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Chen Y, Gao X, Dai X, Xia Y, Zhang X, Sun L, Zhu Y. Integrated Bioinformatics and Experimental Analysis of Long Noncoding RNA Associated-ceRNA as Prognostic Biomarkers in Advanced Stomach Adenocarcinoma. J Cancer 2024; 15:1536-1550. [PMID: 38370380 PMCID: PMC10869988 DOI: 10.7150/jca.89526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 01/10/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Advanced stomach adenocarcinoma (ASTAD) is a highly malignant and prognostically poor stage of gastric cancer. Recently, long noncoding RNA (lncRNA) was found to play a crucial role, including as competing endogenous RNA (ceRNA) in cancer. However, studies on large-scale sample in ASTAD are still lacking, thus we constructed the ceRNA network of ASTAD to explore its molecular mechanism. METHODS We compared the expression of mRNAs, lncRNAs and miRNAs between ASTAD and normal tissues utilizing RNA-Seq and miRNA-seq Data from The Cancer Genome Atlas (TCGA). GO and KEGG enrichment analysis were executed for annotating the functions of differentially expressed mRNAs. Subsequently, we investigated the expression correlations between the differentially expressed lncRNAs and their respective mRNAs by constructing a ceRNA network. Kaplan-Meier survival analysis was used to assess the relationship between high/low risk scores based on this network with patient prognosis in TCGA training cohort and GSE15459 validation cohort. In vitro functional assays were employed to verify the cancer-promoting effects of key lncRNAs in the ceRNA network and their possible mechanisms. RESULTS In ASTAD tissues, a total of 176 lncRNAs, 124 miRNAs, and 2205 mRNAs were identified as differentially expressed. Our constructed ceRNA network consisted 6 differentially expressed lncRNAs (PVT1, MAGI2-AS3, KCNQ1OT1, LINC02086, AC125807.2 and LINC02535), 25 miRNAs and 130 mRNAs, and the risk score derived from these lincRNAs could predict ASTAD patient outcomes. Key lncRNA LINC02086 was experimentally verified to enhance proliferation and migration of gastric cancer cells by competitively binding to miR-93a-5p with MMP3. CONCLUSION Our comprehensive ceRNA network for ASTAD provides valuable insights into its molecular mechanisms, and LINC02086 may be used as an innovative target for clinical treatment.
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Affiliation(s)
- Yixin Chen
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310006, China
| | - Xin Gao
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310006, China
| | - Xinyang Dai
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310006, China
| | - Yuwei Xia
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310006, China
| | - Xinran Zhang
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310006, China
| | - Leitao Sun
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310006, China
- Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Ying Zhu
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou 310006, China
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Zhang R, Tao Y, Huang J. The Application of MicroRNAs in Glaucoma Research: A Bibliometric and Visualized Analysis. Int J Mol Sci 2023; 24:15377. [PMID: 37895056 PMCID: PMC10607922 DOI: 10.3390/ijms242015377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Glaucoma is similar to a neurodegenerative disorder and leads to global irreversible loss of vision. Despite extensive research, the pathophysiological mechanisms of glaucoma remain unclear, and no complete cure has yet been identified for glaucoma. Recent studies have shown that microRNAs can serve as diagnostic biomarkers or therapeutic targets for glaucoma; however, there are few bibliometric studies that focus on using microRNAs in glaucoma research. Here, we have adopted a bibliometric analysis in the field of microRNAs in glaucoma research to manifest the current tendencies and research hotspots and to present a visual map of the past and emerging tendencies in this field. In this study, we retrieved publications in the Web of Science database that centered on this field between 2007 and 2022. Next, we used VOSviewer, CiteSpace, Scimago Graphica, and Microsoft Excel to present visual representations of a co-occurrence analysis, co-citation analysis, tendencies, hotspots, and the contributions of authors, institutions, journals, and countries/regions. The United States was the main contributor. Investigative Ophthalmology and Visual Science has published the most articles in this field. Over the past 15 years, there has been exponential growth in the number of publications and citations in this field across various countries, organizations, and authors. Thus, this study illustrates the current trends, hotspots, and emerging frontiers and provides new insight and guidance for searching for new diagnostic biomarkers and clinical trials for glaucoma in the future. Furthermore, international collaborations can also be used to broaden and deepen the field of microRNAs in glaucoma research.
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Affiliation(s)
| | | | - Jufang Huang
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha 410013, China; (R.Z.); (Y.T.)
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Tu H, Zhang Q, Xue L, Bao J. Cuproptosis-Related lncRNA Gene Signature Establishes a Prognostic Model of Gastric Adenocarcinoma and Evaluate the Effect of Antineoplastic Drugs. Genes (Basel) 2022; 13:genes13122214. [PMID: 36553481 PMCID: PMC9777654 DOI: 10.3390/genes13122214] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/14/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND One of the most frequent malignancies of the digestive system is stomach adenocarcinoma (STAD). Recent research has demonstrated how cuproptosis (copper-dependent cell death) differs from other cell death mechanisms that were previously understood. Cuproptosis regulation in tumor cells could be a brand-new treatment strategy. Our goal was to create a cuproptosis-related lncRNA signature. Additionally, in order to evaluate the possible immunotherapeutic advantages and drug sensitivity, we attempted to study the association between these lncRNAs and the tumor immune microenvironment of STAD tumors. METHODS The TCGA database was accessed to download the RNA sequencing data, genetic mutations, and clinical profiles for TCGA STAD. To locate lncRNAs related to cuproptosis and build risk-prognosis models, three techniques were used: co-expression network analysis, Cox-regression techniques, and LASSO techniques. Additionally, an integrated methodology was used to validate the models' predictive capabilities. Then, using GO and KEGG analysis, we discovered the variations in biological functions between each group. The link between the risk score and various medications for STAD treatment was estimated using the tumor mutational load (TMB) and tumor immune dysfunction and rejection (TIDE) scores. RESULT We gathered 22 genes linked to cuproptosis based on the prior literature. Six lncRNAs related to cuproptosis were used to create a prognostic marker (AC016394.2, AC023511.1, AC147067.2, AL590705.3, HAGLR, and LINC01094). After that, the patients were split into high-risk and low-risk groups. A statistically significant difference in overall survival between the two groups was visible in the survival curves. The risk score was demonstrated to be an independent factor affecting the prognosis by both univariate and multivariate Cox regression analysis. Different risk scores were substantially related to the various immunological states of STAD patients, as further evidenced by immune cell infiltration and ssGSEA analysis. The two groups had differing burdens of tumor mutations. In addition, immunotherapy was more effective for STAD patients in the high-risk group than in the low-risk group, and risk scores for STAD were substantially connected with medication sensitivity. CONCLUSIONS We discovered a marker for six cuproptosis-associated lncRNAs linked to STAD as prognostic predictors, which may be useful biomarkers for risk stratification, evaluation of possible immunotherapy, and assessment of treatment sensitivity for STAD.
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Affiliation(s)
- Hengjia Tu
- Nanshan School, Guangzhou Medical University, Guangzhou 511436, China
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
- Correspondence: ; Tel.: +86-19860075568
| | - Qingling Zhang
- Nanshan School, Guangzhou Medical University, Guangzhou 511436, China
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Lingna Xue
- Nanshan School, Guangzhou Medical University, Guangzhou 511436, China
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Junrong Bao
- Faculty of Big Data and Computing, Guangdong Baiyun University, No.1 Xueyuan Road, Guangzhou 510450, China
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Integrating Expression Data-Based Deep Neural Network Models with Biological Networks to Identify Regulatory Modules for Lung Adenocarcinoma. BIOLOGY 2022; 11:biology11091291. [PMID: 36138770 PMCID: PMC9495551 DOI: 10.3390/biology11091291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 12/03/2022]
Abstract
Simple Summary The growing evidence suggested that competing endogenous RNAs (ceRNAs) have significant associations with tumor occurrence and progression, yet the regulatory mechanism of them in lung adenocarcinoma remains unclear. Identification of the regulatory modules for lung adenocarcinoma is a critical and fundamental step towards understanding the regulatory mechanisms during carcinogenesis. Deep neural network (DNN) models have become a powerful tool to intelligently recognize the sophisticated relationships of ceRNAs appropriately. In this paper, multiple deep neural network models were constructed using the expression data to identify regulatory modules for lung adenocarcinoma in biological networks. Three identified regulatory modules association with lung adenocarcinoma were validated from three aspects, i.e., literature review, functional enrichment analysis, and an independent dataset. The regulatory relationships between RNAs were validated in various datasets, including CPTAC, TCGA and an expression profile from the GEO database. Our study will contribute to improving the understanding of regulatory mechanisms in the carcinogenesis of lung adenocarcinoma and provide schemes for identifying novel regulatory modules of other cancers. Abstract Lung adenocarcinoma is the most common type of primary lung cancer, but the regulatory mechanisms during carcinogenesis remain unclear. The identification of regulatory modules for lung adenocarcinoma has become one of the hotspots of bioinformatics. In this paper, multiple deep neural network (DNN) models were constructed using the expression data to identify regulatory modules for lung adenocarcinoma in biological networks. First, the mRNAs, lncRNAs and miRNAs with significant differences in the expression levels between tumor and non-tumor tissues were obtained. MRNA DNN models were established and optimized to mine candidate mRNAs that significantly contributed to the DNN models and were in the center of an interaction network. Another DNN model was then constructed and potential ceRNAs were screened out based on the contribution of each RNA to the model. Finally, three modules comprised of miRNAs and their regulated mRNAs and lncRNAs with the same regulation direction were identified as regulatory modules that regulated the initiation of lung adenocarcinoma through ceRNAs relationships. They were validated by literature and functional enrichment analysis. The effectiveness of these regulatory modules was evaluated in an independent lung adenocarcinoma dataset. Regulatory modules for lung adenocarcinoma identified in this study provided a reference for regulatory mechanisms during carcinogenesis.
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Taghehchian N, Alemohammad R, Farshchian M, Asoodeh A, Abbaszadegan MR. Inhibitory role of LINC00332 in gastric cancer progression through regulating cell EMT and stemness. Life Sci 2022; 305:120759. [PMID: 35787995 DOI: 10.1016/j.lfs.2022.120759] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/11/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Gastric cancer (GC) is one of the most common lethal malignancies worldwide. The molecular mechanisms underlying GC early detection are poorly understood. Identifying potential coding and non-coding markers and related pathways in the GC progression is essential. Some Long non-coding RNAs (lncRNAs) reportedly play vital roles during gastric GC development. However, the clinical significance and biological function of LINC00332 in GC remain largely unclear. METHODS The gene expression patterns of GC from an RNAseq dataset (GSE122401) were retrieved from the Gene Expression Omnibus (GEO) database to recognize differentially expressed genes (DEGs) and lncRNAs (DELs) between normal and GC samples through several bioinformatic analysis. The expression of LINC00332 and MMP-13 as a target gene was quantified in fresh frozen tissues obtained from GC patients. In addition, we investigated the potential function of LINC00332 in silico and in vitro. RESULTS The expressions of LINC00332 and MMP-13 were significantly downregulated and upregulated in GC tissues, respectively. A significant inverse correlation between LINC00332 and MMP-13 mRNA expression was observed in tumor samples. The mRNA expression level of mesenchymal markers, stem cell factors, and MMP genes were significantly decreased after the LINC00332 ectopic expression, while epithelial markers expression was significantly increased. The LINC00332 overexpression markedly repressed proliferation, migration, and invasion and did not induce apoptosis in AGS cells. In addition, LINC00332 overexpression notably promoted the E-cadherin protein expression. Moreover, LINC00332 significantly decreased the cisplatin resistance. CONCLUSION Our findings indicated that LINC00332 may be a critical anti-EMT factor and provided a new efficient therapeutic strategy for GC treatment.
