportion of the ceRNA network and can regulate gene expression by competitively binding to miRNAs. This reveals the existence of an RNA-miRNA regulatory pathway and is of great biological significance. CeRNAs, as competitive endogenous RNAs, have revealed a new mechanism of interaction between RNAs. Until now, the role of lncRNA-mediated ceRNAs in breast cancer and their regulatory mechanisms have been elucidated to some extent. Purpose In this study, comprehensive analysis of large-scale invasive breast cancer samples in TCGA were conducted to further explore the developmental mechanism of invasive breast cancer and the potential predictive markers for invasive breast cancer prognosis in the ceRNA network. Methods Abnormal expression profiles of invasive breast cancer associated mRNAs, lncRNAs and miRNAs were obtained from the TCGA database. Through further alignment and prediction of target genes, an abnormal lncRNA-miRNA-mRNA ceRNA network was constructed for invasive breast cancer. Through the overall survival analysis, Identification prognostic bio-markers for invasive breast cancer patients. In addition, we used Cytoscape plug-in BinGo for the different mRNA performance functional cluster analysis. Results Differential analysis revealed that 1059 lncRNAs, 86 miRNAs, and 2138 mRNAs were significantly different in invasive breast cancer samples versus normal samples. Then we construct an abnormal lncRNA-miRNA-mRNA ceRNA network for invasive breast cancer, consisting of 90 DElncRNAs, 18 DEmiRNAs and 26 DEmRNAs.Further, 4 out of 90 lncRNAs, 3 out of 26 mRNAs, and 2 out of 18 miRNAs were useful as prognostic biomarkers for invasive breast cancer patients (P value < 0.05). It is worth noting that based on the ceRNA network, we found that the LINC00466-Hsa-mir-204- NTRK2 LINC00466-hsa-mir-204-NTRK2 axis was present in 9 RNAs associated with the prognosis of invasive breast cancer. Conclusion This study provides an effective bioinformatics basis for further understanding of the molecular mechanism of invasive breast cancerand for predicting outcomes, which can guide the use of invasive breast cancerdrugs and subsequent related research.
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Affiliation(s)
- Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, People's Republic of China
| | - Huayao Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, People's Republic of China
| | - Jing Zhuang
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, People's Republic of China, .,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang 261031, People's Republic of China,
| | - HongXiu Zhang
- Institute of Virology, Jinan Center for Disease Control and Prevention, Jinan 250021, People's Republic of China
| | - Kejia Wang
- College of Basic Medicine, Qingdao University, Qingdao 266071, People's Republic of China
| | - Jing Yang
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, People's Republic of China,
| | - Cun Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, People's Republic of China
| | - Lijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, People's Republic of China, .,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang 261031, People's Republic of China,
| | - Chao Zhou
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, People's Republic of China, .,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang 261031, People's Republic of China,
| | - Changgang Sun
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, People's Republic of China, .,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang 261031, People's Republic of China,
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Song J, Ye A, Jiang E, Yin X, Chen Z, Bai G, Zhou Y, Liu J. Reconstruction and analysis of the aberrant lncRNA-miRNA-mRNA network based on competitive endogenous RNA in CESC. J Cell Biochem 2018; 119:6665-6673. [PMID: 29741786 PMCID: PMC6055788 DOI: 10.1002/jcb.26850] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 03/09/2018] [Indexed: 12/30/2022]
Abstract
A growing body of studies has demonstrated that long non-coding RNA (lncRNA) are regarded as the primary section of the ceRNA network. This is thought to be the case owing to its regulation of protein-coding gene expression by functioning as miRNA sponges. However, functional roles and regulatory mechanisms of lncRNA-mediated ceRNA in cervical squamous cell carcinoma (CESC), as well as their use for potential prediction of CESC prognosis, remains unknown. The aberrant expression profiles of mRNA, lncRNA, and miRNA of 306 cervical squamous cancer tissues and three adjacent cervical tissues were obtained from the TCGA database. A lncRNA-mRNA-miRNA ceRNA network in CESC was constructed. Meanwhile, Gene Ontology (GO) and KEGG pathway analysis were performed using Cytoscape plug-in BinGo and DAVID database. We identified a total of 493 lncRNA, 70 miRNA, and 1921 mRNA as differentially expressed profiles. An aberrant lncRNA-mRNA-miRNA ceRNA network was constructed in CESC, it was composed of 50 DElncRNA, 18 DEmiRNA, and 81 DEmRNA. According to the overall survival analysis, 3 out of 50 lncRNA, 10 out of 81 mRNA, and 1 out of 18 miRNA functioned as prognostic biomarkers for patients with CESC (P value < 0.05). We extracted the sub-network in the ceRNA network and found that two novel lncRNA were recognized as key genes. These included lncRNA MEG3 and lncRNA ADAMTS9-AS2. The present study provides a new insight into a better understanding of the lncRNA-related ceRNA network in CESC, and the novel recognized ceRNA network will help us to improve our understanding of lncRNA-mediated ceRNA regulatory mechanisms in the pathogenesis of CESC.
