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Yang H, Chen XW, Song XJ, Du HY, Si FC. Baitouweng decoction suppresses growth of esophageal carcinoma cells through miR-495-3p/BUB1/STAT3 axis. World J Gastrointest Oncol 2024; 16:3193-3210. [DOI: 10.4251/wjgo.v16.i7.3193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 04/29/2024] [Accepted: 06/04/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Esophageal carcinoma (EC) is one of the most prevalent cancers in human populations worldwide. Baitouweng decoction is one of the most important Chinese medicine formulas, with the potential to treat cancer.
AIM To investigate the role and mechanism of Baitouweng decoction on EC cells.
METHODS Differentially expressed genes (DEGs) in EC tissues and normal tissues were screened by the cDNA microarray technique and by bioinformatics methods. The target genes of microRNAs were predicted based on the TargetScan database and verified by dual luciferase gene reporter assay. We used Baitouweng decoction to intervene EC cells, and detected the activity of EC9706 and KYSE150 cells by the MTT method. Cell cycle and apoptosis were measured by flow cytometry. The expression of BUB1 mRNA and miR-495-3p was measured by qRT-PCR. The protein levels of BUB1, STAT3, p-STAT3, CCNB1, CDK1, Bax, Caspase3, and Caspase9 were measured by Western blot analysis. The migration and invasion abilities of the cells were measured by wound-healing assay and Transwell invasion assay, respectively.
RESULTS DEGs identified are involved in biological processes, signaling pathways, and network construction, which are mainly related to mitosis. BUB1 was the key hub gene, and it is also a target gene of miR-495-3p. Baitouweng decoction could upregulate miR-495-3p and inhibit BUB1 expression. In vitro experiments showed that Baitouweng decoction significantly inhibited the migration and invasion of EC cells and induced apoptosis and G2/M phase arrest. After treatment with Baitouweng decoction, the expression of Bax, Caspase 3, and Caspase 9 in EC cells increased significantly, while the expression of BUB1, CCNB1, and CDK1 decreased significantly. Moreover, the STAT3 signaling pathway may play an important role in this process.
CONCLUSION Baitouweng decoction has a significant inhibitory effect on EC cell growth. BUB1 is a potential therapeutic target for EC. Further analysis showed that Baitouweng decoction may inhibit the growth of EC cells by upregulating miR-495-3p targeting the BUB1-mediated STAT3 signal pathway.
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Affiliation(s)
- Hui Yang
- Henan Key Laboratory of Traditional Chinese Medicine Syndrome and Prescription in Signaling, Henan International Joint Laboratory of TCM Syndrome and Prescription in Signaling, Traditional Chinese Medicine School, Henan University of Chinese Medicine, Zhengzhou 450046, Henan Province, China
| | - Xiao-Wei Chen
- Henan Key Laboratory of Traditional Chinese Medicine Syndrome and Prescription in Signaling, Henan International Joint Laboratory of TCM Syndrome and Prescription in Signaling, Traditional Chinese Medicine School, Henan University of Chinese Medicine, Zhengzhou 450046, Henan Province, China
| | - Xue-Jie Song
- Henan Key Laboratory of Traditional Chinese Medicine Syndrome and Prescription in Signaling, Henan International Joint Laboratory of TCM Syndrome and Prescription in Signaling, Traditional Chinese Medicine School, Henan University of Chinese Medicine, Zhengzhou 450046, Henan Province, China
| | - Hai-Yang Du
- Henan Key Laboratory of Traditional Chinese Medicine Syndrome and Prescription in Signaling, Henan International Joint Laboratory of TCM Syndrome and Prescription in Signaling, Traditional Chinese Medicine School, Henan University of Chinese Medicine, Zhengzhou 450046, Henan Province, China
| | - Fu-Chun Si
- Henan Key Laboratory of Traditional Chinese Medicine Syndrome and Prescription in Signaling, Henan International Joint Laboratory of TCM Syndrome and Prescription in Signaling, Traditional Chinese Medicine School, Henan University of Chinese Medicine, Zhengzhou 450046, Henan Province, China
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Liu M, Li H, Huo Z, Chen H, Kang X, Xu B. Bioinformatics Research and qRT-PCR Verify Hub Genes and a Transcription Factor-MicroRNA Feedback Network in Intervertebral Disc Degeneration. Appl Biochem Biotechnol 2024; 196:3184-3198. [PMID: 37632659 DOI: 10.1007/s12010-023-04699-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2023] [Indexed: 08/28/2023]
Abstract
The present study explores the potentials of bioinformatics analysis to identify hub genes linked to intervertebral disc degeneration (IDD) and explored the potential molecular mechanism of transcription factor-microRNA regulatory network. Furthermore, the hub genes were identified through quantitative reverse transcriptase PCR (qRT-PCR). GEO database expression profile datasets for candidate genes (GSE124272) were downloaded. Genes that were differentially expressed (DEGs) were detected utilizing limma technique in the R programming language. Search Tool for the Retrieval of Interacting Genes/Proteins and NetworkAnalyst software identified hub genes. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis as well as Gene Ontology annotation of the DEGs were performed using Metascape. Using Bioinformatics data from the TRRUST, StarBase, and TransmiR databases, a TF-miRNA-hub genes network was constructed. qRT-PCR was utilized to confirm the result. As compared to healthy persons, 521 DEGs, comprising 203 down-regulated and 318 up-regulated genes, as well as 7 core genes, were found in people with IDD. Analysis revealed that all seven essential genes were under-expressed. qRT-PCR further confirmed the low expression of these seven important genes. Based on the TRRUST database, 16 TFs that could target five junction genes were then predicted. According to the StarBase database, four miRNAs were linked to crucial genes, while the TransmiR database predicted regulatory connections between four miRNAs and five TFs. The expression of the TP53-(hsa-miR-183-5p)-CCNB1 TF-miRNA-mRNA interaction network was discovered to be correlated with IDD. Throughout this investigation, a network of TF-miRNA-mRNA connections was built for investigation of the probable molecular mechanisms responsible for IDD. The identification of hub genes associated with IDD may reveal promising IDD treatment strategies.
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Affiliation(s)
- Mingli Liu
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Hao Li
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Zhenxin Huo
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Houcong Chen
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Xinjian Kang
- Graduate School, Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300211, China
| | - Baoshan Xu
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, No. 406 Jiefangnan Road, Hexi District, Tianjin, 300211, China.
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Ishaq Y, Ikram A, Alzahrani B, Khurshid S. The Role of miRNAs, circRNAs and Their Interactions in Development and Progression of Hepatocellular Carcinoma: An Insilico Approach. Genes (Basel) 2022; 14:genes14010013. [PMID: 36672755 PMCID: PMC9858589 DOI: 10.3390/genes14010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/06/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a type of malignant tumor. miRNAs are noncoding RNAs and their differential expression patterns are observed in HCC-induced by alcoholism, HBV and HCV infections. By acting as a competing endogenous RNA (ceRNA), circRNA regulates the miRNA function, indirectly controlling the gene expression and leading to HCC progression. In the present study, data mining was performed to screen out all miRNAs and circRNA involved in alcohol, HBV or HCV-induced HCC with statistically significant (≤0.05%) expression levels reported in various studies. Further, the interaction of miRNAs and circRNA was also investigated to explore their role in HCC due to various causative agents. Together, these study data provide a deeper understanding of the circRNA-miRNA regulatory mechanisms in HCC. These screened circRNA, miRNA and their interactions can be used as prognostic biomarkers or therapeutic targets for the treatment of HCC.
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Affiliation(s)
- Yasmeen Ishaq
- Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore (UOL), Lahore 54000, Pakistan
| | - Aqsa Ikram
- Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore (UOL), Lahore 54000, Pakistan
- Correspondence:
| | - Badr Alzahrani
- Department of Clinical Laboratory Sciences, Jouf University, Sakaka 42421, Saudi Arabia
| | - Sana Khurshid
- Department of Molecular Biology, Virtual University of Pakistan, 1-Davis Road, Lahore 54000, Pakistan
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Luo Y, Hu S, Yan P, Wu J, Guo H, Zhao L, Tang Q, Ma J, Long K, Jin L, Jiang A, Li M, Li X, Wang X. Analysis of mRNA and lncRNA Expression Profiles of Breast Muscle during Pigeon ( Columbalivia) Development. Genes (Basel) 2022; 13:genes13122314. [PMID: 36553580 PMCID: PMC9777807 DOI: 10.3390/genes13122314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
The breast muscle is essential for flight and determines the meat yield and quality of the meat type in pigeons. At present, studies about long non-coding RNA (lncRNA) expression profiles in skeletal muscles across the postnatal development of pigeons have not been reported. Here, we used transcriptome sequencing to examine the White-King pigeon breast muscle at four different ages (1 day, 14 days, 28 days, and 2 years old). We identified 12,918 mRNAs and 9158 lncRNAs (5492 known lncRNAs and 3666 novel lncRNAs) in the breast muscle, and 7352 mRNAs and 4494 lncRNAs were differentially expressed in the process of development. We found that highly expressed mRNAs were mainly related to cell-basic and muscle-specific functions. Differential expression and time-series analysis showed that differentially expressed genes were primarily associated with muscle development and functions, blood vessel development, cell cycle, and energy metabolism. To further predict the possible role of lncRNAs, we also conducted the WGCNA and trans/cis analyses. We found that differentially expressed lncRNAs such as lncRNA-LOC102093252, lncRNA-G12653, lncRNA-LOC110357465, lncRNA-G14790, and lncRNA-LOC110360188 might respectively target UBE2B, Pax7, AGTR2, HDAC1, Sox8 and participate in the development of the muscle. Our study provides a valuable resource for studying the lncRNAs and mRNAs of pigeon muscles and for improving the understanding of molecular mechanisms in muscle development.
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Affiliation(s)
- Yi Luo
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Silu Hu
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Peiqi Yan
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jie Wu
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongrui Guo
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Ling Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianzi Tang
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Jideng Ma
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Keren Long
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Long Jin
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Anan Jiang
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuewei Li
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (X.L.); (X.W.)
| | - Xun Wang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (X.L.); (X.W.)