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Affiliation(s)
- Negin Taghehchian
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Reza Alemohammad
- Stem Cell and Regenerative Medicine Research Group, Academic Center for Education, Culture, and Research (ACECR), Khorasan Razavi, Mashhad, Iran
| | - Moein Farshchian
- Stem Cell and Regenerative Medicine Research Group, Academic Center for Education, Culture, and Research (ACECR), Khorasan Razavi, Mashhad, Iran.
| | - Ahmad Asoodeh
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
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Mohsenikia M, Khalighfard S, Alizadeh AM, Khori V, Ghandian Zanjan M, Zare M, Omranipour R, Patrad E, Razavi H, Malekshahi ZV, Bagheri-Hosseinabadi Z. An innovative systematic approach introduced the involved lncRNA-miR-mRNA network in cell cycle and proliferation after conventional treatments in breast cancer patients. Cell Cycle 2022; 21:1753-1774. [PMID: 35470783 PMCID: PMC9302505 DOI: 10.1080/15384101.2022.2070104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION The present study aimed to explore the involved lncRNA-miRNA-mRNA network in the cell cycle and proliferation after conventional treatments in Luminal A breast cancer patients. METHODS The candidate miRNAs (miRs), lncRNAs, and mRNAs were first taken from the Gene Expression Omnibus and TCGA databases. The lncRNA-miR-mRNA network was then constructed using the high-throughput sequencing data. The expression levels of selected targets were measured in the breast cancer and healthy samples by the Real-Time PCR technique and compared with the clinical outcomes by the Kaplan-Meier method. RESULTS Our analysis revealed a group of differentially expressed 3 lncRNAs, 9 miRs, and 14 mRNAs in breast cancer patients. A significant expression decrease of the selected tumor suppressor lncRNAs, miRs, and genes and a substantial expression increase of the selected onco-lncRNAs, oncomiRs, and oncogenes were obtained in the patients compared to the healthy group. The plasma levels of the lncRNAs, miRs, and mRNAs were more significant after the operation, chemotherapy, and radiotherapy than the pre-treatment. The Kaplan-Meier analysis indicated that the patients with a high expression of miR-21, miR-20b, IGF1R, and E2F2 and a low expression of miR-125a, PDCD4, and PTEN had exhibited a shorter overall survival rate. CONCLUSION Our results suggested that the underlying mechanisms of the lncRNA, miRs, and mRNAs and relevant signaling pathways may be considered predictive and therapeutic targets for breast cancer.
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Affiliation(s)
- Maryam Mohsenikia
- Department of Immunology, School of Medicine, Dezful University of Medical Sciences, Dezful, Iran
| | - Solmaz Khalighfard
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ali Mohammad Alizadeh
- Breast Disease Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran.,Cancer Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Khori
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Maziar Ghandian Zanjan
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mohammadreza Zare
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ramesh Omranipour
- Breast Disease Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Elham Patrad
- Cancer Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hengamesadat Razavi
- Cancer Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ziba Veisi Malekshahi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Bagheri-Hosseinabadi
- Department of Clinical Biochemistry, Faculty of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
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Li H, Ye Z, Li Z. Identification of the potential biological target molecules related to primary open-angle glaucoma. BMC Ophthalmol 2022; 22:188. [PMID: 35461232 PMCID: PMC9034601 DOI: 10.1186/s12886-022-02368-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 03/21/2022] [Indexed: 12/31/2022] Open
Abstract
Background To identify the potential biological target molecules and the corresponding interaction networks in primary open-angle glaucoma (POAG) development. Methods The microarray datasets of GSE138125 and GSE27276 concerning lncRNA and mRNA expression profiles in trabecular meshwork of POAG were downloaded from the Gene Expression Omnibus database. The R software was applied to identify differentially expressed (DE) lncRNAs and mRNAs in POAG, and to perform GO and KEGG functional enrichment analysis. Protein–protein interaction (PPI) network and module analysis, and lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network were performed by Cytoscape software. Results A total of 567 DE-mRNAs were identified from GSE138125 and GSE27276, including 298 up-regulated and 269 down-regulated mRNAs, which were found enriching in biological processes of extracellular matrix organization and epidermis development, respectively. KEGG pathway enrichment analysis further revealed that module genes in PPI network were primarily involved in the AGE-PAGE, PI3K-Akt and TGF-β signaling pathways. Moreover, 897 up-regulated and 1036 down-regulated DE-lncRNAs were identified from GSE138125. Through literature review and databases searching, we obtained 712 lncRNA-miRNA and 337 miRNA-mRNA pairs based on the selected eight POAG-related miRNAs. After excluding 702 lncRNAs and 284 mRNAs that were not comprised in the DE-lncRNA and DE-mRNAs, a total of 53 lncRNA nodes, eight miRNA nodes, 10 mRNA nodes, and 78 edges were included in the final ceRNA network. Conclusions This study demonstrated the lncRNA and mRNA expression profiles of trabecular meshwork in POAG patients and the normal controls, and identified potentially ceRNAs and pathways which might improve the pathogenic understanding of this ocular disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12886-022-02368-0.
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Affiliation(s)
- Hongyu Li
- Medical School of Chinese PLA, Beijing, China.,Senior Department of Ophthalmology, the Third Medical Center of PLA General Hospital, Beijing, China
| | - Zi Ye
- Senior Department of Ophthalmology, the Third Medical Center of PLA General Hospital, Beijing, China.
| | - Zhaohui Li
- Medical School of Chinese PLA, Beijing, China. .,Senior Department of Ophthalmology, the Third Medical Center of PLA General Hospital, Beijing, China.
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Zhang X, Dai X, Zhao X, Wang J, Dou J, Zhuang H, Chen N, Zhao H. MiR-874-3p represses the migration and invasion yet promotes the apoptosis and cisplatin sensitivity via being sponged by long intergenic non-coding RNA 00922 (LINC00922) and targeting Glycerophosphodiester Phosphodiesterase Domain Containing 5 (GDPD5) in gastric cancer cells. Bioengineered 2022; 13:7082-7104. [PMID: 35282764 PMCID: PMC9208458 DOI: 10.1080/21655979.2022.2045831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Our study mainly reports the specific mechanisms of microRNA (miR)-874-3p on drug resistance in gastric cancer (GC). Clinical specimen was collected. The upstream long non-coding RNA (lncRNA) and the downstream gene of miR-874-3p were predicted using bioinformatic analysis with the results being ascertained with dual-luciferase reporter assay. The viability, apoptosis, migration and invasion of transfected GC cells with or without cisplatin (DDP) treatment were evaluated by Cell Counting Kit-8 (CCK-8), flow cytometric, Scratch, and Transwell assays. An animal xenograft model was constructed. Expressions of long intergenic non-coding RNA 00922 (LINC00922), miR-874-3p and potential target genes were quantified by quantitative real-time polymerase-chain reaction (qRT-PCR) and Western blot. MiR-874-3p, which was lower-expressed in drug-resistant GC tissues and cells, was upregulated to repress the viability, migration and invasion but enhance the apoptosis and sensitivity in GC cells with or without DDP resistance. Downregulation of miR-874-3p eliminated the effects of silenced LINC00922, a upstream lncRNA of miR-874-3p, on cell viability, apoptosis, migration and invasion, as well as the expressions of Glycerophosphodiester Phosphodiesterase Domain Containing 5 (GDPD5) and the downstream gene of miR-874-3p in DDP-resistant GC cells. GDPD5 silencing diminished the effects of miR-874-3p downregulation on GDPD5 expression, viability, migration and invasion of DDP-resistant GC cells. Additionally, LINC00922 silencing enhanced the inhibitory effect of DDP on tumor growth, whereas reversing the effects of DDP on LINC00922, miR-874-3p and GDPD5 expressions in tumors. MiR-874-3p, an miRNA, which is sponged by LINC00922 and targets GDPD5, inhibits the GC progression yet enhances the DDP sensitivity in GC.
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Affiliation(s)
- Xiaoyu Zhang
- Division of Gastrointestinal Surgery, Department of General Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huaian, Jiangsu, China
| | - Xudong Dai
- Department of General Surgery, Lianshui People's Hospital Affiliated to Kangda College of Nanjing Medical University, Huaian, Jiangsu, China
| | - Xin Zhao
- Division of Gastrointestinal Surgery, Department of General Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huaian, Jiangsu, China
| | - Jian Wang
- Division of Gastrointestinal Surgery, Department of General Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huaian, Jiangsu, China
| | - Jin Dou
- Division of Gastrointestinal Surgery, Department of General Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huaian, Jiangsu, China
| | - Haiwen Zhuang
- Division of Gastrointestinal Surgery, Department of General Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huaian, Jiangsu, China
| | - Ning Chen
- Division of Gastrointestinal Surgery, Department of General Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huaian, Jiangsu, China
| | - Haijian Zhao
- Division of Gastrointestinal Surgery, Department of General Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huaian, Jiangsu, China
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Wang Q, Wang LX, Zhang CY, Bai N, Feng C, Zhang ZM, Wang L, Gao ZZ. LncRNA CRNDE promotes cell proliferation, migration and invasion of ovarian cancer via miR-423-5p/FSCN1 axis. Mol Cell Biochem 2022; 477:1477-1488. [PMID: 35166986 DOI: 10.1007/s11010-022-04382-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/31/2022] [Indexed: 02/06/2023]
Abstract
Ovarian cancer seriously threatens the health of women. LncRNA CRNDE is known to be upregulated in ovarian cancer. However, the mechanism by which CRNDE regulates the progress of ovarian cancer is largely unknown. MTT assay was applied to measure the cell viability. Colony formation assay was used to measure the cell proliferation. Cell migration was tested by wound healing, and Transwell assay was performed to detect cell invasion. In addition, the expression of miR-423-5p, CRNDE and FSCN1 were detected by RT-qPCR and western blotting, respectively. Meanwhile, dual-luciferase reporter assay and RIP assay were performed to explore the correlation between miR-423-5p and CRNDE (or FSCN1). CRNDE and FSCN1 were upregulated in ovarian cancer cells (SKOV3, CAOV-3, IGROV1, A2780 and C13K), while miR-423-5p was downregulated. Moreover, silencing of FSCN1/CRNDE significantly decreased proliferation, migration and invasion of ovarian cancer cells (SKOV3 and CI3K) via suppressing MMP-2 and MMP-9. In addition, CRNDE could sponge miR-423-5p, and FSCN1 was confirmed to be the direct target of miR-423-5p. Furthermore, CRNDE knockdown-induced inhibition of FSCN1 was notably reversed by miR-423-5p downregulation. Knockdown of CRNDE inhibited cell proliferation, migration and invasion of ovarian cancer via miR-423-5p/FSCN1 axis. Thus, CRNDE may serve a new target for ovarian cancer.
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Affiliation(s)
- Qiong Wang
- Department of Pathology, the First Medical Center of PLA General Hospital, Beijing, 100853, China
| | - Ling-Xiong Wang
- Institute of Oncology, the Fifth Medical Center of PLA General Hospital, Beijing, 100853, China
| | - Chun-Yan Zhang
- Birth Defects Prevention and Control Technology Research Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Nan Bai
- The Medicine Clinical Research Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Chen Feng
- Department of Pediatrics, the Seventh Medical Center of PLA General Hospital, Beijing, 100853, China
| | - Zhuo-Mei Zhang
- Department of Obstetrics and Gynecology, the Third Medical Center of PLA General Hospital, No. 69, Yongding Road, Haidian District, Beijing, 100039, China
| | - Liang Wang
- Department of Pathology, the First Medical Center of PLA General Hospital, Beijing, 100853, China
| | - Zhen-Zhen Gao
- Department of Obstetrics and Gynecology, the Third Medical Center of PLA General Hospital, No. 69, Yongding Road, Haidian District, Beijing, 100039, China.
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Hu R, Yu Y, Wang H. The LMCD1-AS1/miR-526b-3p/OSBPL5 axis promotes cell proliferation, migration and invasion in non-small cell lung cancer. BMC Pulm Med 2022; 22:30. [PMID: 35000595 PMCID: PMC8744214 DOI: 10.1186/s12890-022-01820-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/31/2021] [Indexed: 11/10/2022] Open
Abstract
PURPOSE To explore the specific role and regulatory mechanism of oxysterol binding protein like 5 (OSBPL5) in non-small cell lung cancer (NSCLC). METHODS AND RESULTS Quantitative real-time polymerase chain reaction (qRT-PCR) analysis demonstrated that OSBPL5 expression was notably elevated in NSCLC tissues and cell lines, and Kaplan-Meier analysis manifested that high OSBPL5 expression was closely related to the poor prognosis of NSCLC patients. Besides, according to the results from western blot analysis, cell counting kit-8, EdU and Transwell assays, knockdown of OSBPL5 suppressed NSCLC cell proliferation, migration, invasion and epithelial-mesenchymal transition (EMT) process. Additionally, by performing qRT-PCR analysis, luciferase reporter and RNA pull-down assays, we verified that OSBPL5 was a downstream target of miR-526b-3p and long noncoding RNA (lncRNA) LMCD1-AS1 served as a sponge for miR-526b-3p. Moreover, from rescue assays, we observed that OSBPL5 overexpression offset LMCD1-AS1 knockdown-mediated inhibition in cell proliferation, migration, invasion and EMT in NSCLC. CONCLUSIONS This paper was the first to probe the molecular regulatory mechanism of OSBPL5 involving the LMCD1-AS1/miR-526b-3p axis in NSCLC and our results revealed that the LMCD1-AS1/miR-526b-3p/OSBPL5 axis facilitates NSCLC cell proliferation, migration, invasion and EMT, which may offer a novel therapeutic direction for NSCLC.
