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Kadioglu DB, Demirtas CO, Pirim D, Dilber F, Eren F. The preliminary data of gene expressions and bioinformatics analysis of miR-146b-5p and miR-4510 in the Turkish population in HBV-related hepatocellular carcinoma. HEPATOLOGY FORUM 2024; 5:106-112. [PMID: 39006138 PMCID: PMC11237244 DOI: 10.14744/hf.2023.2023.0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/09/2023] [Accepted: 01/02/2024] [Indexed: 07/16/2024]
Abstract
Background and Aim It is reported that miRNAs play an important role in hepatocellular carcinogenesis and may serve as non-invasive biomarkers for hepatocellular carcinoma (HCC). MiR-4510 and miR-146b-5p expression levels have been found to be associated with HCC. However, their associations with hepatitis B virus (HBV)-related HCC (HBV-HCC) are yet to be explored. We aimed to assess the predictive value of expression levels of serum miR-4510 and miR-146b-5p in patients with HBV-HCC and performed bioinformatics analyses based on the miRNA expression profile. Materials and Methods This cross-sectional study used the serum of 16 patients with Chronic Hepatitis B (CHB), 15 hepatitis B virus-related cirrhosis (HBV-cirrhosis), 15 HBV-HCC, and 16 healthy subjects. The total RNA was isolated from serum, and the expression of miRNAs was measured by qRT-PCR, calculated using the 2-ΔΔCt methods. MIENTURNET was used to predict miRNA-target gene interactions. The Network Analyst was used to build protein-protein interactions. Results There was a significant difference in miR-146b-5p between study groups (p=0.009). MiR-146b-5p expression was found to be significantly reduced in HBV-HCC compared to the HBV-cirrhosis group and healthy controls (p=0.005 and p=0.006, respectively). Conclusion The serum miR-146b-5p levels might be a promising tool to be used as a non-invasive diagnostic biomarker for HCC. Our findings shed light on potential biomarkers for the diagnosis of HBV-HCC in terms of selected miRNAs. The target pathways of miR-146b-5p identified by our in-silico analysis to reveal the functional mechanism are "MAPK signaling pathways" and "Pathways in cancer."
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Affiliation(s)
- Duygu Bircan Kadioglu
- Department of Medical Biology, Marmara University School of Medicine, Istanbul, Turkiye
- Institute of Health Sciences, Marmara University, Istanbul, Turkiye
| | - Coskun Ozer Demirtas
- Department of Gastroenterology, Marmara University School of Medicine, Istanbul, Turkiye
| | - Dilek Pirim
- Department of Molecular Biology and Genetics, Bursa Uludag University, Faculty of Arts and Sciences, Bursa, Turkiye
| | - Feyza Dilber
- Department of Gastroenterology, Marmara University School of Medicine, Istanbul, Turkiye
| | - Fatih Eren
- Department of Medical Biology, Marmara University School of Medicine, Istanbul, Turkiye
- Department of Medical Biology, Eastern Mediterranean University School of Medicine, Famagusta, North Cyprus
- Institute of Gastroenterology, Marmara University, Istanbul, Turkiye
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Zhao Z, Shen Y, Zhao J, Chen X. microRNA expression profile of fish erythrocytes. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2020.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chi X, Jiang Y, Chen Y, Lv L, Chen J, Yang F, Zhang X, Pan F, Cai Q. Upregulation of microRNA miR-652-3p is a prognostic risk factor for hepatocellular carcinoma and regulates cell proliferation, migration, and invasion. Bioengineered 2021; 12:7519-7528. [PMID: 34608826 PMCID: PMC8806865 DOI: 10.1080/21655979.2021.1979861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
As powerful regulatory factors, microRNAs (miRNAs) are involved in tumor progression. The current research aimed to excavate the prognostic significance and potential regulatory mechanisms of miR-652-3p in hepatocellular carcinoma (HCC). Expression of miR-652-3p in HCC tissues and cells was exposed by Quantitative real-time polymerase chain reaction (RT-qPCR) assay, and we found that miR-652-3p was elevated in HCC tissues and cells than in the control group (P < 0.05). Then, the relationship between miR-652-3p levels and clinical characteristics was obtained from the Chi-square test. Kaplan-Meier survival analysis and Cox regression model to explore the outcome of miR-652-3p on the prognosis of HCC. The results investigated that overexpression of miR-652-3p was related to clinical tumor-node-metastasis (TNM) stage (P = 0.020) and differentiation (P = 0.031). HCC patients with elevated miR-652-3p levels were correlated with poor overall survival (log-rank, P = 0.007), and maybe a possible prognostic marker for HCC. Finally, CCK-8, colony formation, wound healing and Transwell assay was detected after transfection of HCC cells with miR-652-3p mimic or inhibitor. And the results confirmed that elevation miR-652-3p promoted the proliferation, migration, and invasion of tumor cells (P < 0.05). All data indicated that elevated miR-652-3p is a prognostic marker and would be able to participate in tumor progression of HCC by regulating cell proliferation, migration, and invasion.