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Motahari Rad H, Mowla SJ, Ramazanali F, Rezazadeh Valojerdi M. Characterization of altered microRNAs related to different phenotypes of polycystic ovarian syndrome (PCOS) in serum, follicular fluid, and cumulus cells. Taiwan J Obstet Gynecol 2022; 61:768-779. [PMID: 36088043 DOI: 10.1016/j.tjog.2022.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 10/14/2022] Open
Abstract
OBJECTIVE Polycystic ovarian syndrome (PCOS) is a metabolic syndrome in which steroidogenesis, folliculogenesis, and cellular adhesion play crucial roles in its prognosis. These pathways are controlled and regulated by some small non-coding RNAs called microRNAs (miRs). Several miRs have differential expression in PCOS compared to healthy women, and their dysregulation suggests important roles of miRs in PCOS pathophysiology. However, the role of miRs is still unclear, especially in various phenotypes of PCOS. MATERIALS AND METHODS This study was conducted to evaluate the diagnostic potential of miR-212-3p, miR-490-5p, miR-647, and miR-4643 in different subtypes of PCOS. Accordingly, nineteen PCOS patients with different subtypes based on Rotterdam criteria (A: 8, B: not detected in this study, C: 5, and D: 6 patients) and six control age and BMI matched women under ICSI treatment were selected. The relative expression of miRs was then measured in blood serum before hormonal treatment (S1) and before ovum pickup (S2), follicular fluid (FF), and cumulus cells (CC) in all subjects. Also, the expression of miRs predicted target genes (AMH, AR, CYP11A1, CYP17A1, CYP19A1, GDF9, and HSD17B12) were done in the CC of understudy groups. RESULTS In general, the results indicated that PCOS significantly increased the expression of miR-212-3p, miR-490-5p, and miR-4643 in FF and CCs compared to control. Although these miRs tend to increase in serum 1 of the PCOS patients, the differences were insignificant. However, there was a significant reduction in the expression of miR-647 in FF and CCs between PCOS vs. control. In addition, the miRs had significantly different expressions in various phenotypes of PCOS. For example, high levels of miR-647 in S2 and low levels of miR-490 in FF and miR-212 in CC can differentiate phenotype A from the other. Also, upregulation of miR-212 in FF and miR-4643 in S1 and low levels of this miR in FF can specifically differentiate subtype A from D. On the other hand, high levels of miR-4643 in FF and miR-490 in CC and lower titter of miR-647 can distinguish subtype C from the other. On the other hand, high levels of AMH, AR, CYP11, CYP17, and HSD17 in the hyperandrogenic PCOS and upregulation of CYP19A1 in the hypoandrogenic group can validate the role of selected miRs in the prognosis of PCOS. CONCLUSION Characterization of altered microRNAs in serum, FF, and CCs and their targets in CC showed that the miRs might play critical roles in steroidogenesis and folliculogenesis. These miRs may be used for molecular classification of PCOS subtypes and as biomarkers for PCOS diagnosis.
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Affiliation(s)
- Hanieh Motahari Rad
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Fariba Ramazanali
- Department of Endocrinology and Female Infertility, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Mojtaba Rezazadeh Valojerdi
- Department of Anatomy, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran; Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
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Epi-miRNAs: Regulators of the Histone Modification Machinery in Human Cancer. JOURNAL OF ONCOLOGY 2022; 2022:4889807. [PMID: 35087589 PMCID: PMC8789461 DOI: 10.1155/2022/4889807] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/14/2021] [Indexed: 12/18/2022]
Abstract
Cancer is a leading cause of death and disability worldwide. Epigenetic deregulation is one of the most critical mechanisms in carcinogenesis and can be classified into effects on DNA methylation and histone modification. MicroRNAs are small noncoding RNAs involved in fine-tuning their target genes after transcription. Various microRNAs control the expression of histone modifiers and are involved in a variety of cancers. Therefore, overexpression or downregulation of microRNAs can alter cell fate and cause malignancies. In this review, we discuss the role of microRNAs in regulating the histone modification machinery in various cancers, with a focus on the histone-modifying enzymes such as acetylases, deacetylases, methyltransferases, demethylases, kinases, phosphatases, desumoylases, ubiquitinases, and deubiquitinases. Understanding of microRNA-related aberrations underlying histone modifiers in pathogenesis of different cancers can help identify novel therapeutic targets or early detection approaches that allow better management of patients or monitoring of treatment response.
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Kakar MU, Mehboob MZ, Akram M, Shah M, Shakir Y, Ijaz HW, Aziz U, Ullah Z, Ahmad S, Ali S, Yin Y. Identification of Differentially Expressed Genes Associated with the Prognosis and Diagnosis of Hepatocellular Carcinoma by Integrated Bioinformatics Analysis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4237633. [PMID: 36317111 PMCID: PMC9617698 DOI: 10.1155/2022/4237633] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/29/2022] [Indexed: 02/05/2023]
Abstract
OBJECTIVE The goal of this study was to understand the possible core genes associated with hepatocellular carcinoma (HCC) pathogenesis and prognosis. METHODS GEO contains datasets of gene expression, miRNA, and methylation patterns of diseased and healthy/control patients. The GSE62232 dataset was selected by employing the server Gene Expression Omnibus. A total of 91 samples were collected, including 81 HCC and 10 healthy samples as control. GSE62232 was analysed through GEO2R, and Functional Enrichment Analysis was performed to extract rational information from a set of DEGs. The Protein-Protein Relationship Networking search method has been used for extracting the interacting genes. MCC method was used to calculate the top 10 genes according to their importance. Hub genes in the network were analysed using GEPIA to estimate the effect of their differential expression on cancer progression. RESULTS We identified the top 10 hub genes through CytoHubba plugin. These included BUB1, BUB1B, CCNB1, CCNA2, CCNB2, CDC20, CDK1 and MAD2L1, NCAPG, and NDC80. NCAPG and NDC80 reported for the first time in this study while the remaining from a recently reported literature. The pathogenesis of HCC may be directly linked with the aforementioned genes. In this analysis, we found critical genes for HCC that showed recommendations for future prognostic and predictive biomarkers studies that could promote selective molecular therapy for HCC.
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Affiliation(s)
- Mohib Ullah Kakar
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, School of life Sciences, Beijing Institute of Technology (BIT), Beijing 100081, China
- Faculty of Marine Sciences, Lasbela University of Agriculture, Water and Marine Sciences (LUAWMS), Uthal, Balochistan, Pakistan
| | - Muhammad Zubair Mehboob
- CAS Centre for Excellence in Biotic Interaction, College of Life Sciences, University of Chinese Academy of Science, Beijing 100049, China
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat 50700, Pakistan
| | - Muhammad Akram
- School of Science, Department of Life sciences, University of Management and Technology, Johar Town, Lahore 54770, Pakistan
| | - Muddaser Shah
- Department of Botany, Abdul Wali Khan University, Mardan 23200, Pakistan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat Al-Mauz, P.O. Box 33, Nizwa 616, Oman
| | - Yasmeen Shakir
- Department of Biochemistry, Hazara University, Mansehra, Pakistan
| | - Hafza Wajeeha Ijaz
- CAS Centre for Excellence in Biotic Interaction, College of Life Sciences, University of Chinese Academy of Science, Beijing 100049, China
| | - Ubair Aziz
- Research Centre of Molecular Simulation, National University of Science and Technology, Islamabad, Pakistan
| | - Zahid Ullah
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Sajjad Ahmad
- Faculty of Veterinary and Animal Sciences, Lasbela University of Agriculture, Water and Marine Sciences, LUAWMS, Uthal, 90150 Balochistan, Pakistan
| | - Sikandar Ali
- Dow Institute for Advanced Biological and Animal Research, Dow University of Health Sciences, Ojha Campus, Karachi, Pakistan
| | - Yongxiang Yin
- Department of Pathology, Wuxi Maternity and Child Health Hospital Affiliated to Nanjing Medical University, Wuxi, China
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Identification of key molecular markers in epithelial ovarian cancer by integrated bioinformatics analysis. Taiwan J Obstet Gynecol 2021; 60:983-994. [PMID: 34794761 DOI: 10.1016/j.tjog.2021.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE The current research was aimed to identify candidate genes associated with development and progression of epithelial ovarian carcinoma using bioinformatics analysis. MATERIALS AND METHODS We screened and validated candidate genes associated with carcinogenesis and development of epithelial ovarian carcinoma via bioinformatic analysis in three microarray datasets (GSE14407, GSE29450, and GSE54388) downloaded from the Gene Expression Omnibus (GEO) database. RESULTS Our bioinformatic analysis identified 514 differentially expressed genes (DEGs) and nine candidate hub genes (CCNB1, CDK1, BUB1, CDC20, CCNA2, BUB1B, AURKA, RRM2, and TTK). Survival analysis using the Kaplan-Meier plotter showed that high expression levels of seven candidate genes (CCNB1, RRM2, BUB1, CCNA2, AURKA, CDK1, and BUB1B) were associated with poor overall survival (OS). Gene Expression Profiling Interactive Analysis (GEPIA) revealed a higher expression level of these seven candidate genes in ovarian carcinoma samples than in normal ovarian samples. Immunostaining results from the Human Protein Atlas (HPA) database suggested that the protein expression levels of CCNB1, CCNA2, AURKA, and CDK1 were increased in ovarian cancer tissues. No difference was observed in RRM2 protein expression level between normal ovarian and ovarian cancer samples. Oncomine analysis revealed an association between the expression patterns of BUB1B, CCNA2, AURKA, CCNB1, CDK1, and BUB1 and patient clinicopathological information. Finally, six genes, namely CCNB1, CCNA2, AURKA, BUB1, BUB1B, and CDK1, were identified as hub genes and a transcription factor (TF)-gene regulatory network was constructed to identify TFs, including POLR2A, ZBTB11, KLF9, and ELF1, that were implicated in regulating these hub genes. CONCLUSION Six significant hub DEGs associated with a poor prognosis in epithelial ovarian cancer were identified. These could be potential biomarkers for ovarian cancer patients.
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MiR-490-5p Restrains Progression of Gastric cancer through DTL Repression. Gastroenterol Res Pract 2021; 2021:2894117. [PMID: 34594374 PMCID: PMC8478551 DOI: 10.1155/2021/2894117] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022] Open
Abstract
Gastric cancer (GC) accounts for a main cause of cancer-related deaths. This study sought for molecular mechanism of miR-490-5p/DTL axis in affecting GC progression, thus bringing new hope for treatment of GC. Expression data of differentially expressed miRNAs and mRNAs in GC tissue from TCGA database were analyzed. MiR-490-5p and DTL mRNA expression levels in GC were evaluated with qRT-PCR. Cell viability was confirmed with CCK-8 method. Cell cycle distribution and apoptosis were analyzed with flow cytometry. Cell migratory and invasive potential was proved with Transwell assay. The targeted relationship between DTL and miR-490-5p was analyzed with dual-luciferase assay. The results indicated a decreased miR-490-5p level in GC cells. MiR-490-5p upregulation hampered proliferation, migration, invasion and promote cell apoptosis. DTL was the target of and inversely associated with miR-490-5p, and it could remarkably induce the carcinogenesis of GC. MiR-490-5p mediated GC cell progression by DTL repression. In conclusion, miR-490-5p and DTL may be valuable in diagnosis and treatment for GC.
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Li Y, Tian D, Chen H, Cai Y, Chen S, Duan S. MicroRNA-490-3p and -490-5p in carcinogenesis: Separate or the same goal? Oncol Lett 2021; 22:678. [PMID: 34345303 PMCID: PMC8323007 DOI: 10.3892/ol.2021.12939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
MicroRNA (miR)-490-3p and miR-490-5p, located on chromosome 7q33, are two independent mature products of miR-490 exerting distinct effects on tumor progression. miR-490-3p and miR-490-5p possess antitumor properties. miR-490-3p dysfunction has been associated with malignancies including colorectal cancer, while the abnormal function of miR-490-5p has been more considerably associated with bladder cancer (for example). At present, there are 30 and 11 target genes of miR-490-3p and miR-490-5p, respectively, that have been experimentally verified, of which the cyclin D1 (CCND1) gene is a common target. Through these target genes, miR-490-3p and miR-490-5p are involved in 7 and 3 signaling pathways, respectively, of which only 2 are shared regulatory signaling pathways. The present review introduces two competing endogenous RNA (ceRNA) regulatory networks centered on miR-490-3p and miR-490-5p. These networks may be important promoters of tumor cell proliferation, invasiveness, metastatic potential and apoptosis. Unlike miR-490-5p, miR-490-3p plays a unique role in promoting cancer. However, both are promising molecular markers for early cancer diagnosis and prognosis. In addition, miR-490-3p was also found to be associated with the chemical resistance of cisplatin and paclitaxel. The present review focuses on the abnormal expression of miR-490-3p and miR-490-5p in different tumor types, and their complex ceRNA regulatory networks. The clinical value of miR-490-3p and miR-490-5p in cancer diagnosis, prognosis and treatment is also clarified, and an explanation for the opposing effects of miR-490-3p in tumor research is provided.