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Affiliation(s)
- Rui Hu
- Department of Thoracic Surgery, Shengli Oilfield Central Hospital, 31 Jinan Road, Dongying, 257034, Shandong, China
| | - Yankai Yu
- Department of Thoracic Surgery, Shengli Oilfield Central Hospital, 31 Jinan Road, Dongying, 257034, Shandong, China
| | - Haining Wang
- Department of Thoracic Surgery, Shengli Oilfield Central Hospital, 31 Jinan Road, Dongying, 257034, Shandong, China.
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Liu W, Lin W, Yu L. Long non-coding RNA muscleblind like splicing regulator 1 antisense RNA 1 (LncRNA MBNL1-AS1) promotes the progression of acute myocardial infarction by regulating the microRNA-132-3p/SRY-related high-mobility-group box 4 (SOX4) axis. Bioengineered 2022; 13:1424-1435. [PMID: 34978261 PMCID: PMC8805923 DOI: 10.1080/21655979.2021.2018974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/10/2021] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNA muscleblind like splicing regulator 1 antisense RNA 1 (LncRNA MBNL1-AS1) exerts vital role in various physiological processes. However, its functions in acute myocardial infarction (AMI) are not elucidated. AMI model was constructed using Wistar rats and it was found that LncRNA MBNL1-AS1 was upregulated in AMI model according to the quantitative real-time polymerase chain reaction (qRT-PCR) results. The left ventricular systolic pressure (LVSP), left ventricular end diastolic pressure (LVEDP) and maximum rate of rise/fall of left ventricle pressure (±dp/dt max) were detected through hemodynamics test, which showed that knockdown of MBNL1-AS1 improved cardiac function in AMI model. Next, the myocardial infarction area was estimated by triphenyltetrazole chloride (TTC) staining, and the levels of cardiac troponin I (cTn-I) and creatine kinase-MB (CK-MB) were detected by enzyme-linked immunosorbent assay (ELISA) kit. The results revealed that silencing MBLN1-AS1 alleviated myocardial injury in AMI model. Additionally, MBNL1-AS1 knockdown inhibited apoptosis of myocardial cells and reduced the expression of apoptotic proteins. According to DIANA database and luciferase reporter assay, miR-132-3p was the direct target of MBNL1-AS1 and was negatively regulated by MBNL1-AS1. Furthermore, Targetscan database predicted that SRY-related high-mobility-group box 4 (SOX4) was the direct target of miR-132-3p and was regulated by MBNL1-AS1 through miR-132-3p. Moreover, overexpression of SOX4 partially eliminated effects of MBNL1-AS1 on myocardial cells. In conclusion, this investigation for the first time revealed that LncRNA MBNL1-AS1 was the potential target for treating AMI and expounded the underlying mechanisms of it.
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Affiliation(s)
- Weifeng Liu
- Department of Cardiology, Yantai Yuhuangding Hospital, Qingdao Medical College, Qingdao University, Yantai, China
| | - Wenyuan Lin
- Department of Cardiology, Yantai Yuhuangding Hospital, Qingdao Medical College, Qingdao University, Yantai, China
| | - Liangliang Yu
- Department of Cardiology, Yantai Yuhuangding Hospital, Qingdao Medical College, Qingdao University, Yantai, China
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Wang L, Wang H, Xu K, Xu Y, Wang Y, Wei S, Zhang Z. Exploration of immune-related cells and ceRNA in squamous cell lung cancer. Medicine (Baltimore) 2021; 100:e27058. [PMID: 34477137 PMCID: PMC8415993 DOI: 10.1097/md.0000000000027058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/06/2021] [Indexed: 01/05/2023] Open
Abstract
The treatment for squamous cell lung cancer (SqCLC) is limited, and the prognosis of SqCLC is poor. In this article, we aimed to analyze and identify immune-related cells and competition endogenous RNA (ceRNA) that influence the prognosis of SqCLC. SqCLC and lung adenocarcinoma data were downloaded from TCGA-GDC. A total of 22 types of immune cell fractions were estimated using CIBERSORT. R software was used to identify any significantly different transcriptome data, including mRNA, LncRNA, and miRNA. The univariate cox regression method was applied to screen for prognosis-related lncRNA, miRNA, mRNA and tumor-infiltrating immune cells. There were 504 patients included in this study. There was a higher proportion of memory activated CD4+ T cells and CD8+ T cells in younger women. Follicular helper T (Tfh) cells were predictive of a good prognosis and reflected immune activation in SqCLC. The SFTA1P/NKX2-1-AS1, hsa-mir-503, GREM2 ceRNA axes and NKX2-1-AS1, hsa-mir-96, PROK2 ceRNA axes were found to be important for the immune function, pathogenesis, and prognosis of SqCLC. Collectively, the immune-related ceRNA and tumor-infiltrating immune cells in SqCLC are likely important determinants of SqCLC pathogenesis, prognosis, and immune status.
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Affiliation(s)
- Lijun Wang
- Department of Respiratory Disease, Building 8 of Tongling People's Hospital, Tongling
| | - Hao Wang
- Department of Respiratory Oncology, Anhui Provincial Cancer Hospital (The First Affiliated Hospital of USTC West District), Hefei
| | - Ke Xu
- Department of Respiratory Oncology, Anhui Provincial Cancer Hospital (The First Affiliated Hospital of USTC West District), Hefei
| | - Yehong Xu
- Department of Respiratory Oncology, Anhui Provincial Cancer Hospital (The First Affiliated Hospital of USTC West District), Hefei
| | - Yong Wang
- Department of Respiratory Disease, The Fifth People's Hospital of Fuyang City, Fuyang, Anhui, P.R. China
| | - Song Wei
- Department of Respiratory Oncology, Anhui Provincial Cancer Hospital (The First Affiliated Hospital of USTC West District), Hefei
| | - Zhihong Zhang
- Department of Respiratory Oncology, Anhui Provincial Cancer Hospital (The First Affiliated Hospital of USTC West District), Hefei
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13
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Li P, Wang L, Li P, Hu F, Cao Y, Tang D, Ye G, Li H, Wang D. Silencing of long non-coding RNA XIST represses gastric cancer progression through blocking NFκB pathway via inhibiting HNF4A-mediated transcription of EPHA1. Cancer Gene Ther 2021; 28:307-320. [PMID: 33199830 DOI: 10.1038/s41417-020-00220-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 07/05/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023]
Abstract
Gastric cancer (GC) is a common cancer and a leading cause of cancer-related deaths worldwide. Recent studies have supported the important role of long non-coding RNAs (lncRNAs) in GC progression. This study identified functional significance of X inactive specific transcript (XIST) in GC. The expression of XIST and EPHA1 in GC tissues and cells was measured. Then, dual luciferase reporter gene assay, RNA immunoprecipitation (RIP) assay and Chromatin Immunoprecipitation (ChIP) assay were performed to explore the interaction among XIST, EPHA1 and HNF4A. The effects of XIST on GG progression were evaluated by determining expression of proliferation- and invasion-related proteins (Ki67, PCNA, MMP-2, and MMP-9). Further, the functional role of XIST in GC with the involvement of NFκB pathway was also analyzed. Subsequently, the tumor growth in nude mice was evaluated. High expression of XIST and EPHA1 was observed in GC. XIST elevated EPHA1 expression by recruiting HNF4A. In addition, silencing of XIST inhibited GC progression in vitro and in vivo. Overexpressed XIST and EPHA1 yielded a reversed effect on cell proliferation and invasion. SN50 treatment (inhibitor of NFκB pathway) counteracted the promotive effect on GC cell proliferation and invasion mediated by XIST. The present study unveils that XIST increases the enrichment of HNF4A in the promoter region of EPHA1, thus promoting the deterioration of GC.
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MESH Headings
- Animals
- Cell Line, Tumor
- Cell Proliferation/physiology
- Disease Progression
- Hepatocyte Nuclear Factor 4/antagonists & inhibitors
- Hepatocyte Nuclear Factor 4/metabolism
- Heterografts
- Humans
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- NF-kappa B/metabolism
- RNA, Long Noncoding/antagonists & inhibitors
- RNA, Long Noncoding/biosynthesis
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Receptor, EphA1/genetics
- Receptor, EphA1/metabolism
- Signal Transduction
- Stomach Neoplasms/genetics
- Stomach Neoplasms/metabolism
- Stomach Neoplasms/pathology
- Transcription, Genetic
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Affiliation(s)
- Ping Li
- Department of Central Laboratory, Huaian Tumor Hospital & Huaian Hospital of Huaian City, Huaian, 223200, PR China
- Department of General Surgery, Huaian Tumor Hospital & Huaian Hospital of Huaian City, Huaian, 223200, PR China
- Department of Experimental Surgery-Cancer Metastasis, Medical Faculty Mannheim, Ruprecht Karls University, Mannheim, 68167, Germany
| | - Liuhua Wang
- Department of General Surgery, Northern Jiangsu Province Hospital, Clinical Medical College, Institute of General Surgery-Yangzhou, Yangzhou University, Yangzhou, 225000, PR China
| | - Pengfei Li
- Department of Central Laboratory, Huaian Tumor Hospital & Huaian Hospital of Huaian City, Huaian, 223200, PR China
- Department of General Surgery, Huaian Tumor Hospital & Huaian Hospital of Huaian City, Huaian, 223200, PR China
| | - Fangyong Hu
- Department of Central Laboratory, Huaian Tumor Hospital & Huaian Hospital of Huaian City, Huaian, 223200, PR China
- Department of General Surgery, Huaian Tumor Hospital & Huaian Hospital of Huaian City, Huaian, 223200, PR China
| | - Yi Cao
- Department of Experimental Surgery-Cancer Metastasis, Medical Faculty Mannheim, Ruprecht Karls University, Mannheim, 68167, Germany
| | - Dong Tang
- Department of General Surgery, Northern Jiangsu Province Hospital, Clinical Medical College, Institute of General Surgery-Yangzhou, Yangzhou University, Yangzhou, 225000, PR China
| | - Gang Ye
- Department of General Surgery, Jiangdu People's Hospital of Yangzhou, Yangzhou, 225200, PR China
| | - Hongbo Li
- Department of General Surgery, Jiangdu People's Hospital of Yangzhou, Yangzhou, 225200, PR China.
| | - Daorong Wang
- Department of General Surgery, Northern Jiangsu Province Hospital, Clinical Medical College, Institute of General Surgery-Yangzhou, Yangzhou University, Yangzhou, 225000, PR China
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14
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LncRNA DLEU2 is activated by STAT1 and induces gastric cancer development via targeting miR-23b-3p/NOTCH2 axis and Notch signaling pathway. Life Sci 2021; 277:119419. [PMID: 33785336 DOI: 10.1016/j.lfs.2021.119419] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Gastric cancer (GC) has severely affected the health of patients and caused high mortality around the world. Long non-coding RNAs (lncRNAs) have been validated to play significant roles in biological process of multiple cancers. METHODS Quantitative real-time PCR (RT-qPCR) and western blot analysis were conducted to evaluate the expression levels and protein levels of related genes in GC cells. Functional assays were implemented to explore the effect of deleted in lymphocytic leukemia 2 (DLEU2). The upstream and downstream mechanisms of DLEU2 were verified by mechanism investigations. RESULTS The expression of long non-coding RNA (lncRNA) DLEU2 was observably high in GC cells and tissues. DLEU2 silence depressed the capacities of proliferation, migration and invasion but promoted apoptosis in GC cells. Moreover, DLEU2 was activated by signal transducer and activator of transcription 1 (STAT1) and sequestered microRNA-23b-3p (miR-23b-3p) to modulate the expression of notch receptor 2 (NOTCH2), thereby stimulating Notch signaling pathway. More importantly, DLEU2 contributed to GC progression via targeting miR-23b-3p/NOTCH2 axis. CONCLUSIONS In summary, our research identified the STAT1/DLEU2/miR-23b-3p/NOTCH2/Notch axis in GC development, indicating that DLEU2 might function as a novel biomarker in GC.