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Affiliation(s)
- Xiaobin Chi
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistics Team, Fuzhou, China
| | - Yi Jiang
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistics Team, Fuzhou, China
| | - Yongbiao Chen
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistics Team, Fuzhou, China
| | - Lizhi Lv
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistics Team, Fuzhou, China
| | - Jianwei Chen
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistics Team, Fuzhou, China
| | - Fang Yang
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistics Team, Fuzhou, China
| | - Xiaojin Zhang
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistics Team, Fuzhou, China
| | - Fan Pan
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistics Team, Fuzhou, China
| | - Qiucheng Cai
- Department of Hepatobiliary Surgery, 900 Hospital of the Joint Logistics Team, Fuzhou, China
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Long Noncoding RNA MIR100HG Knockdown Attenuates Hepatocellular Carcinoma Progression by Regulating MicroRNA-146b-5p/Chromobox 6. Gastroenterol Res Pract 2021; 2021:6832518. [PMID: 34381502 PMCID: PMC8352691 DOI: 10.1155/2021/6832518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/08/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
Purpose Hepatocellular carcinoma (HCC) accounts for approximately ninety percent of primary liver cancer. This study attempted to investigate the effects of the long noncoding RNA MIR100HG (MIR100HG) in HCC and the underlying molecular mechanism. Materials and Methods qRT-PCR was implemented to analyze the expression of MIR100HG, microRNA-146b-5p (miR-146b-5p), and Chromobox 6 (CBX6). The correlation between MIR100HG and clinicopathological features of HCC patients was assessed. Additionally, the effects of MIR100HG knockdown on HCC cell viability, migration, and invasion were explored. The interactions among MIR100HG, miR-146b-5p, and CBX6 were confirmed. Furthermore, rescue experiments were conducted to investigate whether MIR100HG knockdown modulates HCC cell behaviors through modulating the miR-146b-5p/CBX6 axis. Results The expression of MIR100HG and CBX6 was enhanced, while miR-146b-5p was inhibited in HCC cells. High MIR100HG expression was positively associated with the TNM tumor stage and Edmondson-Steiner grading in HCC patients. MIR100HG knockdown considerably reduced the HCC cell viability, migration, and invasion. In addition, MIR100HG directly targeted miR-146b-5p, and miR-146b-5p directly targeted CBX6 in HCC cells. Moreover, miR-146b-5p suppression or CBX6 elevation evidently rescued the suppressed viability, migration, and invasion of HCC cells caused by MIR100HG knockdown. Conclusions Knockdown of MIR100HG inhibited the viability, migration, and invasion of HCC cells by targeting the miR-146b-5p/CBX6 axis, offering a potential therapeutic target for HCC therapy.
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Machine Learning Supports Long Noncoding RNAs as Expression Markers for Endometrial Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3968279. [PMID: 32420338 PMCID: PMC7199595 DOI: 10.1155/2020/3968279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/17/2019] [Indexed: 12/19/2022]
Abstract
Uterine corpus endometrial carcinoma (UCEC) is the second most common type of gynecological tumor. Several research studies have recently shown the potential of different ncRNAs as biomarkers for prognostics and diagnosis in different types of cancers, including UCEC. Thus, we hypothesized that long noncoding RNAs (lncRNAs) could serve as efficient factors to discriminate solid primary (TP) and normal adjacent (NT) tissues in UCEC with high accuracy. We performed an in silico differential expression analysis comparing TP and NT from a set of samples downloaded from the Cancer Genome Atlas (TCGA) database, targeting highly differentially expressed lncRNAs that could potentially serve as gene expression markers. All analyses were performed in R software. The receiver operator characteristics (ROC) analyses and both supervised and unsupervised machine learning indicated a set of 14 lncRNAs that may serve as biomarkers for UCEC. Functions and putative pathways were assessed through a coexpression network and target enrichment analysis.