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Affiliation(s)
- Yin Li
- Medical Genetics Center, Ningbo University School of Medicine, Ningbo, Zhejiang 315211, P.R. China
| | - Dongmei Tian
- Medical Genetics Center, Ningbo University School of Medicine, Ningbo, Zhejiang 315211, P.R. China
| | - Hao Chen
- Medical Genetics Center, Ningbo University School of Medicine, Ningbo, Zhejiang 315211, P.R. China
| | - Yuanting Cai
- Medical Genetics Center, Ningbo University School of Medicine, Ningbo, Zhejiang 315211, P.R. China
| | - Sang Chen
- Medical Genetics Center, Ningbo University School of Medicine, Ningbo, Zhejiang 315211, P.R. China
| | - Shiwei Duan
- Medical Genetics Center, Ningbo University School of Medicine, Ningbo, Zhejiang 315211, P.R. China.,School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang 310015, P.R. China
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11
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Jin W, Ye L. KIF4A knockdown suppresses ovarian cancer cell proliferation and induces apoptosis by downregulating BUB1 expression. Mol Med Rep 2021; 24:516. [PMID: 34013367 PMCID: PMC8160479 DOI: 10.3892/mmr.2021.12155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Ovarian cancer is one of the most common lethal gynecological malignancies worldwide. Abnormal kinesin family member 4A (KIF4A) expression has been implicated in ovarian cancer progression; however, the potential mechanism underlying KIF4A in ovarian cancer is not completely understood. The present study aimed to clarify the molecular basis of KIF4A in ovarian cancer. KIF4A and budding uninhibited by benzimidazoles 1 (BUB1) expression levels were detected via reverse transcription-quantitative PCR and western blotting. Cell Counting Kit-8, colony formation, wound healing, TUNEL and flow cytometry assays were performed to assess cell proliferation, migration, apoptosis and cell cycle distribution, respectively. Ki67 expression levels were detected by conducting immunofluorescence assays. The expression levels of migration- and apoptosis-related proteins were measured via western blotting. A co-immunoprecipitation assay was conducted to determine the association between KIF4A and BUB1. The results demonstrated that KIF4A was expressed at significantly higher levels in ovarian cancer cell lines compared with IOSE-80 cells. Compared with the short hairpin RNA-negative control group, KIF4A knockdown significantly inhibited cell viability, colony formation and migration, and markedly induced cell apoptosis. The results indicated that KIF4A could bind to BUB1 and regulate BUB1 expression. BUB1 overexpression weakened KIF4A knockdown-mediated effects on cell viability, colony formation, migration and apoptosis. Overall, the present study demonstrated that KIF4A knockdown suppressed ovarian cancer progression by regulating BUB1, and suggested the potential value of KIF4A and BUB1 as therapeutic targets for ovarian cancer.
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Affiliation(s)
- Wumin Jin
- Reproductive Medicine Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Lianmin Ye
- Department of Intensive Care Unit, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
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12
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HCV Proteins Modulate the Host Cell miRNA Expression Contributing to Hepatitis C Pathogenesis and Hepatocellular Carcinoma Development. Cancers (Basel) 2021; 13:cancers13102485. [PMID: 34069740 PMCID: PMC8161081 DOI: 10.3390/cancers13102485] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary According to the last estimate by the World Health Organization (WHO), more than 71 million individuals have chronic hepatitis C worldwide. The persistence of HCV infection leads to chronic hepatitis, which can evolve into liver cirrhosis and ultimately into hepatocellular carcinoma (HCC). Although the pathogenic mechanisms are not fully understood, it is well established that an interplay between host cell factors, including microRNAs (miRNA), and viral components exist in all the phases of the viral infection and replication. Those interactions establish a complex equilibrium between host cells and HCV and participate in multiple mechanisms characterizing hepatitis C pathogenesis. The present review aims to describe the role of HCV structural and non-structural proteins in the modulation of cellular miRNA during HCV infection and pathogenesis. Abstract Hepatitis C virus (HCV) genome encodes for one long polyprotein that is processed by cellular and viral proteases to generate 10 polypeptides. The viral structural proteins include the core protein, and the envelope glycoproteins E1 and E2, present at the surface of HCV particles. Non-structural (NS) proteins consist of NS1, NS2, NS3, NS4A, NS4B, NS5a, and NS5b and have a variable function in HCV RNA replication and particle assembly. Recent findings evidenced the capacity of HCV virus to modulate host cell factors to create a favorable environment for replication. Indeed, increasing evidence has indicated that the presence of HCV is significantly associated with aberrant miRNA expression in host cells, and HCV structural and non-structural proteins may be responsible for these alterations. In this review, we summarize the recent findings on the role of HCV structural and non-structural proteins in the modulation of host cell miRNAs, with a focus on the molecular mechanisms responsible for the cell re-programming involved in viral replication, immune system escape, as well as the oncogenic process. In this regard, structural and non-structural proteins have been shown to modulate the expression of several onco-miRNAs or tumor suppressor miRNAs.
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13
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Ding L, Ning J, Wang Q, Lu B, Ke H. Retracted: Sevoflurane improves nerve regeneration and repair of neurological deficit in brain damage rats via microRNA-490-5p/CDK1 axis. Life Sci 2021; 271:119111. [PMID: 33513398 DOI: 10.1016/j.lfs.2021.119111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/16/2021] [Accepted: 01/19/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Sevoflurane (Sevo) is neuroprotective in brain damage, thus our objective was to further investigate the impact of Sevo treatment on nerve regeneration and repair of neurological deficit in brain damage rats by regulating miR-490-5p and cyclin-dependent kinases 1 (CDK1). METHODS The rat middle cerebral artery occlusion model was established. miR-490-5p and CDK1 levels in brain tissues were tested. The behavioral changes, the number of glial fibrillary acidic protein (GFAP) positive cells, ionized calcium-binding adapter molecule-1 (Iba-1) and Nestin mRNA expression, the survival and apoptosis of neurons in peripheral tissues of infarct areas were detected by a series of assays. Furthermore, the target relationship between miR-490-5p and CDK1 was verified. RESULTS miR-490-5p was reduced and CDK1 was raised in brain tissues of brain damage rats. Sevo raised miR-490-5p and decreased CDK1 to improve neurological deficits, reduce apoptotic neurons, suppress expression levels of GFAP and Iba-1, and increase Nestin expression and the number of surviving neurons in peripheral tissue in infarct area, and alleviate the pathological changes of brain tissues of brain damage rats. CDK1 was negatively regulated by miR-490-5p. CONCLUSION Our study presents that Sevo treatment is involved in neurogenesis and repair of neurological deficit of brain damage rats via up-regulating miR-490-5p and inhibiting CDK1.
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Affiliation(s)
- Lingling Ding
- Department of Anesthesiology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China.
| | - Jiaqi Ning
- Department of Anesthesiology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China
| | - Qi Wang
- Department of Anesthesiology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China
| | - Bin Lu
- Department of Anesthesiology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China
| | - Hai Ke
- Department of Anesthesiology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, China
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14
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Cheng C, Wu X, Shen Y, Li Q. KIF14 and KIF23 Promote Cell Proliferation and Chemoresistance in HCC Cells, and Predict Worse Prognosis of Patients with HCC. Cancer Manag Res 2020; 12:13241-13257. [PMID: 33380832 PMCID: PMC7767722 DOI: 10.2147/cmar.s285367] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most common human malignant tumors. The prognosis of HCC patients is still unsatisfying. In this study, we performed the integrated bioinformatics analysis to identify potential biomarkers and biological pathways in HCC. Methods Gene expression profiles were obtained from the Gene Expression Omnibus database (GSE55048, GSE55758, and GSE56545) for the screening of the common differentially expressed genes (DEGs) between HCC tissues and matched non-tumor tissues. DEGs were subjected to Gene Ontology, KEGG pathway, and Reactome pathway analysis. The hub genes were identified by using protein–protein interaction (PPI) network analysis. The hub genes in HCC were further subjected to overall survival analysis of HCC patients. The hub genes were further validated by in vitro functional assays. Results A total of 544 common differentially expressed genes were screened from three datasets. Gene Ontology, KEGG and Reactome analysis results showed that DEGs are significantly associated with the biological process of cell cycle, cell division, and DNA replication. PPI network analysis identified 20 hub genes from the DEGs. These hub genes except CENPE were all significantly up-regulated in the HCC tissues when compared to non-tumor tissues. The Kaplan–Meier survival analysis results showed that the high expression of the 20 hub genes was associated with shorter survival of the HCC patients. Further validation studies showed that knockdown of KIF14 and KIF23 both suppressed the proliferative potential, increased the caspase-3/-7 activity, up-regulated Bax expression, and promoted the invasive and migratory abilities in the HCC cells. In addition, knockdown of KIF14 and KIF23 enhanced chemosensitivity to cisplatin and sorafenib in the HCC cells. Finally, the high expression of KIF14 and KIF23 was associated with shorter progression-free survival, recurrence-free survival, and disease-specific survival of patients with HCC. Conclusion In conclusion, the present study performed the integrated bioinformatics analysis and showed that KIF14 and KIF23 silence attenuated cell proliferation, invasion, and migration, and promoted chemosensitivity of HCC cells. KIF14 and KIF23 may serve as potential biomarkers for predicting the worse prognosis of patients with HCC.
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Affiliation(s)
- Chunxia Cheng
- Department of Hepatobiliary Surgery, The Second People's Hospital of Lianyungang, Liangyungang City 222023, People's Republic of China
| | - Xingxing Wu
- Deparment of Pediatric Surgery, The Second People's Hospital of Lianyungang, Liangyungang City 222023, People's Republic of China
| | - Yu Shen
- Department of Hepatobiliary Surgery, The Second People's Hospital of Lianyungang, Liangyungang City 222023, People's Republic of China
| | - Quanxi Li
- Department of Hepatobiliary Surgery, The Second People's Hospital of Lianyungang, Liangyungang City 222023, People's Republic of China
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15
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Guo R, Chu A, Gong Y. Identification of cancer stem cell-related biomarkers in intestinal-type and diffuse-type gastric cancer by stemness index and weighted correlation network analysis. J Transl Med 2020; 18:418. [PMID: 33160391 PMCID: PMC7648412 DOI: 10.1186/s12967-020-02587-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022] Open
Abstract
Background Cancer stem cells (CSCs) play an important role in drug resistance, recurrence, and metastasis of tumors. Considering the heterogeneity of tumors, this study aimed to explore the key genes regulating stem cells in intestinal-type and diffuse-type gastric cancer. Methods RNA-seq data and related clinical information were downloaded from The Cancer Genome Atlas (TCGA). WGCNA was used to clustered differentially expressed genes with similar expression profiles to form modules. Furtherly, based on the mRNA expression-based stemness index (mRNAsi), significant modules and key genes were identified. Next, the expression of key genes was further verified by the Oncomine database. Results MRNAsi scores of GC were significantly higher than that of normal tissue. Additionally, mRNAsi scores of intestinal-type GC (IGC) were significantly higher than that of diffuse-type GC (DGC). WGCNA showed that the blue module of IGC and the brown module of DGC were both the most significantly associated with mRNAsi. We screened out 16 and 43 key genes for IGC and DGC and found that these genes were closely related, respectively. Functional analysis showed the relationship between the key genes confirmed in the Oncomine database and the fate of cells. Conclusions In this study, 16 and 43 genes related to the characteristics of CSCs were identified in IGC and DGC, respectively. These genes were both associated with cell cycle, which could serve as therapeutic targets for the inhibition of stem cells from both types of GC.