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15
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Long non-coding RNA DPP10-AS1 exerts anti-tumor effects on colon cancer via the upregulation of ADCY1 by regulating microRNA-127-3p. Aging (Albany NY) 2021; 13:9748-9765. [PMID: 33744851 PMCID: PMC8064199 DOI: 10.18632/aging.202729] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/01/2020] [Indexed: 02/06/2023]
Abstract
Herein we hypothesized that DPP10-AS1 could affect the development of colon cancer via the interaction with miR-127-3p and adenylate cyclase 1 (ADCY1). After sorting of CD133 positive cells, sphere formation, colony formation, proliferation, invasion, migration, and apoptosis were detected to explore the involvement of DPP10-AS1 and miR-127-3p in the colon cancer stem cell (CCSC) properties through gain- and loss-of function approaches. Furthermore, tumor xenograft in nude mice was conducted to investigate the effect of DPP10-AS1 and miR-127-3p on tumor growth in vivo. Poorly expressed DPP10-AS1 and ADCY1, while highly expressed miR-127-3p were found in CCSCs. Low expression of DPP10-AS1 was correlated with TNM stage, lymphatic node metastasis, and tumor differentiation. Upregulation of DPP10-AS1 increased ADCY1 protein expression, decreased the protein expression of CCSC-related factors, inhibited sphere formation, colony formation, proliferation, invasion and migration, and accelerated apoptosis of HT-29 and SW480 cells by suppressing the expression of miR-127-3p. Further, the above in vitro findings were also confirmed by in vivo assays. Taken together, this study demonstrates that DPP10-AS1 inhibits CCSC proliferation by regulating miR-127-3p and ADCY1, providing fresh insight into a promising novel treatment strategy for colon cancer.
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16
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Zhong Y, Lin H, Li Q, Liu C, Zhong L. Downregulation of long non‑coding RNA GACAT1 suppresses proliferation and induces apoptosis of NSCLC cells by sponging microRNA‑422a. Int J Mol Med 2021; 47:659-667. [PMID: 33416153 PMCID: PMC7797425 DOI: 10.3892/ijmm.2020.4826] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
Increasing evidence has demonstrated the important roles of long non‑coding (lnc) RNA in non‑small cell lung cancer (NSCLC). lncRNA gastric cancer‑associated transcript 1 (GACAT1) has been reported to play an oncogenic role in different types of cancer; however, the function of GACAT1 in NSCLC remains unclear. The present study found that GACAT1 was overexpressed in NSCLC tissues and was associated with poor outcomes in patients with NSCLC. Functional experiments revealed that GACAT1 downregulation inhibited proliferation, induced apoptosis and cell cycle arrest of 2 NSCLC cell lines. GACAT1 was found to target microRNA(miR)‑422a mechanically and negatively regulated miR‑422a expression. Reduced expression of miR‑422a in NSCLC tissues was inversely correlated with that of GACAT1. Furthermore, YY1 transcription factor (YY1) was identified as a downstream miR‑422a target. Reduced expression of GACAT1 inactivated YY1 by sponging miR‑422a in NSCLC cells. YY1 reintroduction reversed the reduced proliferation of NSCLC cells via GACAT1 knockdown. Taken together, these results revealed the novel role of the GACAT1/miR‑422a pathway in the progression of NSCLC cell lines, providing a possible therapeutic strategy for NSCLC treatment.
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Affiliation(s)
- Youqing Zhong
- Department of Respiratory Medicine, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan 571100
| | - Hui Lin
- Department of Anesthesia, Hainan General Hospital, Haikou, Hainan 570311
| | - Qi Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan 571100
| | - Chang Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan 571100
| | - Lei Zhong
- Clinical Laboratory, Ganzhou People's Hospital of Jiangxi Province, Ganzhou, Jiangxi 341000, P.R. China
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17
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Dong R, Zhang B, Tan B, Lin N. Long non-coding RNAs as the regulators and targets of macrophage M2 polarization. Life Sci 2021; 266:118895. [PMID: 33310042 DOI: 10.1016/j.lfs.2020.118895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/16/2020] [Accepted: 12/04/2020] [Indexed: 12/30/2022]
Abstract
Macrophages are immune cells with high heterogeneity and plasticity. M2 polarization is one extreme of the well-established phenotypes of macrophage polarization, and involves in diverse biological processes. The polarization process is initiated at the command of numerous components. Long non-coding RNAs (lncRNAs) are RNAs longer than 200 nucleotides with limited protein-coding capacity. Recent studies have revealed a newly found subset of lncRNAs engaged in the M2 polarization and their potent and multifunctional roles in developing diseases. By interfering with specific signaling pathways and altering the active mode, acting as the sponges of microRNAs or decoys of transcription factors, lncRNAs prompted macrophages to an M2 phenotype. Further, lncRNAs can bind to the genome to regulate the chromatin dynamics or work as a platform for protein complexes tether. Exosomal lncRNAs can also orchestrate the polarization in a paracrine way. To make it easier to interpret the roles of lncRNAs in the M2 polarization, we review the reported lncRNAs according to the underlying mechanisms. Moreover, we discuss the possibilities of targeting macrophages' M2 polarization using the oligonucleotides drugs or clustered regularly interspaced palindromic repeats (CRISPR) technologies to provoke wisdom on the therapeutic strategies.
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Affiliation(s)
- Rong Dong
- Department of Clinical Pharmacy, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Bo Zhang
- Translational Medicine Research Center, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 31006, China
| | - Biqin Tan
- Department of Clinical Pharmacy, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Nengming Lin
- Department of Clinical Pharmacy, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China; Translational Medicine Research Center, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 31006, China.
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18
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Jiang Y, Wang J, Chen J, Wang J, Xu J. Construction and analysis of an aberrant lncRNA-miRNA-mRNA network associated with papillary thyroid cancer. Medicine (Baltimore) 2020; 99:e22705. [PMID: 33157921 PMCID: PMC7647549 DOI: 10.1097/md.0000000000022705] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Accumulating evidence has indicated that long noncoding RNAs (lncRNAs) are the main constituents of competing endogenous RNA (ceRNA) networks. Nonetheless, in the lncRNA-related ceRNA network of papillary thyroid cancer (PTC), the function of cancer-specific lncRNAs, as well as their use for the potential prediction of PTC prognosis, remains unclear. In this study, 384 RNA sequencing (RNA-seq) profiles of PTC patients were attained from The Cancer Genome Atlas (TCGA), an open-source database that offers vast amounts of RNA-seq data, and 75 miRNAs, 495 lncRNAs, and 1099 mRNAs (P < .05 and |logFC| >2) were detected when compared with normal tissues. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed using the Cytoscape plug-in BinGo. An aberrant lncRNA-mRNA-miRNA ceRNA network consisting of 31 differentially expressed (DE)-lncRNAs, 13 DE-miRNAs, and 134 DE-mRNAs was built in TCGA. On the basis of overall survival (OS) analysis, 6 lncRNAs (CCAT1, SYNPR, SFTA1P, HOTAIR, HCG22, and CLDN10) were identified as prognostic biomarkers for patients in TCGA (P < .05). Through qRT-PCR, we designated 6 cancer-specific lncRNAs as having great significance for survival by verifying their expression in the 60 PTC patients who were diagnosed. The qRT-PCR and TCGA results were completely consistent. Our research provides data for further understanding the lncRNA-miRNA-mRNA ceRNA network and elucidating the molecular mechanisms of PTC.
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Affiliation(s)
| | - Jiao Wang
- Department of Endocrinology and Metabolism
| | - Jian Chen
- Department of Hematology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
| | | | - Jixiong Xu
- Department of Endocrinology and Metabolism
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19
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Wu F, Ning L, Zhou R, Shen A. Screening and evaluation of key genes in contributing to pathogenesis of hepatic fibrosis based on microarray data. Eur J Med Res 2020; 25:43. [PMID: 32943114 PMCID: PMC7499914 DOI: 10.1186/s40001-020-00443-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/11/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Hepatic fibrosis (HF), which is characterized by the excessive accumulation of extracellular matrix (ECM) in the liver, usually progresses to liver cirrhosis and then death. To screen differentially expressed (DE) long non-coding RNAs (lncRNAs) and mRNAs, explore their potential functions to elucidate the underlying mechanisms of HF. METHODS The microarray of GSE80601 was downloaded from the Gene Expression Omnibus database, which is based on the GPL1355 platform. Screening for the differentially expressed LncRNAs and mRNAs was conducted between the control and model groups. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to analyze the biological functions and pathways of the DE mRNAs. Additionally, the protein-protein interaction (PPI) network was delineated. In addition, utilizing the Weighted Gene Co-expression Network Analysis (WGCNA) package and Cytoscape software, we constructed lncRNA-mRNA weighted co-expression networks. RESULTS A total of 254 significantly differentially expressed lncRNAs and 472 mRNAs were identified. GO and KEGG analyses revealed that DE mRNAs regulated HF by participating in the GO terms of metabolic process, inflammatory response, response to wounding and oxidation-reduction. DE mRNAs were also significantly enriched in the pathways of ECM-receptor interaction, PI3K-Akt signaling pathway, focal adhesion (FA), retinol metabolism and metabolic pathways. Moreover, 24 lncRNAs associated with 40 differentially expressed genes were observed in the modules of lncRNA-mRNA weighted co-expression network. CONCLUSIONS This study revealed crucial information on the molecular mechanisms of HF and laid a foundation for subsequent genes validation and functional studies, which could contribute to the development of novel diagnostic markers and provide new therapeutic targets for the clinical treatment of HF.
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Affiliation(s)
- Furong Wu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, People's Republic of China
| | - Lijuan Ning
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, People's Republic of China
| | - Ran Zhou
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, People's Republic of China
| | - Aizong Shen
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, People's Republic of China.
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Gastritis Stages in Monozygotic and Dizygotic Dyspeptic Twins. Gastroenterol Res Pract 2020; 2020:9510717. [PMID: 32714389 PMCID: PMC7352144 DOI: 10.1155/2020/9510717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 02/08/2023] Open
Abstract
Background The progression of Helicobacter pylori-associated gastritis towards atrophic gastritis is modulated by host-related and environmental factors. Studies that explore the possible involvement of host-related versus environmental factors in the development of gastritis phenotype induced by H. pylori are highly needed. Aims Our study was aimed at investigating the phenotype of H. pylori-associated gastritis in two cohorts of monozygotic and dizygotic twins, using the OLGA/OLGIM gastritis staging system. Methods Two cohorts of monozygotic (14 pairs) and dizygotic (15 pairs) dyspeptic twins prospectively underwent endoscopy with biopsy sampling based on Sydney protocol. H. pylori status and OLGA/OLGIM stages were assessed and compared. Results The mean age of monozygotic and dizygotic twins was 40.4 and 38.6 years, respectively (p = 0.623). The overall prevalence of H. pylori infection was 51.7%. Among the 14 monozygotic twin pairs, five pairs were H. pylori-positive, four were H. pylori-negative, and five were H. pylori-discordant. Among the 15 dizygotic twin pairs, five pairs were H. pylori-positive, five were H. pylori-negative, and five were H. pylori-discordant. Concordance for antrum atrophy in monozygotic twins was 78.6% (11/14 pairs) and in dizygotic twins 73.3% (11/15 pairs) (p = 0.742). Concordance for corpus atrophy in monozygotic versus dizygotic twins was 92.9% (13/14 pairs) and 86.7% (13/15 pairs), respectively (p = 0.584). Concordance for antrum intestinal metaplasia (IM) in monozygotic twins was 85.7% (12/14 pairs) and in dizygotic 73.3% (11/15 pairs) (p = 0.411). Concordance for corpus IM in monozygotic twins was 85.7% (12/14 pairs) and in dizygotic 86.7% (13/15 pairs) (p = 0.941). Among monozygotic and dizygotic subjects, the stage of gastritis was concordant in both H. pylori-positive and H. pylori-negative subjects. Conclusions In conclusion, histological gastric mucosa alterations in monozygotic and dizygotic twins showed high rates of concordance. Furthermore, OLGA/OLGIM gastritis stages were not modulated by the zygosity of the twins.
