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Li R, Qiu T, Zhou Q, He F, Jie C, Zheng X, Lu Z, Wu Q, Xie C. Histone acetylation-related IncRNA: Potential biomarkers for predicting prognosis and immune response in lung adenocarcinoma, and distinguishing hot and cold tumours. Front Immunol 2023; 14:1139599. [PMID: 37006256 PMCID: PMC10064094 DOI: 10.3389/fimmu.2023.1139599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
BackgroundHistone acetylation-related lncRNAs (HARlncRNAs) play significant roles in various cancers, but their impact on lung adenocarcinoma (LUAD) remains unclear. This study aimed to develop a new HARlncRNA-based prognostic model for LUAD and to explore its potential biological mechanisms.MethodsWe identified 77 histone acetylation genes based on previous studies. HARlncRNAs related to prognosis were screened by co-expression, univariate and multivariate analyses, and least absolute shrinkage selection operator regression (LASSO). Afterward, a prognostic model was established based on the screened HARlncRNAs. We analysed the relationship between the model and immune cell infiltration characteristics, immune checkpoint molecule expression, drug sensitivity, and tumour mutational burden (TMB). Finally, the entire sample was divided into three clusters to further distinguish between hot and cold tumours.ResultsA seven-HARlncRNA-based prognostic model was established for LUAD. The area under the curve (AUC) of the risk score was the highest among all the analysed prognostic factors, indicating the accuracy and robustness of the model. The patients in the high-risk group were predicted to be more sensitive to chemotherapeutic, targeted, and immunotherapeutic drugs. It was worth noting that clusters could effectively identify hot and cold tumours. In our study, clusters 1 and 3 were considered hot tumours that were more sensitive to immunotherapy drugs.ConclusionWe developed a risk-scoring model based on seven prognostic HARlncRNAs that promises to be a new tool for evaluating the prognosis and efficacy of immunotherapy in patients with LUAD.
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Affiliation(s)
- Rumeng Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Tingting Qiu
- Jiangxi Cancer Hospital, The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Clinical Research Center for Cancer, Nanchang, China
| | - Qiangqiang Zhou
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fajian He
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chen Jie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xinyu Zheng
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zeguang Lu
- The Second Clinical College of Guangzhou Medical University, Guangzhou, China
| | - Qiuji Wu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
- *Correspondence: Conghua Xie, ; Qiuji Wu,
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
- *Correspondence: Conghua Xie, ; Qiuji Wu,
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Yalimaimaiti S, Liang X, Zhao H, Dou H, Liu W, Yang Y, Ning L. Establishment of a prognostic signature for lung adenocarcinoma using cuproptosis-related lncRNAs. BMC Bioinformatics 2023; 24:81. [PMID: 36879187 PMCID: PMC9990240 DOI: 10.1186/s12859-023-05192-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
OBJECTIVE To establish a prognostic signature for lung adenocarcinoma (LUAD) based on cuproptosis-related long non-coding RNAs (lncRNAs), and to study the immune-related functions of LUAD. METHODS First, transcriptome data and clinical data related to LUAD were downloaded from the Cancer Genome Atlas (TCGA), and cuproptosis-related genes were analyzed to identify cuproptosis-related lncRNAs. Univariate COX analysis, least absolute shrinkage and selection operator (LASSO) analysis, and multivariate COX analysis were performed to analyze the cuproptosis-related lncRNAs, and a prognostic signature was established. Second, univariate COX analysis and multivariate COX analysis were performed for independent prognostic analyses. Receiver operating characteristic (ROC) curves, C index, survival curve, nomogram, and principal component analysis (PCA) were performed to evaluate the results of the independent prognostic analyses. Finally, gene enrichment analyses and immune-related function analyses were also carried out. RESULTS (1) A total of 1,297 cuproptosis-related lncRNAs were screened. (2) A LUAD prognostic signature containing 13 cuproptosis-related lncRNAs was constructed (NIFK-AS1, AC026355.2, SEPSECS-AS1, AL360270.1, AC010999.2, ABCA9-AS1, AC032011.1, AL162632.3, LINC02518, LINC0059, AL031600.2, AP000346.1, AC012409.4). (3) The area under the multi-indicator ROC curves at 1, 3, and 5 years were AUC1 = 0.742, AUC2 = 0.708, and AUC3 = 0.762, respectively. The risk score of the prognostic signature could be used as an independent prognostic factor that was independent of other clinical indicators. (4) The results of gene enrichment analyses showed that 13 biomarkers were primarily related to amoebiasis, the wnt signaling pathway, hematopoietic cell lineage. The ssGSEA volcano map showed significant differences between high- and low-risk groups in immune-related functions, such as human leukocyte antigen (HLA), Type_II_IFN_Reponse, MHC_class_I, and Parainflammation (P < 0.001). CONCLUSIONS Thirteen cuproptosis-related lncRNAs may be clinical molecular biomarkers for the prognosis of LUAD.