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Affiliation(s)
- Rui Guo
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, Liaoning Province, The First Hospital of China Medical University, No.155 NanjingBei Street, Heping District, Shenyang, 110001, P.R. China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Aining Chu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, Liaoning Province, The First Hospital of China Medical University, No.155 NanjingBei Street, Heping District, Shenyang, 110001, P.R. China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Yuehua Gong
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, Liaoning Province, The First Hospital of China Medical University, No.155 NanjingBei Street, Heping District, Shenyang, 110001, P.R. China. .,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China. .,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China.
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16
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Vinchure OS, Kulshreshtha R. miR-490: A potential biomarker and therapeutic target in cancer and other diseases. J Cell Physiol 2020; 236:3178-3193. [PMID: 33094503 DOI: 10.1002/jcp.30119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/26/2020] [Accepted: 10/10/2020] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that function as posttranscriptional gene regulators. Among a pool of >2600 known human mature miRNAs, only a small subset have been functionally interrogated and a further smaller pool shown to be associated with the pathogenesis of a variety of diseases suggesting their critical role in maintaining homeostasis. Here, we draw your attention to one such miRNA, miR-490, that has been reported to be deregulated in a myriad of diseases (23 diseases) ranging from cardiomyopathy, depression, and developmental disorders to many cancer types (28 cancer types), such as hepatocellular carcinoma, gastric cancer, cancers of the reproductive and central nervous system among others. The prognostic and diagnostic potential of miR-490 has been reported in many diseases including cancer underlining its clinical relevance. We also collate a complex plethora of epigenetic (histone and DNA methylation), transcriptional (TF), and posttranscriptional (lncRNA and circRNA) mechanisms that have been shown to tightly regulate miR-490 levels. The targets of miR-490 involve a range of cancer-related genes involved in the regulation of various cancer hallmarks like cell proliferation, migration, and invasion, apoptotic cell death, angiogenesis, and so forth. Overall, our in-depth review highlights for the first time the emerging role of miR-490 in disease pathology, diagnosis, and prognosis that assigns a unique therapeutic potential to miR-490 in the era of precision medicine.
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Affiliation(s)
- Omkar Suhas Vinchure
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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17
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Wei R, Wang Z, Zhang Y, Wang B, Shen N, E L, Li X, Shang L, Shang Y, Yan W, Zhang X, Ma W, Wang C. Bioinformatic analysis revealing mitotic spindle assembly regulated NDC80 and MAD2L1 as prognostic biomarkers in non-small cell lung cancer development. BMC Med Genomics 2020; 13:112. [PMID: 32795325 PMCID: PMC7437940 DOI: 10.1186/s12920-020-00762-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 08/04/2020] [Indexed: 01/08/2023] Open
Abstract
Background Lung cancer has been the leading cause of tumor related death, and 80% ~ 85% of it is non-small cell lung cancer (NSCLC). Even with the rising molecular targeted therapies, for example EGFR, ROS1 and ALK, the treatment is still challenging. The study is to identify credible responsible genes during the development of NSCLC using bioinformatic analysis, developing new prognostic biomarkers and potential gene targets to the disease. Methods Firstly, three genes expression profiles GSE44077, GSE18842 and GSE33532 were picked from Gene Expression Omnibus (GEO) to analyze the genes with different expression level (GDEs) between NSCLC and normal lung samples, and the cellular location, molecular function and the biology pathways the GDEs enriched in were analyzed. Then, gene function modules of GDEs were explored based on the protein-protein interaction network (PPI), and the top module which contains most genes was identified, followed by containing genes annotation and survival analysis. Moreover, multivariate cox regression analysis was performed in addition to the Kaplan meier survival to narrow down the key genes scale. Further, the clinical pathological features of the picked key genes were explored using TCGA data. Results Three GEO profiles shared a total of 664 GDEs, including 232 up-regulated and 432 down-regulated genes. Based on the GDEs PPI network, the top function module containing a total of 69 genes was identified, and 31 of 69 genes were mitotic cell cycle regulation related. And survival analysis of the 31 genes revealed that 17/31 genes statistical significantly related to NSCLC overall survival, including 4 spindle assembly checkpoints, namely NDC80, BUB1B, MAD2L1 and AURKA. Further, multivariate cox regression analysis identified NDC80 and MAD2L1 as independent prognostic indicators in lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) respectively. Interestingly, pearson correlation analysis indicated strong connection between the four genes NDC80, BUB1B, MAD2L1 and AURKA, and their clinical pathological features were addressed. Conclusions Using bioinformatic analysis of GEO combined with TCGA data, we revealed two independent prognostic indicators in LUAD and LUSC respectively and analyzed their clinical features. However, more detailed experiments and clinical trials are needed to verify their drug targets role in clinical medical use.
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Affiliation(s)
- Rong Wei
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Ziyue Wang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Yaping Zhang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Bin Wang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Ningning Shen
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Li E
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Xin Li
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Lifang Shang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Yangwei Shang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Wenpeng Yan
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Xiaoqin Zhang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Wenxia Ma
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China.
| | - Chen Wang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China.
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18
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Gong DY, Chen X, Yang TL, Wang Y, Guo Y, Zeng JH, Chen SZ. Upregulation of ECT2 is associated with transcriptional program of cancer stem cells and predicts poor clinical outcome in gastric cancer. Oncol Lett 2020; 20:54. [PMID: 32788941 PMCID: PMC7416382 DOI: 10.3892/ol.2020.11915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 07/02/2020] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer remains the third leading cause of cancer-associated mortality worldwide. The identification of prognostic indicators that are associated with clinical characteristics is urgently required. The aim of the present study was to determine the involvement of epithelial cell transforming 2 (ECT2) in gastric cancer. The results of the present study demonstrated that ECT2 expression was upregulated in human gastric cancer samples. Furthermore, high ECT2 expression was associated with advanced Tumor-Node-Metastasis stage and deeper tumor invasion. ECT2 upregulation was further confirmed in several independent publicly available clinical cohorts from the Gene Expression Omnibus database. In addition, patients with gastric cancer, with high ECT2 expression exhibited a significantly shorter overall survival time than those with low ECT2 expression, and Cox regression analysis demonstrated that ECT2 expression was an independent prognostic marker for overall survival time. Characterization of the transcriptome profiles of ECT2 upregulated gastric tumors indicated that ECT2 upregulation may be associated with transcriptional features of cancer stem cells (CSCs). Additionally, BUB1 mitotic checkpoint serine/threonine kinase and E2F transcription factor 7, two genes previously reported to account for the functionality of CSCs, were strongly enriched in ECT2High gastric cancer samples. Taken together, the results of the present study suggest that ECT2 may serve as a novel marker for CSCs and may be a potential prognostic indicator in gastric cancer.
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Affiliation(s)
- Dao-Yin Gong
- Department of Pathology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610072, P.R. China
| | - Xian Chen
- Department of Pathology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610072, P.R. China
| | - Tian-Lin Yang
- Department of Pathology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610072, P.R. China
| | - Yi Wang
- Department of Pathology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610072, P.R. China
| | - Yu Guo
- Geriatric Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610072, P.R. China
| | - Jin-Hao Zeng
- Geriatric Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610072, P.R. China
| | - Shan-Ze Chen
- Department of Pathyphysiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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19
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Zhang H, Chu K, Zheng C, Ren L, Tian R. Pseudogene DUXAP8 Promotes Cell Proliferation and Migration of Hepatocellular Carcinoma by Sponging MiR-490-5p to Induce BUB1 Expression. Front Genet 2020; 11:666. [PMID: 32849765 PMCID: PMC7396656 DOI: 10.3389/fgene.2020.00666] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 06/01/2020] [Indexed: 01/08/2023] Open
Abstract
Hepatocellular Carcinoma (HCC) currently remains one of the most lethal malignancies worldwide. Recently, long non-coding RNAs (lncRNAs) had been demonstrated to play a crucial role in the progression of multiple human cancers, including HCC. In this study, we found that lncRNA DUXAP8 was upregulated in tumor samples and served as an oncogene in HCC. Bioinformatics analysis showed that DUXAP8 was significantly associated with the regulation of centrosome organization, homologous recombination, meiotic cell cycle process, sister chromatid segregation, nuclear chromosome segregation, and RNA export from the nucleus. The knockdown of DUXAP8 significantly suppresses cell proliferation and the cell cycle but induces cell apoptosis in HCC. Mechanically, the present study showed that DUXAP8 serves as a sponge of MiR-490-5p to promote the expression of BUB1 in HCC. Although the underlying regulatory mechanisms of DUXAP8 in HCC require further investigation, this study, for the first time, showed that DUXAP8 can serve as a new therapeutic target for HCC.
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Affiliation(s)
- Haiping Zhang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Kaiqiu Chu
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chunxi Zheng
- Department of Clinical Laboratory, Qingdao Women and Children's Hospital, Qingdao, China
| | - Lisheng Ren
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Runhua Tian
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
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20
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Liu W, Yin C, Liu Y. Circular RNA circ_0091579 Promotes Hepatocellular Carcinoma Proliferation, Migration, Invasion, and Glycolysis Through miR-490-5p/CASC3 Axis. Cancer Biother Radiopharm 2020; 36:863-878. [PMID: 32673066 DOI: 10.1089/cbr.2019.3472] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is one of the most common malignancies with high invasion and metastasis capacities. Circular RNAs (circRNAs) were evidenced to take part in the progression of multifarious cancers, including HCC. However, the role of circ_0091579 in HCC progression has not been fully described. This study aimed to explore the function of circ_0091579 and its potential regulatory mechanism in the progression of HCC. Materials and Methods: The expression of circ_0091579, microRNA-490-5p (miR-490-5p), and cancer susceptibility candidate 3 (CASC3) in HCC tissues and cells was detected by quantitative real-time polymerase chain reaction. The circular characteristic and stability of circ_0091579 were verified by RNase R digestion and actinomycin D reaction assays. Cell proliferation, migration, and invasion were determined by methyl thiazolyl tetrazolium assay and Transwell assay, respectively. The level of glycolysis was evaluated by glucose consumption and lactate production. The levels of proteins were examined by Western blot. The interaction between miR-490-5p and circ_0091579 or CASC3 was certified by Dual-luciferase reporter assay. Results: circ_0091579 and CASC3 were upregulated, while miR-490-5p was downregulated in HCC tissues and cells. Silencing of either circ_0091579 or CASC3 suppressed cell proliferation, migration, invasion, and glycolysis in HCC cells. Moreover, miR-490-5p was verified to directly bind to circ_0091579 and CASC3. Circ_0091579 upregulated CASC3 by sponging miR-490-5p in HCC cells to promote cell proliferation, invasion, and migration. Conclusion: circ_0091579 promoted cell proliferation, migration, invasion, and glycolysis partially through miR-490-5p/CASC3 axis in HCC cells.