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21
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Chen P, Zhang W, Chen Y, Zheng X, Yang D. Comprehensive analysis of aberrantly expressed long non‑coding RNAs, microRNAs, and mRNAs associated with the competitive endogenous RNA network in cervical cancer. Mol Med Rep 2020; 22:405-415. [PMID: 32377727 PMCID: PMC7248517 DOI: 10.3892/mmr.2020.11120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 03/20/2020] [Indexed: 02/06/2023] Open
Abstract
Cervical cancer is a common malignant disease that poses a serious health threat to women worldwide. Growing research efforts have focused on protein‑coding and non‑coding RNAs involved in the tumorigenesis and prognosis of various types of cancer. The potential molecular mechanisms and the interaction among long non‑coding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs require further investigation in cervical cancer. In the present study, lncRNA, miRNA, and mRNA expression profiles of 304 primary tumor tissues from patients with cervical cancer and 3 solid normal tissues from The Cancer Genome Atlas (TCGA) dataset were studied via RNA sequencing (RNA‑seq). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using R package clusterProfiler to annotate the principal functions of differentially expressed (DE) mRNAs. Kaplan‑Meier analysis was also conducted to investigate the effects of DElncRNAs, DEmiRNAs, and DEmRNAs on overall survival. A total of 2,255 mRNAs, 133 miRNAs, and 150 lncRNAs that were differentially expressed were identified with a threshold of P<0.05 and |fold change (FC)|>2. Functional enrichment analysis indicated that DEmRNAs were enriched in cancer‑associated KEGG pathways. Furthermore, 255 mRNAs, 15 miRNAs, and 12 lncRNAs that were significantly associated with overall survival in cervical carcinoma were also identified. Importantly, an miRNA‑mediated competitive endogenous RNA (ceRNA) network was successfully constructed based on the expression profiles of DElncRNAs and DEmRNAs. More importantly, it was found that the lncRNA EPB41L4A‑AS1 may function as a pivotal regulator in carcinoma of the uterine cervix. Taken together, the present study has provided novel insights into investigating the potential mechanisms underlying tumorigenesis, development, and prognosis of cervical cancer, and presented new potential avenues for cancer therapeutics.
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Affiliation(s)
- Peng Chen
- Department of Obstetrics and Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100000, P.R. China
| | - Weiyuan Zhang
- Department of Obstetrics and Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100000, P.R. China
| | - Yu Chen
- Department of Obstetrics and Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100000, P.R. China
| | - Xiaoli Zheng
- Department of Obstetrics and Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100000, P.R. China
| | - Dong Yang
- Department of Obstetrics and Gynecology, Beijing Shijitan Hospital, Capital Medical University, Beijing 100000, P.R. China
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Liu X, Gao L, Ni D, Ma C, Lu Y, Huang X. Candidate genes for predicting the survival of patients with gastric cancer: a study based on The Cancer Genome Atlas (TCGA) database. Transl Cancer Res 2020; 9:2599-2608. [PMID: 35117619 PMCID: PMC8798540 DOI: 10.21037/tcr.2020.02.82] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/08/2020] [Indexed: 01/17/2023]
Abstract
Background Gastric cancer (GC) is the second most frequent cause of cancer-related mortality in the world, and the five-year survival rate for GC remains very low universally. In recent years, it has become a consensus that genetic changes are associated with carcinogenesis of GC, and precision medicine based on genetic changes is one of the most popular treatments for GC patients. However, the association between some genes and GC-related protein signaling pathways is still not well understood. This study revealed that seven genes were closely related to the survival probability in GC patients. Methods We downloaded the gene expression data of GC patients from The Cancer Genome Atlas (TCGA) databases, and integrated bioinformatic analysis was performed, such as differential gene expression analysis, including Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathways analyses, as well as survival analysis. The r package “survival” was used to analyze the Kaplan-Meier survival analysis, which showed the associations between specific gene expressions and the outcomes of patients with GC to identify which genes could be potential prognostic biomarkers. Results This study revealed that seven genes: alcohol dehydrogenase 4 (ADH4), histamine receptor H3 (HRH3), neuropeptide Y2 receptor (NPY2R), apolipoprotein AI (APOA1), N-acetylgalactosaminyltransferase 14 (GALNT14), leucine-rich repeats and IQ motif containing 1 (LRRIQ1), and coiled-coil-domain-containing 57 (CCDC57). These seven genes were closely related to the survival probability of GC patients (P<0.05). Conclusions Our study found seven genes which could be considered as candidate prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Xiqiao Liu
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, China
| | - Liying Gao
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, China
| | - Dongqiong Ni
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, China
| | - Chengao Ma
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, China
| | - Yuping Lu
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, China
| | - Xuan Huang
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, China
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Yao K, Yu Y, Zhang H. Construction for Long Non-Coding RNA (lncRNA)-Associated Competing Endogenous RNA (ceRNA) Network in Human Retinal Detachment (RD) with Proliferative Vitreoretinopathy (PVR). Med Sci Monit 2020; 26:e919871. [PMID: 32103829 PMCID: PMC7061588 DOI: 10.12659/msm.919871] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background The aim of this study was to analyze the long non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) network in human retinal tissues following detachment with proliferative vitreoretinopathy (PVR). Material/Methods Expression data of 19 human detached retinas with PVR and 19 normal retinas from postmortem donors were downloaded from Gene Expression Omnibust (GEO) database (GSE28133). The R package “limma” was utilized to discriminate the dysregulated lncRNA and mRNA profiles. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of differentially expressed mRNAs were performed using R packages “Clusterprofiler.” The ceRNA network of dysregulated genes was constructed by using mircode, miRDB, miRTarBase and TargetScan databases, and was visualized by Cytoscape v3.6.1. Results A total of 23 lncRNAs and 994 mRNAs were identified significantly expressed between the human detached retinas with PVR and the normal retina tissues, with thresholds of |log2FoldChange| >1.0 and adjusted P-value <0.05. The constructed ceRNA network (lncRNA-miRNA-mRNA regulatory axis) included 9 PVR-specific lncRNAs, as well as 27 miRNAs and 73 mRNAs. Conclusions We demonstrated the differential lncRNA expression profile and constructed a lncRNA-associated ceRNA network in human detached retinas with PVR. This may ferret out an unknown ceRNA regulatory network in human retinal detachment with PVR.
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Affiliation(s)
- Ke Yao
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
| | - Yixian Yu
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
| | - Hong Zhang
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
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CFIm25-regulated lncRNA acv3UTR promotes gastric tumorigenesis via miR-590-5p/YAP1 axis. Oncogene 2020; 39:3075-3088. [PMID: 32066878 PMCID: PMC7142022 DOI: 10.1038/s41388-020-1213-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
Accumulating evidences indicate that 3ʹUTR of the coding gene can act as crucial regulators in gastric cancer (GC). However, the detailed mechanisms and responsive targets are not well established. Here, we found that acvr1b gene 3ʹUTR (acv3UTR) was elevated in GC tissue, the expression of which was significantly correlated with advanced pTNM-stage and poor outcome in clinical patients. Forced expression of acv3UTR promoted GC cells growth in vitro and in vivo. Mechanistically, our results suggested that acv3UTR functioned as an oncogenic competing endogenous RNA via sponging miR-590-5p and enhancing YAP1 level. Tumor suppressor miR-590-5p was a molecular module in acv3UTR regulatory axis, the forced expression of which led to impairing of oncogenic potential of acv3UTR. The positive correlation of acv3UTR and YAP1 expression, and the negative correlation of acv3UTR and miR-590-5p expression, were verified in GC patients. Moreover, CFIm25 was identified as a key regulator contributing to acv3UTR aberrant expression in GC binding to UGUA-264 motif. Overall, our finding defines a mechanism for understanding the potential role of acv3UTR transcription in GC tumorigenesis, and indicates a correlation between 3ʹUTR trans-regulatory effect and GC development.
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Yan XY, Zhang JJ, Zhong XR, Yu SH, Xu L, Tian R, Sun LK, Su J. The LINC00365/SCGB2A1 (Mammaglobin B) Axis Down-Regulates NF-κB Signaling and Is Associated with the Progression of Gastric Cancer. Cancer Manag Res 2020; 12:621-631. [PMID: 32095083 PMCID: PMC6995300 DOI: 10.2147/cmar.s223699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/05/2019] [Indexed: 02/06/2023] Open
Abstract
PURPOSE A lack of early diagnostic biomarkers and therapeutic targets has led to poor prognosis for gastric cancer patients. However, the analysis of cancer-associated genomic data has been shown to be effective in identifying potential markers. Recently, the long non-coding RNA LINC00365 and SCGB2A1 gene (as known as mammaglobin B) were predicted to be co-expressed in gastric cancer based on the Gene Expression Omnibus database. However, their precise role in gastric cancer tumors is still not clear. METHODS The expressions of LINC00365 and SCGB2A1 in gastric cancer tissues were investigated using qPCR and their expressions were detected in a gastric cancer tissue microarray by in situ hybridization and immunohistochemical staining. The functions of LINC00365 in BGC-823 and MGC-803 gastric cancer cells were tested using the MTT assay, flow cytometry, colony formation assay, EDU staining, immunofluorescence and luciferase assay. RESULTS We found that LINC00365 and SCGB2A1 mRNA were both expressed at low levels in 30 cases of gastric cancer. Gastric cancer tissue microarray analysis indicated that LINC00365 and SCGB2A1 were expressed at low levels in tumor tissue, and low expression of both factors correlated with shorter survival time. Functional studies showed that LINC00365 overexpression significantly inhibited gastric cancer cell viability through the impairment of proliferation rather than the promotion of apoptosis. Furthermore, overexpressed LINC00365 upregulated SCGB2A1 in gastric cancer cell lines. Immuno-fluorescence and luciferase assay analysis indicated that LINC00365 overexpression inhibited the NF-κB pro-survival signaling pathway. Consistent with the effects of LINC00365, SCGB2A1 upregulation also reduced cell survival and inactivated NF-κB. CONCLUSION Collectively, our findings revealed that SCGB2A1 may be the target coding protein regulated by LINC00365 in gastric cancer. LINC00365 and SCGB2A1 may function as tumor suppressors and may serve as potential prognostic and therapeutic markers in gastric cancer treatment.
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Affiliation(s)
- Xiao-Yu Yan
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin130021, People’s Republic of China
| | - Juan-Juan Zhang
- Department of Basic Medicine, HeXi University, Zhangye, Gansu734000, People’s Republic of China
| | - Xin-Ru Zhong
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin130021, People’s Republic of China
| | - Si-Hang Yu
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin130021, People’s Republic of China
| | - Long Xu
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin130021, People’s Republic of China
| | - Rui Tian
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin130021, People’s Republic of China
| | - Lian-Kun Sun
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin130021, People’s Republic of China
| | - Jing Su
- Key Laboratory of Pathobiology, Ministry of Education, Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin130021, People’s Republic of China
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Competitive Endogenous RNA Network Construction and Comparison of Lung Squamous Cell Carcinoma in Smokers and Nonsmokers. DISEASE MARKERS 2019; 2019:5292787. [PMID: 31885738 PMCID: PMC6914966 DOI: 10.1155/2019/5292787] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 10/19/2019] [Accepted: 11/14/2019] [Indexed: 12/23/2022]
Abstract
Background Lung squamous cell carcinoma (LUSC) is a subtype of highly malignant lung cancer with poor prognosis, for which smoking is the main risk factor. However, the underlying genetic and molecular mechanisms of smoking-related LUSC remain largely unknown. Methods We mined existing LUSC-related mRNA, miRNA, and lncRNA transcriptome data and corresponding clinical data from The Cancer Genome Atlas (TCGA) database and divided them into smoking and nonsmoking groups, followed by differential expression analysis. Functional enrichment analysis of the unique differentially expressed mRNAs of the two groups was performed using the DAVID database. Subsequently, the lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network of LUSC in smoking and nonsmoking groups was constructed. Finally, survival analyses were performed to determine the effects of differentially expressed lncRNAs/mRNAs/miRNAs that were involved in the ceRNA network on overall survival and to discover the hub genes. Results A total of 1696 lncRNAs, 125 miRNAs, and 3246 mRNAs and 1784 lncRNAs, 96 miRNAs, and 3229 mRNAs with differentially expressed profiles were identified in the smoking and nonsmoking groups, respectively. The ceRNA network and survival analysis revealed four lncRNAs (LINC00466, DLX6-AS1, LINC00261, and AGBL1), one miRNA (hsa-mir-210), and two mRNAs (CITED2 and ENPP4), with the potential as biomarkers for smoking-related LUSC diagnosis and prognosis. Conclusion Taken together, our research has identified the differences in the ceRNA regulatory networks between smoking and nonsmoking LUSC, which could lay the foundation for future clinical research.