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Wu C, Tang G, Wang X, Zhang J, Chen S, Lu C, Zhang D, Li Y. Micro-RNA-21 rs1292037 A>G polymorphism can predict hepatocellular carcinoma prognosis (HCC), and plays a key role in cell proliferation and ischemia-reperfusion injury (IRI) in HCC cell model of IRI. Saudi Med J 2020; 41:383-392. [PMID: 32291425 PMCID: PMC7841620 DOI: 10.15537/smj.2020.4.24994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 02/03/2020] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES To assess the predictive function of miR-21 rs1292037 A greater than G polymorphism in survival and ischemia-reperfusion injury (IRI) in hepatocellular carcinoma (HCC) patients. METHODS The experiment was carried out between July 2018 and July 2019, whereas the prospective clinical study was carried out between January 2014 and January 2019. In this study, 62 HCC patients with hepatitis B virus (HBV), 17 HCC patients without HBV, and 13 healthy controls were investigated. Micro-RNA-21 levels in the blood were identified using quantitative reverse-transcription polymerase chain reaction (qRT-PCR) and allele specific PCR for miR-21 rs1292037. Partial hepatectomy was performed in all patients, and the tumor development indicators and survival time were evaluated in a subsequent follow-up. Cell-based simulated IRI model of HCC huh7 cell line was used to determine the functions of miR-21 with respect to IRI and proliferation. RESULTS Micro-RNA-21 levels were significantly increased in HCC patients. Furthermore, an miR- 21 rs1292037 A greater than G polymorphism was found to be significantly associated with HCC prognosis and severity of liver injury after hepatectomy. In vitro study revealed that miR-21 might prevent IRI from occurring, and can induce proliferation in HCC huh7 cells. These functions of miR-21 were demonstrated to be triggered by IL-12A inhibition. CONCLUSION Micro-RNA-21 rs1292037 A greater than G polymorphism can predict IRI and tumor progression by regulating the miR-21/IL-12A.axis.
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Affiliation(s)
- Chaoyu Wu
- Department of Infectious Diseases, Linyi Central Hospital, Linyi, China. E-mail.
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Zhang E, Li X. LncRNA SOX2-OT regulates proliferation and metastasis of nasopharyngeal carcinoma cells through miR-146b-5p/HNRNPA2B1 pathway. J Cell Biochem 2019; 120:16575-16588. [PMID: 31099048 DOI: 10.1002/jcb.28917] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is an aggressive malignancy with a high mortality on account of its frequent metastasis and poor prognosis. An extensive body of investigations has proven that long noncoding RNAs are implicated in a variety of biological processes. Although SOX2-OT has been reported to play an oncogenic role in osteosarcoma, the mechanism of SOX2-OT-driven NPC progression is still obscure. The aim of this study was to elucidate the biological function of SOX2-OT and the related possible mechanism in NPC. In our study, SOX2-OT was notably elevated in NPC samples and cells. Further, a high expression level of SOX2-OT was correlated with poor clinical outcomes of NPC. Results from loss-of-function experiments suggested that knockdown of SOX2-OT repressed cell proliferation, arrested cell cycle, facilitated cell apoptosis, and inhibited cell metastasis of NPC. To further investigate the molecular mechanism of SOX2-OT, miR-146b-5p was found to directly bind to SOX2-OT, which mediated the role of SOX2-OT in NPC tumorigenesis. In addition, HNRNPA2B1 was a target of miR-146b-5p and SOX2-OT modulated the expression of HNRNPA2B1 through competitively binding to miR-146b-5p. At last, we discovered that SOX2-OT regulated NPC progression by targeting miR-146b-5p/HNRNPA2B1 pathway, which may provide more innovative targets for the treatment of patients with NPC.