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Affiliation(s)
- Wei Liu
- Department of Laboratory, Luhe Hospital Affiliated to Capital Medical University, Beijing, China
| | - Changbin Yin
- Department of Laboratory, Luhe Hospital Affiliated to Capital Medical University, Beijing, China
| | - Yue Liu
- Department of Research and Development Center, DAAN Gene Co., Ltd. of Sun Yat-Sen University, Guangzhou, China
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21
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Identification of Glioma Cancer Stem Cell Characteristics Based on Weighted Gene Prognosis Module Co-Expression Network Analysis of Transcriptome Data Stemness Indices. J Mol Neurosci 2020; 70:1512-1520. [PMID: 32451841 DOI: 10.1007/s12031-020-01590-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/13/2020] [Indexed: 12/27/2022]
Abstract
Glioma is the most common primary brain tumor in humans and the most deadly. Stem cells, which are characterized by therapeutic resistance and self-renewal, play a critical role in glioma, and therefore the identification of stem cell-related genes in glioma is important. In this study, we collected and evaluated the epigenetically regulated-mRNA expression-based stemness index (EREG-mRNAsi) of The Cancer Genome Atlas (TCGA, http://www.ncbi.nlm.nih.gov/ ) for glioma patient samples, corrected through tumor purity. After EREG-mRNAsi correction, glioma pathological grade and survival were analyzed. The differentially expressed gene (DEG) co-expression network was constructed by weighted gene co-expression network analysis (WGCNA) in TCGA glioma samples to find modules of interest and key genes. Gene ontology (GO) and pathway-enrichment analysis were performed to identify the function of significant genetic modules. Protein-protein interaction (PPI) and co-expression network analysis of key genes was performed for further analysis. In this experiment, we found that corrected EREG-mRNAsi was significantly up-regulated in glioma samples and increased with glioma grade, with G4 having the highest stemness index. Patients with higher corrected EREG-mRNAsi scores had worse overall survival. Fifty-one DEGs in the brown gene module were found to be positively related to EREG-mRNAsi via WGCNA. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that chromosome segregation and cell cycle molecular function were the major functions in key DEGs. Among these key DEGs, BUB1 showed high connectivity and co-expression, and also high connectivity in PPI. Fifty-one key genes were verified to play a critical role in glioma stem cells. These genes may serve as primary therapeutic targets to inhibit the activity of glioma stem cells.
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Zhang L, Makamure J, Zhao D, Liu Y, Guo X, Zheng C, Liang B. Bioinformatics analysis reveals meaningful markers and outcome predictors in HBV-associated hepatocellular carcinoma. Exp Ther Med 2020; 20:427-435. [PMID: 32537007 PMCID: PMC7281962 DOI: 10.3892/etm.2020.8722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 12/05/2019] [Indexed: 12/18/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common type of malignant neoplasm of the liver with high morbidity and mortality. Extensive research into the pathology of HCC has been performed; however, the molecular mechanisms underlying the development of hepatitis B virus-associated HCC have remained elusive. Thus, the present study aimed to identify critical genes and pathways associated with the development and progression of HCC. The expression profiles of the GSE121248 dataset were downloaded from the Gene Expression Omnibus database and the differentially expressed genes (DEGs) were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) analyses were performed by using the Database for Annotation, Visualization and Integrated Discovery. Subsequently, protein-protein interaction (PPI) networks were constructed for detecting hub genes. In the present study, 1,153 DEGs (777 upregulated and 376 downregulated genes) were identified and the PPI network yielded 15 hub genes. GO analysis revealed that the DEGs were primarily enriched in ‘protein binding’, ‘cytoplasm’ and ‘extracellular exosome’. KEGG analysis indicated that DEGs were accumulated in ‘metabolic pathways’, ‘chemical carcinogenesis’ and ‘fatty acid degradation’. After constructing the PPI network, cyclin-dependent kinase 1, cyclin B1, cyclin A2, mitotic arrest deficient 2 like 1, cyclin B2, DNA topoisomerase IIα, budding uninhibited by benzimidazoles (BUB)1, TTK protein kinase, non-SMC condensin I complex subunit G, NDC80 kinetochore complex component, aurora kinase A, kinesin family member 11, cell division cycle 20, BUB1B and abnormal spindle microtubule assembly were identified as hub genes based on the high degree of connectivity by using Cytoscape software. In addition, overall survival (OS) and disease-free survival (DFS) analyses were performed using the Gene Expression Profiling Interactive Analysis online database, which revealed that the increased expression of all hub genes were associated with poorer OS and DFS outcomes. Receiver operating characteristic curves were constructed using GraphPad prism 7.0 software. The results confirmed that 15 hub genes were able to distinguish HCC form normal tissues. Furthermore, the expression levels of three key genes were analyzed in tumor and normal samples of the Human Protein Atlas database. The present results may provide further insight into the underlying mechanisms of HCC and potential therapeutic targets for the treatment of this disease.
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Affiliation(s)
- Lijie Zhang
- Department of Radiology, Hubei Key Laboratory of Molecular Imaging, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Joyman Makamure
- Department of Radiology, Hubei Key Laboratory of Molecular Imaging, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Dan Zhao
- Department of Radiology, Hubei Key Laboratory of Molecular Imaging, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Yiming Liu
- Department of Radiology, Hubei Key Laboratory of Molecular Imaging, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xiaopeng Guo
- Department of Radiology, Hubei Key Laboratory of Molecular Imaging, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Chuansheng Zheng
- Department of Radiology, Hubei Key Laboratory of Molecular Imaging, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Bin Liang
- Department of Radiology, Hubei Key Laboratory of Molecular Imaging, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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Guo Q, Ke XX, Liu Z, Gao WL, Fang SX, Chen C, Song YX, Han H, Lu HL, Xu G. Evaluation of the Prognostic Value of STEAP1 in Lung Adenocarcinoma and Insights Into Its Potential Molecular Pathways via Bioinformatic Analysis. Front Genet 2020; 11:242. [PMID: 32265985 PMCID: PMC7099762 DOI: 10.3389/fgene.2020.00242] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/28/2020] [Indexed: 12/19/2022] Open
Abstract
Background Upregulation of the six-transmembrane epithelial antigen of prostate-1 (STEAP1) is closely associated with prognosis of numerous malignant cancers. However, its role in lung adenocarcinoma (LUAD), the most common type of lung cancer, remains unknown. This study aimed to investigate the role of STEAP1 in the occurrence and progression of LUAD and the potential mechanisms underlying its regulatory effects. Methods STEAP1 mRNA and protein expression were analyzed in 40 LUAD patients via real-time PCR and western blotting, respectively. We accessed the clinical data of 522 LUAD patients from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) to investigate the expression and prognostic role of STEAP1 in LUAD. Further, we performed gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and gene set enrichment analysis (GSEA) to elucidate the potential mechanism underlying the role of STEAP1 in LUAD. The protein-protein interaction (PPI) network of STEAP1 was analyzed using the Search Tool for the Retrieval of Interacting Genes (STRING) database, and hub genes with significant positive and negative associations with STEAP1 were identified and their role in LUAD prognosis was predicted. Results STEAP1 was significantly upregulated in LUAD patients and associated with LUAD prognosis. Further, TCGA data indicated that STEAP1 upregulation is correlated with the clinical prognosis of LUAD. GO and KEGG analysis revealed that the genes co-expressed with STEAP1 were primarily involved in cell division, DNA replication, cell cycle, apoptosis, cytokine signaling, NF-kB signaling, and TNF signaling. GSEA revealed that homologous recombination, p53 signaling pathway, cell cycle, DNA replication, apoptosis, and toll-like receptor signaling were highly enriched upon STEAP1 upregulation. Gene Expression Profiling Interactive Analysis (GEPIA) analysis revealed that the top 10 hub genes associated with STEAP1 expression were also associated with the LUAD prognosis. Conclusion STEAP1 upregulation potentially influences the occurrence and progression of LUAD and its co-expressed genes via regulation of homologous recombination, p53 signaling, cell cycle, DNA replication, and apoptosis. STEAP1 is a potential prognostic biomarker for LUAD.
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Affiliation(s)
- Qiang Guo
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xi-Xian Ke
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zhou Liu
- Department of Cardiac Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Wei-Long Gao
- Department of Cardiac Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Shi-Xu Fang
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Cheng Chen
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yong-Xiang Song
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Hao Han
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Hong-Ling Lu
- Department of Biochemistry, Zunyi Medical University, Zunyi, China
| | - Gang Xu
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
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Identification of the Differentially Expressed Genes of Muscle Growth and Intramuscular Fat Metabolism in the Development Stage of Yellow Broilers. Genes (Basel) 2020; 11:genes11030244. [PMID: 32110997 PMCID: PMC7140879 DOI: 10.3390/genes11030244] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/10/2020] [Accepted: 02/20/2020] [Indexed: 02/04/2023] Open
Abstract
High-quality chicken meat is an important source of animal protein for humans. Gene expression profiles in breast muscle tissue were determined, aiming to explore the common regulatory genes relevant to muscle and intramuscular fat (IMF) during the developmental stage in chickens. Results show that breast muscle weight (BMW), breast meat percentage (BMP, %), and IMF (%) continuously increased with development. A total of 256 common differentially expressed genes (DEGs) during the developmental stage were screened. Among them, some genes related to muscle fiber hypertrophy were upregulated (e.g., CSRP3, LMOD2, MUSTN1, MYBPC1), but others (e.g., ACTC1, MYL1, MYL4) were downregulated from Week 3 to Week 18. During this period, expression of some DEGs related to the cells cycle (e.g., CCNB3, CCNE2, CDC20, MCM2) changed in a way that genetically suggests possible inhibitory regulation on cells number. In addition, DEGs associated with energy metabolism (e.g., ACOT9, CETP, LPIN1, DGAT2, RBP7, FBP1, PHKA1) were found to regulate IMF deposition. Our data identified and provide new insights into the common regulatory genes related to muscle growth, cell proliferation, and energy metabolism at the developmental stage in chickens.