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Affiliation(s)
- Jukun Song
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province, China
| | - Aizhu Ye
- Department of Clinical Laboratory, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province, China
| | - Enli Jiang
- Department of Obstetrics and Gynecology, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province, China
| | - Xinhai Yin
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province, China
| | - Zhu Chen
- Guiyang Hospital of Stomatology, Medical College, Zunyi Medical College, Guiyang, China
| | - Guohui Bai
- Special Key Laboratory of Oral Diseases Research, Stomatological Hospital Affiliated to Zunyi Medical College, Zunyi, Guizhou Province, China
| | - Yu Zhou
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou Province, China
| | - Jianguo Liu
- Special Key Laboratory of Oral Diseases Research, Stomatological Hospital Affiliated to Zunyi Medical College, Zunyi, Guizhou Province, China
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Leonardi GC, Accardi G, Monastero R, Nicoletti F, Libra M. Ageing: from inflammation to cancer. IMMUNITY & AGEING 2018; 15:1. [PMID: 29387133 PMCID: PMC5775596 DOI: 10.1186/s12979-017-0112-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 12/28/2017] [Indexed: 02/08/2023]
Abstract
Ageing is the major risk factor for cancer development. Hallmark of the ageing process is represented by inflammaging, which is a chronic and systemic low-grade inflammatory process. Inflammation is also a hallmark of cancer and is widely recognized to influence all cancer stages from cell transformation to metastasis. Therefore, inflammaging may represent the biological phenomena able to couple ageing process with cancer development. Here we review the molecular and cellular pathway involved in age-related chronic inflammation along with its potential triggers and their connection with cancer development.
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Affiliation(s)
- Giulia C Leonardi
- 1Department of Biomedical and Biotechnological Sciences, Pathology and Oncology Section, University of Catania, Catania, Italy
| | - Giulia Accardi
- 2Department of Pathobiology and Medical Biotechnologies, Immunosenescence and Ageing Group, University of Palermo, Palermo, Italy
| | - Roberto Monastero
- 3Department of Experimental Biomedicine and Clinical Neurosciences, Neurology Section, University of Palermo, Palermo, Italy
| | - Ferdinando Nicoletti
- 1Department of Biomedical and Biotechnological Sciences, Pathology and Oncology Section, University of Catania, Catania, Italy
| | - Massimo Libra
- 1Department of Biomedical and Biotechnological Sciences, Pathology and Oncology Section, University of Catania, Catania, Italy
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Zinger A, Cho WC, Ben-Yehuda A. Cancer and Aging - the Inflammatory Connection. Aging Dis 2017; 8:611-627. [PMID: 28966805 PMCID: PMC5614325 DOI: 10.14336/ad.2016.1230] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/30/2016] [Indexed: 12/13/2022] Open
Abstract
Aging and cancer are highly correlated biological phenomena. Various cellular processes such as DNA damage responses and cellular senescence that serve as tumor suppressing mechanisms throughout life result in degenerative changes and contribute to the aging phenotype. In turn, aging is considered a pro-tumorigenic state, and constitutes the single most important risk factor for cancer development. However, the causative relations between aging and cancer is not straight forward, as these processes carry contradictory hallmarks; While aging is characterized by tissue degeneration and organ loss of function, cancer is a state of sustained cellular proliferation and gain of new functions. Here, we review the molecular and cellular pathways that stand in the base of aging related cancer. Specifically, we deal with the inflammatory perspective that link these two processes, and suggest possible molecular targets that may be exploited to modify their courses.