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Affiliation(s)
- Enqin Zhang
- Department of Otorhinolaryngology, Ankang in Shaanxi Province Chinese Traditional Medicine Hospital, Ankang, Shaanxi, China
| | - Xueping Li
- Department of Otorhinolaryngology, Ankang in Shaanxi Province Chinese Central Medicine Hospital, Ankang, Shaanxi, China
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Lin H, Zhang Z. Diagnostic value of a microRNA signature panel in exosomes for patients with hepatocellular carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:1478-1487. [PMID: 31933965 PMCID: PMC6947065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 02/22/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the fifth most frequently diagnosed cancer worldwide and the second most frequent cause of cancer death. The aim of this study is to investigate the early diagnostic value of a panel of peripheral blood exosomal micro-RNAs (miRNAs) in patients with HCC compared with patients with Hepatitis B virus (HBV) and hepatocirrhosis. PATIENTS AND METHODS Blood samples from 72 patients with HCC, 72 patients with hepatocirrhosis and 72 patients with HBV were obtained at Beijing Friendship Hospital, Capital Medical University. The miRNA expression levels were detected by real-time polymerase chain reaction (RT-PCR). Areas under curve (AUCs) were used to compare diagnostic values of plasmic and exosomal miRNAs. RESULTS We screened plasmic and exosomal solutions of 3 HCC, 3 cirrhosis and 3 HBV patients to perform miRNA microarray analysis. Three distinctly differential microRNAs including miRNA-26a, miRNA-29c, and miRNA-21 were selected to perform further evaluation. First, we found that the expressions of miRNA-26a, miRNA-29c, and miRNA-21 were significantly lower in patients with HCC compared with cirrhotic and HBV group in both exosomes and plasma. Second, we found miRNA-26a, miRNA-29c, and miRNA-21 were significantly down-regulated in HCC tumor tissues compared with normal tissues. Thirdly, we found miRNAs in exosomes had better diagnostic value for patients with HCC compared with plasmic miRNAs among different groups. CONCLUSIONS In conclusion, we found that the expression of miRNA-26a, miRNA-29c, and miRNA-21 were significantly lower in patients with HCC, and we confirmed miRNA-26a, miRNA-29c, and miRNA-21 could be identified as independent diagnostic biomarkers for patients with HCC.
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Affiliation(s)
- Huajun Lin
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University Beijing, People's Republic of China
| | - Zhongtao Zhang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University Beijing, People's Republic of China
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Yao Q, Chen Y, Zhou X. The roles of microRNAs in epigenetic regulation. Curr Opin Chem Biol 2019; 51:11-17. [PMID: 30825741 DOI: 10.1016/j.cbpa.2019.01.024] [Citation(s) in RCA: 266] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/10/2019] [Accepted: 01/25/2019] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs, approximately 18-25 nucleotides in length, now recognized as one of the major regulatory gene families in eukaryotes. Recent advances have been made in understanding the complicated roles of miRNAs in epigenetic regulation. miRNAs, as epigenetic modulators, affect the protein levels of the target mRNAs without modifying the gene sequences. Moreover, miRNAs can also be regulated by epigenetic modifications, including DNA methylation, RNA modification, and histone modifications. The reciprocal actions of miRNAs and epigenetic pathway appear to form a miRNA-epigenetic feedback loop and have an extensive influence on gene expression proliferation. The dysregulation of the miRNA-epigenetic feedback loop interferes with the physiological and pathological processes and contributes to variety of diseases. In this review, we focus on the reciprocal interconnection of miRNAs in epigenetic regulation, with the aim of offering new insights into the epigenetic regulatory mechanism that can be used to combat diseases.
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Affiliation(s)
- Qian Yao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, PR China
| | - Yuqi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, PR China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, PR China.
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Wen DY, Huang JC, Wang JY, Pan WY, Zeng JH, Pang YY, Yang H. Potential clinical value and putative biological function of miR-122-5p in hepatocellular carcinoma: A comprehensive study using microarray and RNA sequencing data. Oncol Lett 2018; 16:6918-6929. [PMID: 30546424 PMCID: PMC6256359 DOI: 10.3892/ol.2018.9523] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 12/12/2017] [Indexed: 02/07/2023] Open
Abstract
In order to determine the diagnostic efficacy of microRNA (miR)-122-5p and to identify the potential molecular signaling pathways underlying the function of miR-122-5p in hepatocellular carcinoma (HCC), the expression profiles of data collected from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and literature databases were analyzed, along with any associations between clinicopathological characteristics and the diagnostic value of miR-122-5p in HCC. The intersection of 12 online prediction databases and differentially expressed genes from TCGA and GEO were utilized in order to select the prospective target genes of miR-122-5p in HCC. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction network (PPI) analyses were subsequently performed based on the selected target genes. The average expression level of miR-122-5p was decreased in HCC patients compared with controls from TCGA database (P<0.001), and the downregulation of miR-122-5p was significantly associated with HCC tissues (P<0.001), tumor vascular invasion (P<0.001), metastasis (P=0.001), sex (P=0.006), virus infection status (P=0.001) and tissue (compared with serum; P<0.001) in cases from the GEO database. The pooled sensitivity and specificity for miR-122-5p to diagnose HCC were 0.60 [95% confidence interval (CI), 0.48–0.71] and 0.81 (95% CI, 0.70–0.89), respectively. The area under the curve (AUC) value was 0.76 (95% CI, 0.72–0.80), while in Meta-DiSc 1.4, the AUC was 0.76 (Q*=0.70). The pooled sensitivity and specificity were 0.60 (95% CI, 0.57–0.62) and 0.79 (95% CI, 0.76–0.81), respectively. A total of 198 overlapping genes were selected as the potential target genes of miR-122-5p, and 7 genes were defined as the hub genes from the PPI network. Cell division cycle 6 (CDC6), minichromosome maintenance complex component 4 (MCM4) and MCM8, which serve pivotal functions in the occurrence and development of HCC, were the most significant hub genes. The regulation of cell proliferation for cellular adhesion and the biosynthesis of amino acids was highlighted in the GO and KEGG pathway analyses. The downregulation of miR-122-5p in HCC demonstrated diagnostic value, worthy of further attention. Therefore, miR-122-5p may function as a tumor suppressor by modulating genome replication.