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Wang J, Zhang X, Yao H, Le Y, Zhou W, Li J, Lu L, Chen M, Li X. MiR-490-5p functions as tumor suppressor in childhood neuroblastoma by targeting MYEOV. Hum Cell 2020; 33:261-271. [DOI: 10.1007/s13577-019-00302-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/11/2019] [Indexed: 12/24/2022]
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Zeng L, Fan X, Wang X, Deng H, Zhang K, Zhang X, He S, Li N, Han Q, Liu Z. Bioinformatics Analysis based on Multiple Databases Identifies Hub Genes Associated with Hepatocellular Carcinoma. Curr Genomics 2019; 20:349-361. [PMID: 32476992 PMCID: PMC7235396 DOI: 10.2174/1389202920666191011092410] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 08/27/2019] [Accepted: 08/30/2019] [Indexed: 02/07/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the most common liver cancer and the mechanisms of hepatocarcinogenesis remain elusive. Objective This study aims to mine hub genes associated with HCC using multiple databases. Methods Data sets GSE45267, GSE60502, GSE74656 were downloaded from GEO database. Differentially expressed genes (DEGs) between HCC and control in each set were identified by limma software. The GO term and KEGG pathway enrichment of the DEGs aggregated in the datasets (aggregated DEGs) were analyzed using DAVID and KOBAS 3.0 databases. Protein-protein interaction (PPI) network of the aggregated DEGs was constructed using STRING database. GSEA software was used to verify the biological process. Association between hub genes and HCC prognosis was analyzed using patients' information from TCGA database by survminer R package. Results From GSE45267, GSE60502 and GSE74656, 7583, 2349, and 553 DEGs were identified respectively. A total of 221 aggregated DEGs, which were mainly enriched in 109 GO terms and 29 KEGG pathways, were identified. Cell cycle phase, mitotic cell cycle, cell division, nuclear division and mitosis were the most significant GO terms. Metabolic pathways, cell cycle, chemical carcinogenesis, retinol metabolism and fatty acid degradation were the main KEGG pathways. Nine hub genes (TOP2A, NDC80, CDK1, CCNB1, KIF11, BUB1, CCNB2, CCNA2 and TTK) were selected by PPI network and all of them were associated with prognosis of HCC patients. Conclusion TOP2A, NDC80, CDK1, CCNB1, KIF11, BUB1, CCNB2, CCNA2 and TTK were hub genes in HCC, which may be potential biomarkers of HCC and targets of HCC therapy.
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Affiliation(s)
- Lu Zeng
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, P.R. China.,Xi'an Medical University, Xi'an 710021, Shaanxi Province, P.R. China
| | - Xiude Fan
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, P.R. China
| | - Xiaoyun Wang
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, P.R. China
| | - Huan Deng
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, P.R. China
| | - Kun Zhang
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, P.R. China
| | - Xiaoge Zhang
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, P.R. China
| | - Shan He
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, P.R. China.,Xi'an Medical University, Xi'an 710021, Shaanxi Province, P.R. China
| | - Na Li
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, P.R. China
| | - Qunying Han
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, P.R. China
| | - Zhengwen Liu
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, P.R. China
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Xu CY, Dong JF, Chen ZQ, Ding GS, Fu ZR. MiR-942-3p Promotes the Proliferation and Invasion of Hepatocellular Carcinoma Cells by Targeting MBL2. Cancer Control 2019; 26:1073274819846593. [PMID: 31046434 PMCID: PMC6501494 DOI: 10.1177/1073274819846593] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs (miRNAs), a subgroup of small noncoding RNAs, play critical roles in tumor growth and metastasis. Accumulating evidence shows that the dysregulation of miRNAs is associated with the progression of hepatocellular carcinoma (HCC). However, the molecular mechanism by which miR-942-3p contributes to HCC remains undocumented. The association between miR-942-3p expression and the clinicopathological characteristics in HCC patients was analyzed by The Cancer Genome Atlas data set. The targets of miR-942-3p were identified by bioinformatic analysis and dual luciferase report assay. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and Transwell assays were performed to assess the functional role of miR-942-3p in HCC cells. Consequently, we found that miR-942-3p expression level was elevated in HCC tissues and cell lines as compared with the normal tissues and was associated with the pathological stage and tumor node metastasis (TNM) stage, acting as an independent prognostic factor of poor survival in patients with HCC. Ectopic expression of miR-942-3p enhanced the proliferation and invasive potential of HCC cells, but inhibition of miR-942-3p expression had the opposite effects. Mannose-binding lectin 2 (MBL2) was further identified as a direct target of miR-942-3p and possessed a negative correlation with miR-942-3p expression and unfavorable survival in patients with HCC. Restoration of MBL2 inhibited the progression of HCC cells and attenuated the tumor-promoting effects induced by miR-942-3p. In conclusion, miR-942-3p may act as an oncogenic factor in HCC cells by targeting MBL2 and provide a potential marker for patients with HCC.
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Affiliation(s)
- Chun-Yang Xu
- 1 Department of Organ Transplantation, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Jun-Feng Dong
- 1 Department of Organ Transplantation, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zi-Qi Chen
- 1 Department of Organ Transplantation, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Guo-Shan Ding
- 1 Department of Organ Transplantation, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhi-Ren Fu
- 1 Department of Organ Transplantation, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
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Zhang L, Gao X, Zhou X, Qin Z, Wang Y, Li R, Tang M, Wang W, Zhang W. Identification of key genes and microRNAs involved in kidney Wilms tumor by integrated bioinformatics analysis. Exp Ther Med 2019; 18:2554-2564. [PMID: 31555364 PMCID: PMC6755433 DOI: 10.3892/etm.2019.7870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 06/27/2019] [Indexed: 12/11/2022] Open
Abstract
Wilms tumor (WT) is one of the most common types of pediatric solid tumors; however, its molecular mechanisms remain unclear. The present study aimed to identify key genes and microRNAs (miRNAs), and to predict the underlying molecular mechanisms of WT using integrated bioinformatics analysis. Original gene expression profiles were downloaded from the Gene Expression Omnibus (GEO; accession, GSE66405) and The Cancer Genome Atlas (TCGA) databases. Similarly, miRNA expression patterns were downloaded from GEO (accession, GSE57370) and TCGA. R version 3.5.0 software was used to identify differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) using the limma and edgeR packages. Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology analyses were performed to examine the biological functions of the DEGs. Additionally, a protein-protein interaction (PPI) network was constructed to screen hub gene modules using Cytoscape software. By predicting target genes of the DEMs and integrating them with DEGs, the present study constructed a miRNA-mRNA regulatory network to predict the possible molecular mechanism of WT. Expression of hub genes was validated using the Oncomine database. A total of 613 genes and 29 miRNAs were identified to be differentially expressed in WT. By constructing a PPI network and screening hub gene modules, 5 upregulated genes, including BUB1 mitotic checkpoint serine/threonine kinase, BUB1B mitotic checkpoint serine/threonine kinase B, cell division cycle protein 45, cyclin B2 and pituitary tumor-transforming 1. These genes were identified to be associated with the cell cycle pathway, which suggested that these genes may serve important roles in WT. In addition, a miRNA-mRNA regulatory network was constructed and comprised 16 DEMs and 19 DEGs. In conclusion, key genes, miRNAs and the mRNA-miRNA regulatory network identified in the present study may improve understanding of the underlying molecular mechanisms in the occurrence and development of WT, and may aid the identification of potential biomarkers and therapeutic targets.
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Affiliation(s)
- Lei Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Xian Gao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Xiang Zhou
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Zhiqiang Qin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Yi Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Ran Li
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Min Tang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Wei Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Wei Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
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Liang C, Zhang Y, Zhang Y, Li R, Wang Z, Wei Z, Guo J. The prognostic value of LINC01296 in pan-cancers and the molecular regulatory mechanism in hepatocellular carcinoma: a comprehensive study based on data mining, bioinformatics, and in vitro validation. Onco Targets Ther 2019; 12:5861-5885. [PMID: 31410029 PMCID: PMC6650622 DOI: 10.2147/ott.s205853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/21/2019] [Indexed: 12/12/2022] Open
Abstract
Background and aims This study aimed to clarify the prognostic role of LINC01296 in various cancers, and to evaluate its effect on proliferation, metastasis, and the cell cycle in hepatocellular carcinoma (HCC) by data mining, bioinformatics, and in vitro validation. Methods The prognostic role of LINC01296 in cancer patients was assessed by searching the PubMed, Embase, Web of Science, and Gene Expression Omnibus databases and calculating pooled hazard ratios (HRs) with 95% confidence intervals (CIs); this prognostic role was also evaluated using The Cancer Genome Atlas (TCGA). We detected LINC01296 expression in HCC cell lines, and lentivirus-mediated small interfering RNAs were used to silence LINC01296 in MHCC97H and Hep3B cells to explore the role of LINC01296 in cell proliferation, metastasis, and cell cycle progression with in vitro validation and bioinformatics. Results The results indicated that LINC01296 overexpression was associated with poor overall survival (OS) and disease-free survival (DFS) in various cancers; however, LINC01296 expression was not associated with recurrence-free survival (RFS). Similar results were found with TCGA, which showed that LINC01296 expression was associated with the pathologic stage, tumor size, and differentiation in Asian cancer patients. Additionally, bioinformatics analysis revealed expression of 394 related genes, which indicated that LINC01296 could be involved in the tumorigenesis and progression of HCC. In vitro gene silencing experiments indicated that LINC01296 downregulation repressed cell proliferation, cell cycle progression, and the metastatic potential of HCC through the regulation of BUB1, CCNA2, and CDK1 expression. Conclusion This study demonstrated that LINC01296 expression is related to poor OS and DFS in a variety of cancer types and that LINC01296 has an oncogenic role in HCC.
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Affiliation(s)
- Chaojie Liang
- Department of General Surgery, First Hospital/First Clinical College of Shanxi Medical University, Taiyuan, Shanxi 030001, People's Republic of China
| | - Yongping Zhang
- Department of General Surgery, First Hospital/First Clinical College of Shanxi Medical University, Taiyuan, Shanxi 030001, People's Republic of China
| | - Yu Zhang
- Department of General Surgery, First Hospital/First Clinical College of Shanxi Medical University, Taiyuan, Shanxi 030001, People's Republic of China
| | - Ruihuan Li
- Department of General Surgery, First Hospital/First Clinical College of Shanxi Medical University, Taiyuan, Shanxi 030001, People's Republic of China
| | - Zhimin Wang
- Department of General Surgery, First Hospital/First Clinical College of Shanxi Medical University, Taiyuan, Shanxi 030001, People's Republic of China
| | - Zhigang Wei
- Department of General Surgery, First Hospital/First Clinical College of Shanxi Medical University, Taiyuan, Shanxi 030001, People's Republic of China
| | - Jiansheng Guo
- Department of General Surgery, First Hospital/First Clinical College of Shanxi Medical University, Taiyuan, Shanxi 030001, People's Republic of China
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Yu H, Zhang S, Ibrahim AN, Deng Z, Wang M. Serine/threonine kinase BUB1 promotes proliferation and radio-resistance in glioblastoma. Pathol Res Pract 2019; 215:152508. [PMID: 31272759 DOI: 10.1016/j.prp.2019.152508] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/30/2019] [Accepted: 06/20/2019] [Indexed: 10/26/2022]
Abstract
BUB1 (Budding uninhibited by benzimidazoles 1), a mitotic checkpoint serine/threonine kinase, has been linked in numerous cancers to pro-tumorigenic phenomena including elevation of cellular proliferation, tumor growth, metastatic potential, and poorer patient prognosis. However, the role of BUB1 in glioblastoma remains poorly investigated. In this study, clinical analyses determined significant enrichment of BUB1 in glioblastoma with direct correlation of elevated expression to poorer prognosis in glioma patients. Genetic inhibition of BUB1 in glioblastoma tumor cells via shRNA silencing diminished both proliferative ability and tumorigenicity in vitro and in vivo. Silencing of BUB1 was additionally determined to promote the cytotoxic effect of irradiation on glioblastoma tumor cells, and investigation of the underlying pathways revealed the roles of DNA mismatch repair, spliceosome and c-Myc pathways. Mechanistically, FOXM1 was determined to positively regulate transcription of BUB1 via direct promoter region binding. For validation, pharmacologic inhibition through administration of a BUB1 inhibitor demonstrated attenuated glioblastoma cellular proliferation in vitro as well as delayed tumor growth with prolonged survival in vivo. Collectively, this study demonstrates a novel therapeutic target for glioblastoma in the form of BUB1, which plays a pivotal role in GBM proliferative and radio-resistance capacities in a FOXM1-dependant manner.