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Affiliation(s)
- Adar Zinger
- 1Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - William C Cho
- 2Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Arie Ben-Yehuda
- 1Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Etebari K, Asgari S. Revised annotation of Plutella xylostella microRNAs and their genome-wide target identification. INSECT MOLECULAR BIOLOGY 2016; 25:788-799. [PMID: 27515977 DOI: 10.1111/imb.12263] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The diamondback moth, Plutella xylostella, is the most devastating pest of brassica crops worldwide. Although 128 mature microRNAs (miRNAs) have been annotated from this species in miRBase, there is a need to extend and correct the current P. xylostella miRNA repertoire as a result of its recently improved genome assembly and more available small RNA sequence data. We used our new ultra-deep sequence data and bioinformatics to re-annotate the P. xylostella genome for high confidence miRNAs with the correct 5p and 3p arm features. Furthermore, all the P. xylostella annotated genes were also screened to identify potential miRNA binding sites using three target-predicting algorithms. In total, 203 mature miRNAs were annotated, including 33 novel miRNAs. We identified 7691 highly confident binding sites for 160 pxy-miRNAs. The data provided here will facilitate future studies involving functional analyses of P. xylostella miRNAs as a platform to introduce novel approaches for sustainable management of this destructive pest.
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Affiliation(s)
- K Etebari
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - S Asgari
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
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Zeng G, Xun W, Wei K, Yang Y, Shen H. MicroRNA-27a-3p regulates epithelial to mesenchymal transition via targeting YAP1 in oral squamous cell carcinoma cells. Oncol Rep 2016; 36:1475-82. [DOI: 10.3892/or.2016.4916] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/30/2016] [Indexed: 11/06/2022] Open
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Zhang Q, Xu M, Qu Y, Li Z, Zhang Q, Cai X, Lu L. Analysis of the differential expression of circulating microRNAs during the progression of hepatic fibrosis in patients with chronic hepatitis B virus infection. Mol Med Rep 2015; 12:5647-54. [PMID: 26299203 PMCID: PMC4581744 DOI: 10.3892/mmr.2015.4221] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 05/08/2015] [Indexed: 01/06/2023] Open
Abstract
Considering the limitations of liver biopsy, reliable non‑invasive serum biomarkers of liver fibrosis are required for early diagnosis. The present study analyzed the expression profile of circulating micro (mi)RNAs during the development and progression of hepatic fibrosis in patients with chronic hepatitis B virus (HBV) infection, aiming to identify novel earlier diagnostic biomarkers. Fresh plasma samples were collected from 50 patients diagnosed with chronic HBV infection and hepatic fibrosis. These patients were classified into five groups (S0, S1, S2, S3 and S4; n=10 per group) based on Scheuer's staging criteria. The differential expression of the circulating miRNAs was determined by performing miRNA microarray hybridization. Finally, the target genes of the miRNAs were predicted and classified using gene ontology analysis. A total of 140 miRNAs were detected in the S1‑S4 patient groups, and their expression levels were >2‑fold higher compared with those in the S0 group. The numbers of miRNAs differentially expressed in the S1‑S4 patient groups were 48, 97, 84 and 56, respectively, with 12 miRNAs differentially expressed at all stages, 10 of which were upregulated and two of which were downregulated. The target genes of the miRNAs identified were found to be involved in 100 signal transduction pathways, the majority of which affected hepatic fibrosis via the TGF‑/Smad, Wnt, MAPK, Jak/STAT and VEGF pathways. The differential expression levels of miRNAs were closely associated with the staging of hepatic fibrosis. The results of the present study provide evidence to facilitate the development and application of non‑invasive biomarkers for earlier diagnosis of hepatic fibrosis.