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Ouyang D, Li R, Li Y, Zhu X. Construction of a Competitive Endogenous RNA Network in Uterine Corpus Endometrial Carcinoma. Med Sci Monit 2019; 25:7998-8010. [PMID: 31650984 PMCID: PMC6825398 DOI: 10.12659/msm.915798] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 06/28/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) affect post-transcriptional regulation by interfering with microRNAs (miRNAs), and by acting as competitive endogenous RNAs (ceRNAs). The roles and mechanisms of lncRNAs as ceRNAs in the progression and prognosis of uterine corpus endometrial carcinoma are not well understood. MATERIAL AND METHODS We analyzed high-throughput transcriptome data downloaded from The Cancer Genome Atlas database for 548 patients with uterine corpus endometrial carcinoma, and the we constructed a ceRNA network. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses of differentially expressed messenger RNAs (DE-mRNAs) were performed using R software. Kaplan-Meier survival curves were generated for all RNAs in the ceRNA network. RESULTS We identified 2612 messenger RNAs (mRNAs), 1111 lncRNAs, and 187 miRNAs that were differentially expressed in uterine corpus endometrial carcinoma. We then identified mutual regulatory relationships between lncRNA-miRNA pairs and miRNA-mRNA pairs. A ceRNA regulatory network for uterine corpus endometrial carcinoma was successfully constructed, and consisted of 87 lncRNAs, 74 mRNAs, and 20 miRNAs. Nine lncRNAs, 3 miRNAs, and 22 mRNAs were associated with prognosis of uterine corpus endometrial carcinoma. We also analyzed the linear relationships between the expression of the 9 DE-lncRNAs and 22 DE-mRNAs with prognostic value. CONCLUSIONS Our study showed that the lncRNAs C2orf48 and LINC00261 might be key regulators of uterine corpus endometrial carcinoma and might serve as prognostic indicators. Our study contributes to the understanding of the molecular mechanisms of uterine corpus endometrial carcinoma, and it identifies lncRNAs that might serve as prognostic markers and therapeutic targets.
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Affiliation(s)
- Dong Ouyang
- Department of Obstetrics and Gynecology, Akesu Hospital of Traditional Chinese Medicine, Akesu, Xinjiang, P.R. China
| | - Ruyi Li
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Yaxian Li
- Department of Obstetrics and Gynecology, Akesu Hospital of Traditional Chinese Medicine, Akesu, Xinjiang, P.R. China
| | - Xueqiong Zhu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
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Jiang Y, Chen J, Chen G. Long noncoding RNA IRAIN acts as tumor suppressor via miR-125b in multiple myeloma. Oncol Lett 2019; 18:6787-6794. [PMID: 31788123 DOI: 10.3892/ol.2019.11012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 09/07/2019] [Indexed: 01/15/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are aberrantly expressed in a variety of cancer types. The lncRNA IGF1R antisense imprinted non-protein coding RNA (IRAIN) is associated with various cancer types, yet the role of IRAIN in multiple myeloma (MM) progression remains unclear. In the present study it was identified that IRAIN may act as a tumor suppressor in MM, whilst microRNA (miR)-125b may promote tumorigenesis. Downregulation of IRAIN significantly increased the expression of miR-125b. Furthermore, by using dual-luciferase reporter assays, IRAIN was identified as a target of miR-125b. Knockdown of IRAIN promoted MM cell proliferation in vitro. Thus, expression levels of IRAIN may be used to predict the clinical prognosis of patients with MM and may be a novel therapeutic target for treating MM.
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Affiliation(s)
- Yanxia Jiang
- Hematology Department, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Jian Chen
- Hematology Department, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Guoan Chen
- Hematology Department, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
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Pan H, Guo C, Pan J, Guo D, Song S, Zhou Y, Xu D. Construction of a Competitive Endogenous RNA Network and Identification of Potential Regulatory Axis in Gastric Cancer. Front Oncol 2019; 9:912. [PMID: 31637209 PMCID: PMC6787165 DOI: 10.3389/fonc.2019.00912] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/02/2019] [Indexed: 12/31/2022] Open
Abstract
Background: Increasing studies has found that long non-coding RNAs (lncRNAs) play critical roles in carcinogenesis, but the underlying mechanisms remain unclear. The aim of this study is to construct a competitive endogenous RNA (ceRNA) network and to identify potential regulatory axis in gastric cancer (GC). Methods: Differentially expressed (DE) mRNAs, miRNAs, and lncRNAs were obtained by analyzing the RNA expression profiles of stomach adenocarcinoma (STAD) retrieved from The Cancer Genome Atlas (TCGA) database. The lncRNA-miRNA-mRNA regulatory networks of GC were constructed by comprehensive bioinformatics methods including functional annotation, RNA-RNA interactomes prediction, correlation analysis, and survival analysis. The interactions and correlations among ceRNAs were validated by experiments on cancer tissues and cell lines. Results: A total of 41 lncRNAs, 9 miRNAs, and 10 mRNAs were identified and selected to establish the ceRNA regulatory network of GC. Several ceRNA regulatory axes, which consist of 18 lncRNAs, 4 miRNAs, and 6 mRNAs, were obtained from the network. A potential ADAMTS9-AS2/miR-372/CADM2 axis which perfectly conformed to the ceRNA theory was further analyzed. qRT-PCR showed that ADAMTS9-AS2 knockdown remarkably increased miR-372 expression but reduced CADM2 expression, whereas ADAMTS9-AS2 overexpression had the opposite effects. Dual luciferase reporter assay indicated that miR-372 could bound to the ADAMTS9-AS2 and the 3′UTR of CADM2. Conclusion: The constructed novel ceRNA network and the potential regulatory axes might provide a novel approach of the exploring the potential mechanisms of development in GC. The ADAMTS9-AS2/miR-372/CADM2 could act as a promising target for GC treatment.
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Affiliation(s)
- Hongda Pan
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chunmiao Guo
- The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Jingxin Pan
- The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Dongwei Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shibo Song
- Department of Gastrointestinal Surgery, Beijing Hospital, Beijing, China
| | - Ye Zhou
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dazhi Xu
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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30
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Lu L, Wu M, Lu Y, Zhao Z, Liu T, Fu W, Li W. MicroRNA-424 regulates cisplatin resistance of gastric cancer by targeting SMURF1 based on GEO database and primary validation in human gastric cancer tissues. Onco Targets Ther 2019; 12:7623-7636. [PMID: 31571913 PMCID: PMC6756437 DOI: 10.2147/ott.s208275] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/29/2019] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Cisplatin (DDP) based chemotherapy regimens are widely used in advanced gastric cancer (GC). Drug resistance often limited the clinical benefits of cisplatin regimen. The mechanisms of cisplatin resistance have not been fully revealed. Therefore, further exploration of the relevant molecular mechanisms is urgently needed. PATIENTS AND METHODS DDP resistance associated miRNA of GC microarray dataset GSE86195 was obtained from the National Center for Biotechnology Information (NCBI) GEO database, GEO2R was applied to compare the samples in two different groups under the same experimental conditions. |log2(Fold Change) | (log2(FC)) was selected as the criteria to screen the statistically significant DE-miRNAs. StarBaseV3.0 was used to predict the target genes of the DE-miRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of target genes of DE-miRNAs were carried out using DAVID. The STRING database was applied to estimate the correlations between target genes. Analysis of hubgenes by coremine and The Human Protein Atlas (THPA). Initial expression validations of miR-424 and miR-491-5p, SMURF1 and BCL2L1 were carried out using clinical pathological specimens by RT-PCR. RESULTS A total of 13 Differential expression-miRNAs (DE-miRNAs) were identified in DDP chemoresistant cells, including 9 upregulated miRNAs and 4 downregulated miRNAs. SMURF1 and BCL2L1 were screened as the critical genes in DDP-resistant GC, which were regulated by miR-424 and miR-491-5p respectively. The results of validation of hub genes expression in GC tissues indicated that in DFS<1-year group, the expression of miR-424 decreased significantly, notably upregulated expression of SMURF1 was also detected. CONCLUSION Our results implied that miR-424, as a tumor suppressor, could deregulate SMURF1 in DDP-resistant GC cells.
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Affiliation(s)
- Li Lu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Menglin Wu
- Radiology Department, Second Hospital of Tianjin Medical University, Tianjin, People’s Republic of China
| | - Yaoheng Lu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Zhicheng Zhao
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Tong Liu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Weihua Fu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Weidong Li
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
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Jiang H, Wu F, Jiang N, Gao J, Zhang J. Reconstruction and analysis of competitive endogenous RNA network reveals regulatory role of long non‑coding RNAs in hepatic fibrosis. Mol Med Rep 2019; 20:4091-4100. [PMID: 31545470 PMCID: PMC6797987 DOI: 10.3892/mmr.2019.10682] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 08/12/2019] [Indexed: 12/19/2022] Open
Abstract
Hepatic fibrosis (HF), one of the leading global health problems, is defined as aberrant and excess production of extracellular matrix components. The pathogenesis of HF is complex and poorly understood. Long non‑coding RNAs (LncRNAs) can interact with microRNAs (miRNAs) as competing endogenous RNAs (ceRNAs) to regulate the expression of target genes, which play a significant role in the initiation and progression of HF. In the present study, the LncRNA‑associated ceRNA network was reconstructed based on LncRNA, miRNA and mRNA expression profiles that were downloaded from National Center for Biotechnology Information Gene Expression Omnibus. Bioinformatics assessments including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed with Database for Annotation, Visualization and Integration Discovery. The ceRNA network was composed of 220 LncRNA nodes, 24 miRNA nodes, 164 mRNA nodes and 1,149 edges. Functional assays identified that a total of 338 GO terms and 25 pathways, including regulation of cytokine and collagen, and the transforming growth factor‑β and Toll‑like receptor signaling pathways, were significantly enriched. In addition, 4 LncRNAs (NONMMUT036242, XR_877072, XR_378619 and XR_378418) were highly related to HF and thereby chosen as key LncRNAs. The present study uncovered a ceRNA network that could further the understanding of the mechanisms underlying HF development and provide potential novel markers for clinical diagnosis and targets for treatment.
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Affiliation(s)
- Hui Jiang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, P.R. China
| | - Furong Wu
- Department of Pharmacy, Anhui Provincial Hospital, Hefei, Anhui 230001, P.R. China
| | - Nannan Jiang
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, P.R. China
| | - Jiarong Gao
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, P.R. China
| | - Jiafu Zhang
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230031, P.R. China
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He Y, Liu C, Song P, Pang Z, Mo Z, Huang C, Yan T, Sun M, Fa X. Investigation of miRNA- and lncRNA-mediated competing endogenous RNA network in cholangiocarcinoma. Oncol Lett 2019; 18:5283-5293. [PMID: 31612038 PMCID: PMC6781644 DOI: 10.3892/ol.2019.10852] [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: 08/29/2018] [Accepted: 03/08/2019] [Indexed: 12/17/2022] Open
Abstract
Cholangiocarcinoma (CCA) is a biliary malignancy which is prone to lymphatic metastasis and has a high mortality rate. This disease lacks effective therapeutic targets and prognostic molecular biomarkers. The aim of the current study was to investigate differentially expressed genes and elucidate their association with CCA and the underlying mechanisms of action. mRNAs, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) obtained from 36 CCA samples and nine normal samples from The Cancer Genome Atlas were integrated. Subsequently, 1,095 differentially expressed (DE) mRNAs and 75 DE miRNAs were identified using a threshold of |log2 fold change|>2 and an adjusted P<0.01. Weighted gene co-expression network analysis was used to identify the DEmRNAs that could be key target genes in CCA. A total of 12 hub DEmRNAs were identified as targetable genes. Furthermore, the hub DEmRNAs-DElncRNAs pairs were identified using the miRTarBase and miRcode databases. Cytoscape software was used to construct and visualize the protein-protein interactions and the competing endogenous RNA network. Survival time analysis and correlation analysis were used to further evaluate the hub genes. The results obtained in the current study suggested that spalt like transcription factor 3 and OPCML intronic transcript 1 may serve an important role in the development and progression of CCA.