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Affiliation(s)
- Hai Yu
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Suojun Zhang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430073, China
| | - Ahmed N Ibrahim
- Department of Neurology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Zhong Deng
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Maode Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
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Abdeyrim A, Cheng X, Lian M, Tan Y. miR‑490‑5p regulates the proliferation, migration, invasion and epithelial‑mesenchymal transition of pharyngolaryngeal cancer cells by targeting mitogen‑activated protein kinase kinasekinase 9. Int J Mol Med 2019; 44:240-252. [PMID: 31115491 PMCID: PMC6559303 DOI: 10.3892/ijmm.2019.4196] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/08/2019] [Indexed: 11/05/2022] Open
Abstract
MicroRNA (miRNA/miR) has been identified to be a promising tool in treating pharyngolaryngeal cancer. The present study aimed to investigate the role of miR‑490‑5p in the regulation of proliferation, migration, invasion and epithelial‑mesenchymal transition (EMT) of pharyngolaryngeal cancer cells. The data of miR‑490‑5p expression levels of 45 cases were obtained from the People's Hospital of Xinjiang Uygur Autonomous Region, and the prediction of the target of miR‑490‑5p was conducted by bioinformatics and verified using a luciferase assay. Cell viability was determined by cell counting kit‑8. Migration and invasion rates were measured by wound healing test and Transwell apparatus, respectively. Colony formation rate was measured by plate colony formation assay. mRNA and protein levels were determined by quantitative polymerase chain reaction and western blotting, respectively. miR‑490‑5p expression was significantly depressed in primary pharyngolaryngeal cancer tissues and cell lines, leading to an unfavorable prognosis. Evidently, miR‑490‑5p overexpression decreased the cell viabilities of BICR 18 and FaDu cells. Mechanically, miR‑490‑5p could target mitogen‑activated protein kinase kinasekinase 9 (MAP3K9). The overexpression of MAP3K9 could promote cell viability, migration and invasion rates, EMT process and ability of cloning, miR‑490‑5p could target MAP3K9 and further modulate the proliferation, migration, invasion and EMT of pharyngolaryngeal cancer cells. The results of the present study provide a novel entry point to the treatment of pharyngolaryngeal cancer.
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Affiliation(s)
- Arikin Abdeyrim
- Department of Otorhinolaryngology Head and Neck Surgery, The People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, Xinjiang 830001, P.R. China
| | - Xiuqin Cheng
- Department of Otorhinolaryngology Head and Neck Surgery, The People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, Xinjiang 830001, P.R. China
| | - Meng Lian
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100005, P.R. China
| | - Yuanyouan Tan
- Department of Otorhinolaryngology Head and Neck Surgery, The People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, Xinjiang 830001, P.R. China
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Luo J, Si ZZ, Li T, Li JQ, Zhang ZQ, Chen GS, Qi HZ, Yao HL. MicroRNA-146a-5p enhances radiosensitivity in hepatocellular carcinoma through replication protein A3-induced activation of the DNA repair pathway. Am J Physiol Cell Physiol 2019; 316:C299-C311. [PMID: 30462539 DOI: 10.1152/ajpcell.00189.2018] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hepatocellular carcinoma (HCC) is known for its high mortality rate worldwide. Based on intensive studies, microRNA (miRNA) expression functions in tumor suppression. Therefore, we aimed to evaluate the contribution of miR-146a-5p to radiosensitivity in HCC through the activation of the DNA damage repair pathway by binding to replication protein A3 (RPA3). First, the limma package of R was performed to differentially analyze HCC expression chip, and regulative miRNA of RPA3 was predicted. Expression of miR-146a-5p, RPA3, and DNA damage repair pathway-related factors in tissues and cells was determined. The effects of radiotherapy on the expression of miR-146a-5p and RPA3 as well as on cell radiosensitivity, proliferation, cell cycle, and apoptosis were also assessed. The results showed that there exists a close correlation between miR-146a and the radiotherapy effect on HCC progression through regulation of RPA3 and the DNA repair pathway. The positive rate of ATM, pCHK2, and Rad51 in HCC tissues was higher when compared with that of the paracancerous tissues. SMMC-7721 and HepG2 cell proliferation were significantly inhibited following 8 Gy 6Mv dose. MiR-146a-5p restrained the expression of RPA3 and promoted the expression of relative genes associated with the DNA repair pathway. In addition, miR-146a-5p overexpression suppresses cell proliferation and enhances radiosensitivity and cell apoptosis in HCC cells. In conclusion, the present study revealed that miR-146a-5p could lead to the restriction of proliferation and the promotion of radiosensitivity and apoptosis in HCC cells through activation of DNA repair pathway and inhibition of RPA3.
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Affiliation(s)
- Jing Luo
- Department of Organ Transplantation and General Surgery, Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhong-Zhou Si
- Department of Organ Transplantation and General Surgery, Second Xiangya Hospital of Central South University, Changsha, China
| | - Ting Li
- Department of Organ Transplantation and General Surgery, Second Xiangya Hospital of Central South University, Changsha, China
| | - Jie-Qun Li
- Department of Organ Transplantation and General Surgery, Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhong-Qiang Zhang
- Department of Organ Transplantation and General Surgery, Second Xiangya Hospital of Central South University, Changsha, China
| | - Guang-Shun Chen
- Department of Organ Transplantation and General Surgery, Second Xiangya Hospital of Central South University, Changsha, China
| | - Hai-Zhi Qi
- Department of Organ Transplantation and General Surgery, Second Xiangya Hospital of Central South University, Changsha, China
| | - Hong-Liang Yao
- Department of Gastrointestinal Surgery, Second Xiangya Hospital of Central South University, Changsha, China
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Giunti L, Da Ros M, De Gregorio V, Magi A, Landini S, Mazzinghi B, Buccoliero AM, Genitori L, Giglio S, Sardi I. A microRNA profile of pediatric glioblastoma: The role of NUCKS1 upregulation. Mol Clin Oncol 2019; 10:331-338. [PMID: 30847170 PMCID: PMC6388501 DOI: 10.3892/mco.2019.1795] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/10/2018] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs/miRs) are a novel class of gene regulators that may be involved in tumor chemoresistance. Recently, specific miRNA expression profiles have been identified in adult glioblastoma (aGBM), but there are only limited data available on the role of miRNAs in pediatric GBM (pGBM). In the present study, the expression profile of miRNAs was examined in seven pGBMs and three human GBM cell lines (U87MG, A172 and T98G), compared with a non-tumoral pool of pediatric cerebral cortex samples by microarray analysis. A set of differentially expressed miRNAs was identified, including miR-490, miR-876-3p, miR-876-5p, miR-448 and miR-137 (downregulated), as well as miR-501-3p (upregulated). Through bioinformatics analysis, a series of target genes was predicted. In addition, similar gene expression patterns in pGBMs and cell lines was confirmed. Of note, drug resistant T98G cells had upregulated nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS1) expression, a protein overexpressed in many tumors that serves an important role in cell proliferation and progression. On the basis of the present preliminary report, it could be intriguing to further investigate the relationship between each of the identified differentially expressed miRNAs and NUCKS1, in order to clarify their involvement in the multi-drug resistance mechanism of pGBMs.
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Affiliation(s)
- Laura Giunti
- Medical Genetics Unit, Meyer Children's University Hospital, I-50139 Florence, Italy
| | - Martina Da Ros
- Neuro-Oncology Unit, Department of Pediatric Oncology, Meyer Children's University Hospital, I-50139 Florence, Italy
| | - Veronica De Gregorio
- Neuro-Oncology Unit, Department of Pediatric Oncology, Meyer Children's University Hospital, I-50139 Florence, Italy
| | - Alberto Magi
- Department of Experimental and Clinical Medicine, University of Florence, I-50139 Florence, Italy
| | - Samuela Landini
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences 'Mario Serio', University of Florence, I-50139 Florence, Italy
| | - Benedetta Mazzinghi
- Nephrology and Dialysis Unit, Meyer Children's University Hospital, I-50139 Florence, Italy
| | | | - Lorenzo Genitori
- Neurosurgery Unit, Meyer Children's University Hospital, I-50139 Florence, Italy
| | - Sabrina Giglio
- Medical Genetics Unit, Meyer Children's University Hospital, I-50139 Florence, Italy.,Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences 'Mario Serio', University of Florence, I-50139 Florence, Italy
| | - Iacopo Sardi
- Neuro-Oncology Unit, Department of Pediatric Oncology, Meyer Children's University Hospital, I-50139 Florence, Italy
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Tang D, Zhao X, Zhang L, Wang Z, Wang C. Identification of hub genes to regulate breast cancer metastasis to brain by bioinformatics analyses. J Cell Biochem 2018; 120:9522-9531. [PMID: 30506958 DOI: 10.1002/jcb.28228] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 11/15/2018] [Indexed: 12/30/2022]
Abstract
Breast cancer with metastasis especially brain metastasis represents a significant cause of morbidity and mortality in patients. In this study, we aimed to investigate the hub genes and potential molecular mechanism in brain metastasis breast cancer. Expression profiles of the genes were extracted from the Gene Expression Omnibus (GEO) database. GO and KEGG pathway enrichment analyses were conducted at Database for Annotation, Visualization, and Integrated Discovery. Protein-protein interaction (PPI) network was established by STRING database constructed by Cytoscape software. Hub genes were identified by the molecular complex detection (MCODE) plugin and the CytoHubba plugin. The transcription factor (TF) that regulates the expression of hub genes was analyzed using the NetworkAnalyst algorithm. Kaplan-Meier curve was used to analyze the effects of hub genes on overall survival. Two GEO databases (GSE100534 and GSE52604) were downloaded from GEO databases. A total of 102 overlapped genes were identified, and the top five KEGG pathways enriched were pathways in cancer, HTLV-I infection, focal adhesion, ECM-receptor interaction, and protein digestion and absorption. By combing the results of MCODE and CytoHubba, a total of 10 hub genes were selected. Kaplan-Meier curve showed that ANLN, BUB1, TTK, and SKA3 were closely associated with the overall survival of breast cancer patients. TF analysis results showed that E2F4, KDM5B, and MYC were crucial regulators for these four hub genes. The current study based on the GEO database provided novel understanding regarding the mechanism of breast cancer metastasis to brain and may provide novel therapeutic targets.