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Affiliation(s)
- Qingqing Zhang
- Department of Gastroenterology, Shanghai First People's Hospital, Shanghai Jiao‑Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Mingyi Xu
- Department of Gastroenterology, Shanghai First People's Hospital, Shanghai Jiao‑Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Ying Qu
- Department of Gastroenterology, Shanghai First People's Hospital, Shanghai Jiao‑Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Zhenghong Li
- Department of Gastroenterology, Shanghai First People's Hospital, Shanghai Jiao‑Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Qidi Zhang
- Department of Gastroenterology, Shanghai First People's Hospital, Shanghai Jiao‑Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Xiaobo Cai
- Department of Gastroenterology, Shanghai First People's Hospital, Shanghai Jiao‑Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Lungen Lu
- Department of Gastroenterology, Shanghai First People's Hospital, Shanghai Jiao‑Tong University School of Medicine, Shanghai 200080, P.R. China
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23
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Shervington L, Patil H, Shervington A. Could the Anti-Chaperone VER155008 Replace Temozolomide for Glioma Treatment. J Cancer 2015; 6:786-94. [PMID: 26185541 PMCID: PMC4504115 DOI: 10.7150/jca.12251] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/11/2015] [Indexed: 12/16/2022] Open
Abstract
Cancer inducible molecular chaperone HSP90 is of great importance as an anticancer target. Proteomic analysis showed that inhibiting HSP90 by the geldanamycin derivative, 17-AAG elevated the expression of the co-chaperone Hsp70. In this study we used HSP90 selective inhibitor 17-AAG and HSP70/90 dual inhibitor, VER155008 (VER) in U87-MG glioma cells. miRNAs microarray technology was used to evaluate the efficacy of these inhibitory drugs compared with temozolomide (TMZ), used as a standard treatment for glioma. Microarrays data identified 154 differentially expressed miRNAs using stringent or unstringent parameters. 16 miRNAs were overlapped between treatments, 13 upregulated and one downregulated miRNA were overlapped between TMZ and VER. The miRNA target prediction software was used for these overlapped miRNAs and identified 6 of the 13 upregulated miRNAs target methyltransferase genes. The IC50, together with Akt and HSP70 and 90 protein level data favour VER and TMZ to 17-AAG, however due to the selectivity of VER to cancer cells as a potent antichaperon, it may be more favourable to the standard TMZ.
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Affiliation(s)
| | | | - Amal Shervington
- Brain Tumour North West, Faculty of Science and Technology, University of Central Lancashire, Preston, PR1 2HE. UK
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24
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Leitão AL, Costa MC, Enguita FJ. A guide for miRNA target prediction and analysis using web-based applications. Methods Mol Biol 2015; 1182:265-77. [PMID: 25055918 DOI: 10.1007/978-1-4939-1062-5_23] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
MiRNAs are small noncoding RNAs which act by binding to the 3'UTR of mRNA transcripts to exert a negative regulatory effect. The miRNA binding to its target follows rules based on the base complementarity of the seed sequence (2-9 first nucleotides of the miRNA sequence). Several algorithms have been developed to predict miRNA binding to genomic targets and its physiological consequences. This chapter will describe several practical aspects for the use of miRNA target prediction algorithms taking advantage of their web interfaces as well as how to produce integrative results in a graphical manner.
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Affiliation(s)
- Ana Lúcia Leitão
- Departamento de Ciências e Tecnologia da Biomassa, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, Caparica, 2829-516, Portugal
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25
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Callegari S, Gastaldello S, Faridani OR, Masucci MG. Epstein-Barr virus encoded microRNAs target SUMO-regulated cellular functions. FEBS J 2014; 281:4935-50. [DOI: 10.1111/febs.13040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 08/11/2014] [Accepted: 09/02/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Simone Callegari
- Department of Cell and Molecular Biology; Karolinska Institutet; Stockholm Sweden
| | - Stefano Gastaldello
- Department of Cell and Molecular Biology; Karolinska Institutet; Stockholm Sweden
| | - Omid R. Faridani
- Department of Cell and Molecular Biology; Karolinska Institutet; Stockholm Sweden
| | - Maria G. Masucci
- Department of Cell and Molecular Biology; Karolinska Institutet; Stockholm Sweden
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26
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Bacalini MG, Friso S, Olivieri F, Pirazzini C, Giuliani C, Capri M, Santoro A, Franceschi C, Garagnani P. Present and future of anti-ageing epigenetic diets. Mech Ageing Dev 2014; 136-137:101-15. [DOI: 10.1016/j.mad.2013.12.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 12/06/2013] [Accepted: 12/20/2013] [Indexed: 12/13/2022]