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Affiliation(s)
- Yanxin He
- Department of Surgery, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450014, P.R. China
| | - Chao Liu
- Department of Surgery, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450014, P.R. China
| | - Pan Song
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450014, P.R. China
| | - Zhigang Pang
- Department of Surgery, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450014, P.R. China
| | - Zhuomao Mo
- College of Traditional Chinese Medicine of Jinan University, Institute of Integrated Traditional Chinese and Western Medicine of Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Chuiguo Huang
- Department of Urology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450014, P.R. China
| | - Tingting Yan
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong 999077, P.R. China
| | - Meng Sun
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450014, P.R. China
| | - Xianen Fa
- Department of Surgery, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450014, P.R. China
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Zhang L, Mao J. Long-Chain Noncoding RNA PVT1 Gene Polymorphisms Are Associated with the Risk and Prognosis of Colorectal Cancer in the Han Chinese Population. Genet Test Mol Biomarkers 2019; 23:728-736. [PMID: 31509024 DOI: 10.1089/gtmb.2019.0078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background: To investigate the association between long-chain noncoding RNA (lncRNA) plasmacytoma variant translocation 1 (PVT1) gene polymorphisms and the risk and prognosis of colorectal cancer (CRC) in the Han Chinese population. Methods: A cohort of 225 Han Chinese CRC patients and 225 healthy controls was analyzed for the PVT1 gene genotypes at the loci rs1221464062, rs1366023633, rs1252200336, and rs1273526412. The levels of PVT1 mRNA, hsa-miR-455-5p, and hsa-miR-455-3p in both cancerous tissues and paracancerous normal tissues of the CRC patients were determined by reverse transcription polymerase chain reaction. The survival rate of CRC patients was recorded after 3 years of follow-up. Results: The risk of developing CRC in subjects with the ID genotype of the PVT1 gene locus rs1252200336 was 2.71 times higher compared with the type II genotype; and the D allele was a risk factor for CRC. The survival of CRC patients with the ID/DD genotypes of the PVT1 gene rs1252200336 locus was significantly lower compared with the II genotype. In both the cancerous tissues and the paracancerous normal tissues of CRC patients, the level of lncRNA PVT1 was negatively correlated with the hsa-miR-455-5p and hsa-miR-455-3p levels. In subjects carrying the ID/DD genotypes of the PVT1 gene rs1252200336 locus, the level of the lncRNA PVT1 in cancerous tissues was significantly higher compared with the II genotype, whereas the hsa-miR-455-3p level was significantly lower compared with the II genotype. Conclusion: The PVT1 gene rs1252200336 locus polymorphisms are associated with the risk of developing CRC in the Han Chinese population. The rs1252200336 locus deletion mutation (D) may impact the binding of hsa-miR-455-5p to the lncRNA PVT1 and its role in the development and progression of CRC.
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Affiliation(s)
- Lei Zhang
- Department of Anorectal Surgery, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Jiehong Mao
- Department of Anorectal Surgery, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
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Wang J, Ding Y, Wu Y, Wang X. Identification of the complex regulatory relationships related to gastric cancer from lncRNA‐miRNA‐mRNA network. J Cell Biochem 2019; 121:876-887. [DOI: 10.1002/jcb.29332] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Jie Wang
- Laboratory of Media Design and Software Technology Jiangnan University Wuxi Jiangsu China
| | - Yanrui Ding
- Laboratory of Media Design and Software Technology Jiangnan University Wuxi Jiangsu China
- Key Laboratory of Industrial Biotechnology Jiangnan University Wuxi Jiangsu China
| | - Yanyan Wu
- Laboratory of Media Design and Software Technology Jiangnan University Wuxi Jiangsu China
| | - Xiaxia Wang
- Laboratory of Media Design and Software Technology Jiangnan University Wuxi Jiangsu China
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Nie ML, Han J, Huang HC, Guo T, Huangfu LT, Cheng XJ, Li XM, Du H, Li QD, Wen XZ, Ji JF. The novel lncRNA p4516 acts as a prognostic biomarker promoting gastric cancer cell proliferation and metastasis. Cancer Manag Res 2019; 11:5375-5391. [PMID: 31354346 PMCID: PMC6578592 DOI: 10.2147/cmar.s201793] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/05/2019] [Indexed: 12/18/2022] Open
Abstract
Purpose: Emerging evidence has shown that long noncoding RNAs (lncRNAs) participate in oncogenesis and tumor progression. We previously found a novel lncRNA p4516 which was closely associated with prognosis by preliminary study of lncRNA expression profile from paired tumors and nontumor tissues in 198 gastric cancer (GC) patients. However, the exact biological functions and the underlying molecular mechanisms of p4516 in gastric tumorigenesis still remain unclear. Materials and methods: The RNA fluorescence in situ hybridization (RNA-FISH) analysis, cytoplasmic and nuclear RNA isolation and qRT-PCR were applied to determine the subcellular localization of p4516. Expression levels of p4516 were assessed using qRT-PCR in both GC cell lines and in 142 primary GC tissues. Correlations between p4516 expression and GC patients’ clinicopathological parameters were analyzed. Gain- and loss-of-function experiments were employed to investigate the role of p4516 in proliferation, migration and invasion both in vitro and in vivo. In addition, Western blotting and immunohistochemical staining were used to examine the protein expression levels. Results: LncRNA p4516 was mainly localized in the nucleus of GC cells and p4516 tended to have higher expression levels in GC cells compared to the normal gastric mucosa-derived cells GES-1. Furthermore, higher expression levels of p4516 correlated with worse clinical outcomes in GC patients and acted as an independent prognostic biomarker. Functional analysis revealed that p4516 participated in the regulation of GC cell proliferation, invasion and migration both in vivo and in vitro. Moreover, p4516 was involved in epithelial–mesenchymal transition (EMT) in GC cells. Conclusion: Our study demonstrated the oncogenic role of novel lncRNA p4516 in the gastric carcinogenesis for the first time. High expression of p4516 may act as prognostic marker in patient with gastric cancer.
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Affiliation(s)
- Meng-Lin Nie
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Jing Han
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Han-Chen Huang
- Key Laboratory of RNA Biology, Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.,Centre for Cognitive Machines and Computational Health (CMaCH), The School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ting Guo
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Long-Tao Huangfu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Xiao-Jing Cheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Xiao-Mei Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Hong Du
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Qing-Da Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Xian-Zi Wen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China
| | - Jia-Fu Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital & Institute, Beijing, People's Republic of China.,Department of Gastrointestinal Surgery, Peking University Cancer Hospital, Beijing, People's Republic of China
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Meng J, Chen Y, Zhang C. Protective impacts of long noncoding RNA taurine-upregulated 1 against lipopolysaccharide-evoked injury in MRC-5 cells through inhibition of microRNA-127. J Cell Biochem 2019; 120:14928-14935. [PMID: 31017717 DOI: 10.1002/jcb.28755] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Pneumonia is a respiratory disease, which is triggered by pathogenic microorganisms or physical/chemical factors. Increasing evidence confirmed the vital impacts of long noncoding RNAs on various inflammatory diseases. Nonetheless, the influence of taurine-upregulated 1 (TUG1) in pneumonia remains vague. The research tried to disclose the protective impacts of TUG1 against lipopolysaccharide (LPS)-evoked injury in MRC-5 cells. METHODS MRC-5 cells were disposed with LPS to construct pulmonary injury model. Then, pc-TUG1 vector was transfected into MRC-5 cells and the influence of overexpressed TUG1 in cell viability, apoptosis, and pro-inflammatory cytokines in LPS-disposed cells were evaluated. The correlation between TUG1 and microRNA (miR)-127 was estimated via utilizing real-time quantitative polymerase chain reaction (RT-qPCR), meanwhile whether miR-127 affected the impacts of TUG1 on LPS-injured MRC-5 cells was explored. Besides, NF-κB and p38MAPK pathways were evaluated to understand the dormant mechanisms. RESULTS LPS administration apparently evoked inflammatory injury in MRC-5 cells by restraining cell viability, accelerating apoptosis, and enhancing TNF-α and IL-6 productions. But, TUG1 lightened LPS-evoked pro-inflammatory response in MRC-5 cells. In addition, miR-127 was repressed by overexpressed TUG1, meanwhile the protective impacts of TUG1 against LPS-evoked inflammatory injury in MRC-5 cells were overturned by overexpressed miR-127. Finally, we disclosed that TUG1 hindered the activation of NF-κB and p38MAPK pathways via restraining miR-127. CONCLUSIONS These explorations testified that taurine-upregulated 1 (TUG1) protected MRC-5 cells against lipopolysaccharide (LPS)-evoked inflammatory injury via hindering miR-127/NF-κB/p38MAPK axis.
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Affiliation(s)
- Jie Meng
- Department of Pediatrics, Jining No.1 People's Hospital, Jining, China
| | - Yan Chen
- Department of Pediatrics, Jining No.1 People's Hospital, Jining, China
| | - Cunxue Zhang
- Department of Pediatrics, Jining No.1 People's Hospital, Jining, China
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Tuersong T, Li L, Abulaiti Z, Feng S. Comprehensive analysis of the aberrantly expressed lncRNA‑associated ceRNA network in breast cancer. Mol Med Rep 2019; 19:4697-4710. [PMID: 31059025 PMCID: PMC6522813 DOI: 10.3892/mmr.2019.10165] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 04/01/2019] [Indexed: 12/11/2022] Open
Abstract
Previous studies have suggested that long non-coding RNAs (lncRNAs) are closely associated with human diseases, particularly cancer, including cancer of the lung, breast and stomach. A variety of lncRNAs are abnormally expressed in cancer and participate in several pathways including cell proliferation and apoptosis; these elements are closely associated with the development of cancer. The Cancer Genome Atlas (TCGA) is an important cancer database. It consists of clinical data, genomic variation, mRNA, microRNA (miRNA) and lncRNAs expression, methylation and other data for various types of human cancer. In the present study, differential expression of RNA was identified using the edgeR package. A total 1,222 RNA sequencing profiles from patients with breast cancer were downloaded from TCGA. A competing endogenous RNA (ceRNA) network was constructed for breast cancer based on miRcode and miRTarBase. The top 10 lncRNAs were selected using Cox regression analysis. Survival analysis was performed using Kaplan-Meier analysis. A total of 1,028 breast cancer-associated lncRNAs and 89 miRNAs (fold change >2; P<0.05) were identified; among these, 93 lncRNAs and 19 miRNAs were included in the ceRNA network. Subsequently, 10 basic lncRNAs were selected and their associations with overall survival were identified. In addition, 5 lncRNAs (ADAM metallopeptidase with thrombospondin type 1 motif 9-antisense RNA 1, AL513123.1, chromosome 10 open reading frame 126, long intergenic non-protein coding RNA 536 and Wilms tumor 1 antisense RNA) were identified to be significantly associated with overall survival (P<0.05, log rank test). These results suggested that mRNAs, lncRNAs and miRNAs were involved in pathological mechanisms of breast cancer. The newly-identified ceRNA network included 93 breast cancer-specific lncRNAs, 19 miRNAs and 27 mRNAs. The results of the present study highlight the potential of lncRNAs in understanding the development and pathogenesis of breast cancer, and suggest novel concepts and an experimental basis for the identification of prognostic biomarkers and therapeutic targets for breast cancer.