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Affiliation(s)
- Dong-Yue Wen
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jia-Cheng Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jie-Yu Wang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Wen-Ya Pan
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jiang-Hui Zeng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yu-Yan Pang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hong Yang
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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Falcon T, Freitas M, Mello AC, Coutinho L, Alvares-da-Silva MR, Matte U. Analysis of the Cancer Genome Atlas Data Reveals Novel Putative ncRNAs Targets in Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2018; 2018:2864120. [PMID: 30046591 PMCID: PMC6038674 DOI: 10.1155/2018/2864120] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/17/2018] [Indexed: 12/14/2022]
Abstract
Hepatocellular carcinoma (HCC) is the prevalent type of primary liver malignancy. Different noncoding RNAs (ncRNAs) that negatively regulate gene expression, such as the microRNAs and the long ncRNAs (lncRNAs), have been associated with cell invasiveness and cell dissemination, tumor recurrence, and metastasis in HCC. To evaluate which regulatory ncRNAs might be good candidates to disrupt HCC proliferation pathways, we performed both unsupervised and supervised analyses of HCC expression data, comparing samples of solid tumor tissue (TP) and adjacent tissue (NT) of a set of patients, focusing on ncRNAs and searching for common mechanisms that may shed light in future therapeutic options. All analyses were performed using the R software. Differential expression (total RNA and miRNA) and enrichment analyses (Gene Ontology + Pathways) were performed using the package TCGABiolinks. As a result, we improved the set of lncRNAs that could be the target of future studies in HCC, highlighting the potential of FAM170B-AS1 and TTN-AS1.
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Affiliation(s)
- Tiago Falcon
- Gene Therapy Center, Experimental Research Center, Hospital de Clínicas de Porto Alegre, 90035-903 Porto Alegre, RS, Brazil
| | - Martiela Freitas
- Gene Therapy Center, Experimental Research Center, Hospital de Clínicas de Porto Alegre, 90035-903 Porto Alegre, RS, Brazil
- Post-Graduation Program on Genetics and Molecular Biology, UFRGS, 91501-970 Porto Alegre, RS, Brazil
| | - Ana Carolina Mello
- Gene Therapy Center, Experimental Research Center, Hospital de Clínicas de Porto Alegre, 90035-903 Porto Alegre, RS, Brazil
- Graduation Program on Biotechnology/Bioinformatics, UFRGS, 91501-970 Porto Alegre, RS, Brazil
| | - Laura Coutinho
- Gene Therapy Center, Experimental Research Center, Hospital de Clínicas de Porto Alegre, 90035-903 Porto Alegre, RS, Brazil
- Graduation Program on Biotechnology/Bioinformatics, UFRGS, 91501-970 Porto Alegre, RS, Brazil
| | - Mario R. Alvares-da-Silva
- Gastroenterology and Hepatology Division, Hospital de Clinicas de Porto Alegre, Brazil
- Graduate Program on Gastroenterology and Hepatology, Department of Internal Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ursula Matte
- Gene Therapy Center, Experimental Research Center, Hospital de Clínicas de Porto Alegre, 90035-903 Porto Alegre, RS, Brazil
- Post-Graduation Program on Genetics and Molecular Biology, UFRGS, 91501-970 Porto Alegre, RS, Brazil
- Department of Genetics, UFRGS, 91501-970 Porto Alegre, RS, Brazil
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