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27
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Li W, Kong LB, Li JT, Guo ZY, Xue Q, Yang T, Meng YL, Jin BQ, Wen WH, Yang AG. MiR-568 inhibits the activation and function of CD4⁺ T cells and Treg cells by targeting NFAT5. Int Immunol 2013; 26:269-81. [PMID: 24355664 DOI: 10.1093/intimm/dxt065] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
CD4(+) T cells play critical roles in orchestrating adaptive immune responses. Their activation and proliferation are critical steps that occur before they execute their biological functions. Despite the important role of this process, the underlying molecular events are not fully understood. MicroRNAs (miRNAs) have been shown to play important roles in lymphocyte development and function. However, the miRNAs that regulate T-cell differentiation, activation and proliferation are still largely unknown. In our previous study, using a miRNA array, we found that several miRNAs (including miR-202, 33b, 181c, 568 and 576) are differentially expressed between resting and activated CD4(+) T cells. In this study, we focused on the function of miR-568 during CD4(+) T-cell activation. We showed that the expression level of miR-568 decreased during the activation of T cells, including Jurkat cells and human peripheral blood CD4(+) T cells. When Jurkat or human peripheral blood CD4(+) T cells were transfected with miR-568 mimics, cell activation was significantly inhibited, as shown by the inhibited expression of activation markers such as CD25, CD69 and CD154; decreased IL-2 production; and inhibited cell proliferation. Using software predictions and confirmatory experiments, we demonstrated that nuclear factor of activated T cells 5 (NFAT5) is a target of miR-568. Treg cells are an important CD4(+) T-cell subpopulation, so we also evaluated the function of miR-568 in Treg-cell activation and differentiation. We showed that the miR-568 level decreased, while the NFAT5 protein level increased during CD4(+)CD25(+) Treg-cell activation, and the transfection of miR-568 mimics inhibited the NFAT5 expression, inhibited the production of both TGF-β and IL-10 and also inhibited the proliferation of Treg cells. Our further study showed that over-expression of miR-568 can inhibit Treg-cell differentiation and can inhibit the suppressive effect of these cells on effector cells. In addition, inhibition of NFAT5 by siRNA-mediated knockdown can inhibit the activation and differentiation of Treg cells. These findings reveal that miR-568 can inhibit the activation and function of both CD4(+) T cells and Treg cells by targeting NFAT5. Since miR-568 plays an important role in both CD4(+) T cells and Treg cells, these findings may provide leads for the development of novel treatments for human inflammatory and autoimmune diseases.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Cancer Biology, Department of Immunology, Fourth Military Medical University, Xi'an 710032, China
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28
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Olivieri F, Rippo MR, Monsurrò V, Salvioli S, Capri M, Procopio AD, Franceschi C. MicroRNAs linking inflamm-aging, cellular senescence and cancer. Ageing Res Rev 2013; 12:1056-68. [PMID: 23688930 DOI: 10.1016/j.arr.2013.05.001] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/30/2013] [Accepted: 05/08/2013] [Indexed: 01/01/2023]
Abstract
Epidemiological and experimental data demonstrate a strong correlation between age-related chronic inflammation (inflamm-aging) and cancer development. However, a comprehensive approach is needed to clarify the underlying molecular mechanisms. Chronic inflammation has mainly been attributed to continuous immune cells activation, but the cellular senescence process, which may involve acquisition of a senescence-associated secretory phenotype (SASP), can be another important contributor, especially in the elderly. MicroRNAs (miRs), a class of molecules involved in gene expression regulation, are emerging as modulators of some pathways, including NF-κB, mTOR, sirtuins, TGF-β and Wnt, that may be related to inflammation, cellular senescence and age-related diseases, cancer included. Interestingly, cancer development is largely avoided or delayed in centenarians, where changes in some miRs are found in plasma and leukocytes. We identified miRs that can be considered as senescence-associated (SA-miRs), inflammation-associated (inflamma-miRs) and cancer-associated (onco-miRs). Here we review recent findings concerning three of them, miR-21, -126 and -146a, which target mRNAs belonging to the NF-κB pathway; we discuss their ability to link cellular senescence, inflamm-aging and cancer and their changes in centenarians, and provide an update on the possibility of using miRs to block accumulation of senescent cells to prevent formation of a microenvironment favoring cancer development and progression.
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