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Affiliation(s)
- Tayier Tuersong
- Department of Pharmacology, Pharmacy College, Xinjiang Medical University, Ürümqi, Xinjiang Uyghur Autonomous Region 830001, P.R. China
| | - Linlin Li
- Department of Pharmacology, Pharmacy College, Xinjiang Medical University, Ürümqi, Xinjiang Uyghur Autonomous Region 830001, P.R. China
| | - Zumureti Abulaiti
- Department of Internal Medicine, Traditional Medical College, Xinjiang Medical University, Ürümqi, Xinjiang Uyghur Autonomous Region 830001, P.R. China
| | - Shumei Feng
- Department of Histology and Embryology, Basic Medical Sciences College, Xinjiang Medical University, Ürümqi, Xinjiang Uyghur Autonomous Region 830001, P.R. China
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Zhang H, Wang Z, Wu J, Ma R, Feng J. Long noncoding RNAs predict the survival of patients with colorectal cancer as revealed by constructing an endogenous RNA network using bioinformation analysis. Cancer Med 2019; 8:863-873. [PMID: 30714675 PMCID: PMC6434209 DOI: 10.1002/cam4.1813] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/20/2018] [Accepted: 09/10/2018] [Indexed: 12/19/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are aberrantly expressed in various cancers types and can function as competing endogenous RNAs (ceRNAs), which promote and maintain tumor initiation and progression. In this study, we explored the functional roles and regulatory mechanisms of lncRNAs as ceRNAs in colorectal cancer and their clinical potential as biomarkers. The RNA sequencing profiles of patients with colorectal cancer were downloaded from TCGA database, and 62 lncRNAs, 30miRNAs, and 59 mRNAs were identified to comprise the ceRNA network (fold change > 2, P < 0.01). Functional enrichment analysis suggested that the target genes of the ceRNA network may be involved in the pathways related to cancer, including the signaling pathway that regulates the pluripotency of stem cells, wnt signaling pathway, hippo signaling pathway, basal cell carcinoma, and colorectal cancer. Univariate and multivariate Cox's proportional hazard regression model revealed that five (H19, MIR31HG, HOTAIR, WT1‐AS, and LINC00488) out of 62 lncRNAs were closely related to the overall survival (OS) (P < 0.05). Furthermore, the five‐lncRNA model could be an independent prognostic model in colorectal cancer. We computed for the risk function and constructed a risk score based on the five lncRNAs. Results showed that patients with high‐risk scores have poor survival rates. Additionally, combing the risk score and other clinicopathological features, we can better predict the patient's survival probabilities. Furthermore, we validate our model in the GSE38832 dataset. Collectively, our study has provided a deeper understanding of the lncRNA‐related ceRNA regulatory mechanism in CRC and identified five‐lncRNA model, which could be considered as candidate prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Hui Zhang
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Nanjing, Jiangsu, China.,Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Nanjing, Jiangsu, China.,Jiangsu Institute of Cancer Research, Nanjing, Jiangsu, China
| | - Zhuo Wang
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Nanjing, Jiangsu, China.,Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Nanjing, Jiangsu, China.,Jiangsu Institute of Cancer Research, Nanjing, Jiangsu, China
| | - Jianzhong Wu
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Nanjing, Jiangsu, China.,Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Nanjing, Jiangsu, China.,Jiangsu Institute of Cancer Research, Nanjing, Jiangsu, China
| | - Rong Ma
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Nanjing, Jiangsu, China.,Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Nanjing, Jiangsu, China.,Jiangsu Institute of Cancer Research, Nanjing, Jiangsu, China
| | - Jifeng Feng
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Nanjing, Jiangsu, China.,Research Center for Clinical Oncology, Jiangsu Cancer Hospital, Nanjing, Jiangsu, China.,Jiangsu Institute of Cancer Research, Nanjing, Jiangsu, China
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Xu N, Wu YP, Yin HB, Xue XY, Gou X. Molecular network-based identification of competing endogenous RNAs and mRNA signatures that predict survival in prostate cancer. J Transl Med 2018; 16:274. [PMID: 30286759 PMCID: PMC6172814 DOI: 10.1186/s12967-018-1637-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/16/2018] [Indexed: 12/31/2022] Open
Abstract
Background The aim of the study is described the regulatory mechanisms and prognostic values of differentially expressed RNAs in prostate cancer and construct an mRNA signature that predicts survival. Methods The RNA profiles of 499 prostate cancer tissues and 52 non-prostate cancer tissues from TCGA were analyzed. The differential expression of RNAs was examined using the edgeR package. Survival was analyzed by Kaplan–Meier method. microRNA (miRNA), messenger RNA (mRNA), and long non-coding RNA (lncRNA) networks from the miRcode database were constructed, based on the differentially expressed RNAs between non-prostate and prostate cancer tissues. Results A total of 773 lncRNAs, 1417 mRNAs, and 58 miRNAs were differentially expressed between non-prostate and prostate cancer samples. The newly constructed ceRNA network comprised 63 prostate cancer-specific lncRNAs, 13 miRNAs, and 18 mRNAs. Three of 63 differentially expressed lncRNAs and 1 of 18 differentially expressed mRNAs were significantly associated with overall survival in prostate cancer (P value < 0.05). After the univariate and multivariate Cox regression analyses, 4 mRNAs (HOXB5, GPC2, PGA5, and AMBN) were screened and used to establish a predictive model for the overall survival of patients. Our ROC curve analysis revealed that the 4-mRNA signature performed well. Conclusion These ceRNAs may play a critical role in the progression and metastasis of prostate cancer and are thus candidate therapeutic targets and potential prognostic biomarkers. A novel model that incorporated these candidates was established and might provide more powerful prognostic information in predicting survival in prostate cancer.
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Affiliation(s)
- Ning Xu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Rd., Yuzhong District, Chongqing, 400016, China.,Departments of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Yu-Peng Wu
- Departments of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Hu-Bin Yin
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Rd., Yuzhong District, Chongqing, 400016, China
| | - Xue-Yi Xue
- Departments of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Xin Gou
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Rd., Yuzhong District, Chongqing, 400016, China.
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Hu H, Wu J, Li D, Zhou J, Yu H, Ma L. Knockdown of lncRNA MALAT1 attenuates acute myocardial infarction through miR-320-Pten axis. Biomed Pharmacother 2018; 106:738-746. [DOI: 10.1016/j.biopha.2018.06.122] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/20/2018] [Accepted: 06/21/2018] [Indexed: 12/19/2022] Open
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Gao S, Zhao ZY, Wu R, Zhang Y, Zhang ZY. Prognostic value of long noncoding RNAs in gastric cancer: a meta-analysis. Onco Targets Ther 2018; 11:4877-4891. [PMID: 30147339 PMCID: PMC6098423 DOI: 10.2147/ott.s169823] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background In the last few years, accumulating evidence has indicated that numerous long noncoding RNAs (lncRNAs) are abnormally expressed in gastric cancer (GC) and are associated with the survival of GC patients. This study aimed to conduct a meta-analysis on 19 lncRNAs (AFAP1 antisense RNA 1 [AFAP1-AS1], CDKN2B antisense RNA 1 [ANRIL], cancer susceptibility 15 [CASC15], colon cancer associated transcript 2 [CCAT2], gastric adenocarcinoma associated, positive CD44 regulator, long intergenic noncoding RNA [GAPLINC], H19, imprinted maternally expressed transcript [H19], HOX transcript antisense RNA [HOTAIR], HOXA distal transcript antisense RNA [HOTTIP], long intergenic non-protein coding RNA 673 [LINC00673], metastasis-associated lung adenocarcinoma transcript 1 [MALAT1], maternally expressed 3 [MEG3], promoter of CDKN1A antisense DNA damage activated RNA [PANDAR], Pvt1 oncogene [PVT1], SOX2 overlapping transcript [Sox2ot], SPRY4 intronic transcript 1 [SPRY4-IT1], urothelial cancer associated 1 [UCA1], X inactive specific transcript [XIST], ZEB1 antisense RNA 1 [ZEB1-AS1] and ZNFX1 antisense RNA 1 [ZFAS1]) to systematically estimate their prognostic value in GC. Methods The qualified literature was systematically searched in PubMed, Web of Science, Embase and Cochrane Database of Systematic Reviews (up to March 16, 2018), and one meta-analysis relating to the relationship between lncRNA expression and overall survival (OS) of GC patients was performed. The only evaluation criterion of survival results was OS. Results A total of 6,095 GC patients and 19 lncRNAs from 51 articles were included in the present study. Among the listed 19 lncRNAs, 18 lncRNAs (other than SPRY4-IT1) showed a significantly prognostic value (P<0.05). Conclusion This meta-analysis suggested that the abnormally expressed lncRNAs (AFAP1-AS1, ANRIL, CASC15, CCAT2, GAPLINC, H19, HOTAIR, HOTTIP, LINC00673, MALAT1, MEG3, PANDAR, PVT1, Sox2ot, UCA1, XIST, ZEB1-AS1 and ZFAS1) were significantly associated with the survival of GC patients, among which AFAP1-AS1, CCAT2, LINC00673, PANDAR, PVT1, Sox2ot, ZEB1-AS1 and ZFAS1 were strong candidates in predicting the prognosis of GC patients.
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Affiliation(s)
- Song Gao
- The Second Department of Clinical Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China,
| | - Zhi-Ying Zhao
- Division of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Rong Wu
- The Second Department of Clinical Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China,
| | - Yue Zhang
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China,
| | - Zhen-Yong Zhang
- The Second Department of Clinical Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China,
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Zhu N, Hou J, Wu Y, Liu J, Li G, Zhao W, Ma G, Chen B, Song Y. Integrated analysis of a competing endogenous RNA network reveals key lncRNAs as potential prognostic biomarkers for human bladder cancer. Medicine (Baltimore) 2018; 97:e11887. [PMID: 30170380 PMCID: PMC6392549 DOI: 10.1097/md.0000000000011887] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Human bladder cancer (BCa) is one of the most commonly diagnosed malignancies worldwide. It has high recurrence rates and low-grade malignancy, thus representing an important public health concern. An increasing number of studies suggest that long-noncoding RNAs (lncRNAs) play important roles in various biological processes and disease pathologies, including cancer.We analyzed the expression profiles of lncRNA, miRNA, and mRNA, along with the clinical information of BCa patients collected from the Cancer Genome Atlas database to identify lncRNA biomarkers for prognosis. We also constructed an lncRNA-miRNA-mRNA global triple network (competitive endogenous RNA network) by bioinformational approach.This BCa lncRNA-miRNA-mRNA network consisted of 23 miRNA nodes, 52 mRNA nodes, 59 lncRNA nodes, and 365 edges. Subsequent gene ontology (GO) and pathway analyses were performed using BinGO for Cytoscape and Database for Annotation, Visualization, and Integration Discovery, respectively, highlighting important GO terms and pathways that were enriched in the network. Subnetworks were created using 3 key lncRNAs (MAGI2-AS3, ADAMTS9-AS2, and LINC00330), revealing associations with BCa-linked mRNAs and miRNAs. Finally, an analysis of significantly differentiating RNAs found 6 DElncRNAs (AC112721.1, ADAMTS9-AS1, ADAMTS9-AS2, HCG22, MYO16-AS1, and SACS-AS1), 1 DEmiRNA (miRNA-195), and 6 DEmRNAs (CCNB1, FAM129A, MAP1B, TMEM100, AIFM3, and HOXB5) that correlated with BCa patient survival.Our results provide a novel perspective from which to study the lncRNA-related ceRNA network in BCa, contributing to the development of future diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
| | - Jingyi Hou
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical College, Chengde
| | - Yuanhao Wu
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin
| | - Jinxin Liu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical College, Chengde
| | - Geng Li
- China-Japan Friendship Hospital, Beijing
| | - Wenjia Zhao
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Guiyun Ma
- Affiliated Hospital of Chengde Medical College
| | - Bin Chen
- Affiliated Hospital of Chengde Medical College
| | - Youxin Song
- Affiliated Hospital of Chengde Medical College
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Noncoding RNA:RNA Regulatory Networks in Cancer. Int J Mol Sci 2018; 19:ijms19051310. [PMID: 29702599 PMCID: PMC5983611 DOI: 10.3390/ijms19051310] [Citation(s) in RCA: 787] [Impact Index Per Article: 131.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/20/2018] [Accepted: 04/25/2018] [Indexed: 02/08/2023] Open
Abstract
Noncoding RNAs (ncRNAs) constitute the majority of the human transcribed genome. This largest class of RNA transcripts plays diverse roles in a multitude of cellular processes, and has been implicated in many pathological conditions, especially cancer. The different subclasses of ncRNAs include microRNAs, a class of short ncRNAs; and a variety of long ncRNAs (lncRNAs), such as lincRNAs, antisense RNAs, pseudogenes, and circular RNAs. Many studies have demonstrated the involvement of these ncRNAs in competitive regulatory interactions, known as competing endogenous RNA (ceRNA) networks, whereby lncRNAs can act as microRNA decoys to modulate gene expression. These interactions are often interconnected, thus aberrant expression of any network component could derail the complex regulatory circuitry, culminating in cancer development and progression. Recent integrative analyses have provided evidence that new computational platforms and experimental approaches can be harnessed together to distinguish key ceRNA interactions in specific cancers, which could facilitate the identification of robust biomarkers and therapeutic targets, and hence, more effective cancer therapies and better patient outcome and survival.
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