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Affiliation(s)
- Dongyang Tang
- Department of Experimental Management Center, Henan Institute of Science and Technology, Xinxiang, China
| | - Xin Zhao
- Department of Pharmacy, Xinxiang Central Hospital, Xinxiang, China
| | - Li Zhang
- Department of architecture, College of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
| | - Zhiwei Wang
- Department of Experimental Management Center, Henan Institute of Science and Technology, Xinxiang, China
| | - Cheng Wang
- Department of pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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Wang H, Chen W, Jin M, Hou L, Chen X, Zhang R, Zhang J, Zhu J. CircSLC3A2 functions as an oncogenic factor in hepatocellular carcinoma by sponging miR-490-3p and regulating PPM1F expression. Mol Cancer 2018; 17:165. [PMID: 30470261 PMCID: PMC6260990 DOI: 10.1186/s12943-018-0909-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/01/2018] [Indexed: 02/08/2023] Open
Abstract
Background Non-coding RNAs (ncRNAs) have been reported to participate in tumor progression by regulating gene expression. Previous studies showed that protein phosphatase Mg2+/Mn2+ dependent 1F (PPM1F) acts a dual role in cancer growth and metastasis. But, the underlying mechanisms by which ncRNAs regulate PPM1F expression in hepatocellular carcinoma (HCC) are poorly understood. Methods The association between PPM1F or miR-490-3p expression and clinicopathological features and prognosis in patients with HCC was analyzed by TCGA RNA-sequencing data. CircSLC3A2 was identified to bind with miR-490-3p by bioinformatic analysis, and the binding sites between miR-490-3p and PPM1F or circSLC3A2 were confirmed by dual luciferase report and RNA immunoprecipitation (RIP) assays. The localization and clinical significance of miR-490-3p and circSLC3A2 in patients with HCC were investigated by fluorescence in situ hybridization (FISH). MTT, Agar, and Transwell assays were conducted to evaluate the effects of miR-490-3p or circSLC3A2 on cell proliferation and invasive potential. Results The expression of PPM1F or miR-490-3p was associated with poor survival and tumor recurrence, and acted as an independent prognostic factor in patients with HCC. Re-expression of miR-490-3p inhibited HCC cell proliferation and invasion by targeting PPM1F, but its inhibitor reversed these effects. Moreover, circSLC3A2, predominantly localized in the cytoplasm, exhibited an oncogenic role by sponging miR-490-3p and regulating PPM1F expression, and harbored a positive correlation with poor survival in patients with HCC. Conclusion CircSLC3A2 acts as an oncogenic factor in HCC by sponging miR-490-3p and regulating PPM1F expression. Electronic supplementary material The online version of this article (10.1186/s12943-018-0909-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongjian Wang
- The Fifth Department of Digestion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China
| | - Wei Chen
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China
| | - Ming Jin
- Department of Clinical Medicine, Ningbo University School of Medicine, Ningbo, 315211, Zhejiang Province, China
| | - Lidan Hou
- Department of Gastroenterology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoyu Chen
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China
| | - Rui Zhang
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China
| | - Jing Zhang
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China.
| | - Jinshui Zhu
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China
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Henriques AC, Ribeiro D, Pedrosa J, Sarmento B, Silva PMA, Bousbaa H. Mitosis inhibitors in anticancer therapy: When blocking the exit becomes a solution. Cancer Lett 2018; 440-441:64-81. [PMID: 30312726 DOI: 10.1016/j.canlet.2018.10.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/12/2018] [Accepted: 10/02/2018] [Indexed: 12/11/2022]
Abstract
Current microtubule-targeting agents (MTAs) remain amongst the most important antimitotic drugs used against a broad range of malignancies. By perturbing spindle assembly, MTAs activate the spindle assembly checkpoint (SAC), which induces mitotic arrest and subsequent apoptosis. However, besides toxic side effects and resistance, mitotic slippage and failure in triggering apoptosis in various cancer cells are limiting factors of MTAs efficacy. Alternative strategies to target mitosis without affecting microtubules have, thus, led to the identification of small molecules, such as those that target spindle Kinesins, Aurora and Polo-like kinases. Unfortunately, these so-called second-generation of antimitotics, encompassing mitotic blockers and mitotic drivers, have failed in clinical trials. Our recent understanding regarding the mechanisms of cell death during a mitotic arrest pointed out apoptosis as the main variable, providing an opportunity to control the cell fates and influence the effectiveness of antimitotics. Here, we provide an overview on the second-generation of antimitotics, and discuss possible strategies that exploit SAC activity, mitotic slippage/exit and apoptosis induction, in order to improve the efficacy of anticancer strategies that target mitosis.
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Affiliation(s)
- Ana C Henriques
- CESPU, Instituto de Investigação e Formação Avançada Em Ciências e Tecnologias da Saúde, Instituto Universitário de Ciências da Saúde, Gandra PRD, Portugal; INEB, Instituto Nacional de Engenharia Biomédica, Universidade Do Porto, Porto, Portugal
| | - Diana Ribeiro
- CESPU, Instituto de Investigação e Formação Avançada Em Ciências e Tecnologias da Saúde, Instituto Universitário de Ciências da Saúde, Gandra PRD, Portugal; Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade Do Porto, Porto, Portugal
| | - Joel Pedrosa
- CESPU, Instituto de Investigação e Formação Avançada Em Ciências e Tecnologias da Saúde, Instituto Universitário de Ciências da Saúde, Gandra PRD, Portugal
| | - Bruno Sarmento
- CESPU, Instituto de Investigação e Formação Avançada Em Ciências e Tecnologias da Saúde, Instituto Universitário de Ciências da Saúde, Gandra PRD, Portugal; INEB, Instituto Nacional de Engenharia Biomédica, Universidade Do Porto, Porto, Portugal; i3S - Instituto de Investigação e Inovação Em Saúde, Universidade Do Porto, Porto, Portugal
| | - Patrícia M A Silva
- CESPU, Instituto de Investigação e Formação Avançada Em Ciências e Tecnologias da Saúde, Instituto Universitário de Ciências da Saúde, Gandra PRD, Portugal
| | - Hassan Bousbaa
- CESPU, Instituto de Investigação e Formação Avançada Em Ciências e Tecnologias da Saúde, Instituto Universitário de Ciências da Saúde, Gandra PRD, Portugal; Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade Do Porto, Porto, Portugal.
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Yu Y, Cai O, Wu P, Tan S. MiR‐490‐5p inhibits the stemness of hepatocellular carcinoma cells by targeting
ECT2. J Cell Biochem 2018; 120:967-976. [PMID: 30206962 DOI: 10.1002/jcb.27459] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/17/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Yuanjie Yu
- Department of Gastroenterology Renmin Hospital of Wuhan University Wuhan Hubei China
- Hubei Key Laboratory of Digestive System Disease Wuhan Hubei China
| | - Ou Cai
- Department of Gastroenterology Renmin Hospital of Wuhan University Wuhan Hubei China
- Hubei Key Laboratory of Digestive System Disease Wuhan Hubei China
| | - Pengbo Wu
- Department of Gastroenterology Renmin Hospital of Wuhan University Wuhan Hubei China
- Hubei Key Laboratory of Digestive System Disease Wuhan Hubei China
| | - Shiyun Tan
- Department of Gastroenterology Renmin Hospital of Wuhan University Wuhan Hubei China
- Hubei Key Laboratory of Digestive System Disease Wuhan Hubei China
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Xu L, Li T, Ding W, Cao Y, Ge X, Wang Y. Combined seven miRNAs for early hepatocellular carcinoma detection with chronic low-dose exposure to microcystin-LR in mice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 628-629:271-281. [PMID: 29438936 DOI: 10.1016/j.scitotenv.2018.02.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 06/08/2023]
Abstract
Aberrant miRNA expression has been detected in various tumor tissues, which may be considered as a marker for early cancer diagnosis. One miRNA has multiple downstream target genes, which can be regulated by multiple upstream other miRNAs. Hence, this dynamic regulation is likely characterized by volatility, and thus, finding the appropriate time point for tests becomes essential for the use of miRNAs as an early marker of tumor diagnosis. In this study, we established a chronic liver cancer progression model in mice by using low doses of the harmful substance microcystin-LR (MC-LR). On the basis of miRNAs microarray assay, we further tested seven miRNAs that showed characteristic expression changes in pre-hepatocarcinogenesis. Our results showed that the levels of four miRNAs (miR-122-5p, miR-125-5p, miR-199a-5p, and miR-503-5p) decreased dramatically, whereas those of two miRNAs (miR-222-5p and miR-590-5p) increased significantly in the early stages, which were all accompanied by an increase in atypia of hepatocytes. MiR-490-5p was a sensitive molecular, suitable only for evaluation of pathological changes in young mice. Therefore the combination the seven of miRNAs for a set may prove to be an effective method in healthy assessment of environmental toxicants for detection of hepatocarcinogenesis caused by hazardous materials.
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Affiliation(s)
- Lizhi Xu
- Basic Medical Education Center, Nanjing University School of Medicine, Nanjing, Jiangsu 210093, People's Republic of China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, Jiangsu 210093, People's Republic of China.
| | - Tianfeng Li
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, Jiangsu 210093, People's Republic of China; Center for Reproductive Medicine, The Affiliated Shenzhen City Maternity and Child Healthcare Hospital of Southern Medical University, Shenzhen, Guangdong 518017, People's Republic of China
| | - Weidong Ding
- Basic Medical Education Center, Nanjing University School of Medicine, Nanjing, Jiangsu 210093, People's Republic of China
| | - Yu Cao
- Basic Medical Education Center, Nanjing University School of Medicine, Nanjing, Jiangsu 210093, People's Republic of China
| | - Xiaolong Ge
- Basic Medical Education Center, Nanjing University School of Medicine, Nanjing, Jiangsu 210093, People's Republic of China
| | - Yaping Wang
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, Jiangsu 210093, People's Republic of China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, Jiangsu 210093, People's Republic of China
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Fang ZQ, Li MC, Zhang YQ, Liu XG. MiR-490-5p inhibits the metastasis of hepatocellular carcinoma by down-regulating E2F2 and ECT2. J Cell Biochem 2018; 119:8317-8324. [PMID: 29932246 DOI: 10.1002/jcb.26876] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/21/2018] [Indexed: 01/07/2023]
Abstract
We intended to evaluate miR-490-5p expression in hepatocellular carcinoma (HCC) tissues and detect the potential targets of miR-490-5p. In vitro experiments were conducted to further investigate the biological function of miR-490-5p on HCC cell metastasis. We investigated the abnormally expressed miRNAs in HCC tissues, and the miR-490-5p expression level was detected by qRT-PCR. E2F2 and ECT2 were proved to be the potential targets of miR-490-5p by luciferase reporter assay. The expression levels of E2F2 and ECT2 were determined using Western blot. Transwell assay was used to analyse the impact of miR-490-5p on metastasis of HCC cells. Four high-expressed miRNAs, and seven low-expressed miRNAs, including miR-490-5p, were detected in HCC tissues. The expression level of miR-490-5p was connected with the tumor size, tumor node metastasis (TNM) stage, and survival ratio of HCC patients. E2F2 and ECT2 were the targets of miR-490-5p, and miR-490-5p inhibited HCC cell metastasis through down-regulating the expressions of E2F2 and ECT2. The over-expressed miR-490-5p could restrain the metastasis of HCC cells by down-regulating E2F2 and ECT2 expression levels.
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Affiliation(s)
- Zheng-Qing Fang
- School of Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Mao-Chun Li
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yu-Qin Zhang
- Department of Medicine, Anhui No. 2 Provincial People's Hospital, Hefei, Anhui, China
| | - Xiang-Guo Liu
- College of Chinese and Western Medicine (School of Life Science), Anhui University of Chinese Medicine, Hefei, Anhui, China
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