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Affiliation(s)
- Saiyidan Yalimaimaiti
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Xiaoqiao Liang
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Haili Zhao
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Hong Dou
- Xinjiang Uygur Autonomous Region Occupational Disease Hospital, Urumqi, 830011, Xinjiang, China
| | - Wei Liu
- Xinjiang Uygur Autonomous Region Occupational Disease Hospital, Urumqi, 830011, Xinjiang, China
| | - Ying Yang
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Li Ning
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China.
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Pan T, Wang H, Wang S, Liu F. Long Non-Coding RNA LINC01929 Facilitates Cell Proliferation and Metastasis as a Competing Endogenous RNA Against MicroRNA miR-1179 in Non-Small Cell Lung Carcinoma. Br J Biomed Sci 2022; 79:10598. [PMID: 35996496 PMCID: PMC9329516 DOI: 10.3389/bjbs.2022.10598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022]
Abstract
Introduction: Non-small cell lung carcinoma (NSCLC) constitutes most lung cancers and has a poor prognosis. LncRNAs are a potential repository for the discovery of cancer prognostic markers. This study explored the role of LINC01929 in NSCLC, both the clinical prognostic significance and the mechanism of its influence on cells. Materials and Methods: LINC01929 levels in 143 pairs of NSCLC tissues and non-cancerous tissues were detected by RT-qPCR. Kaplan-Meier curves and multivariate Cox regression assays were generated for evaluating the prognostic values of LINC01929. To evaluate the cellular function, an XTT assay and transwell invasion assays were performed. Results: LINC01929 was up-regulated in NSCLC tissues compared with healthy tissues. A positive correlation was observed between LINC01929 expression level and tumor T (p = 0.002) or N stage (p = 0.010). Patients with higher LINC01929 levels had shorter overall survival (p = 0.009). Compared with other factors, high LINC01929 expression was significantly associated with poor survival in univariate Cox analysis (HR: 2.485, 95%CI: 1.220–5.060, p = 0.012). After multivariate Cox regression assays, LINC01929 was a independent prognostic factor (HR: 3.021, 95%CI: 1.377–6.628, p = 0.006). miR-1179 was a target miRNA of LINC01929. Inhibited expression of LINC01929 significantly reduced the proliferation, migration, and invasion of NSCLC cells by targeting miR-1179. Discussion: This study revealed the upregulation of LINC01929 in NSCLC. This study supports previous studies showing LINC01929 as a potential prognostic factor for NSCLC.
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Affiliation(s)
- Tinghong Pan
- Department of Thoracic Surgery, Yidu Central Hospital of Weifang, Weifang, China
| | - Hui Wang
- Department of Thoracic Surgery, Yidu Central Hospital of Weifang, Weifang, China
| | - Shuai Wang
- Department of Thoracic Surgery, Yidu Central Hospital of Weifang, Weifang, China
| | - Feng Liu
- Department of Cardiothoracic Surgery, Zhucheng People’s Hospital, Weifang, China
- *Correspondence: Feng Liu, , orcid.org/0000-0002-3218-9173
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Ji Y, Yang Y, Yin Z. Polymorphisms in lncRNA CCAT1 on the susceptibility of lung cancer in a Chinese northeast population: A case-control study. Cancer Med 2022; 12:500-512. [PMID: 35650713 PMCID: PMC9844612 DOI: 10.1002/cam4.4902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/04/2022] [Accepted: 05/15/2022] [Indexed: 02/06/2023] Open
Abstract
OBJECT To explore the association of rs1948915, rs7013433 in long noncoding RNA (lncRNA) CCAT1 and rs6983267 in MYC enhancer region with the risk of lung cancer in a Chinese northeast population, a case-control study was conducted. METHODS The hospital-based case-control study contained 669 lung cancer patients and 697 healthy controls. Taqman® Probe allele resolution was used for genotyping. The differences between the case-control groups were analyzed using Student t-test and chi-square test. Logistic regression analysis was used to assess the relationship between the genotypes and the risk of lung cancer. Cross-generation analysis was used to explore the relationship between gene-environment interaction and lung cancer. RESULTS There was no association between the three selected single-nucleotide polymorphisms (SNPs) and the susceptibility of lung cancer. Rs1948915 CT was correlated with lung adenocarcinoma. In female stratification, rs1948915 CT/CC was associated with a decreased susceptibility of lung cancer significantly. Additionally, the additive and multiplicative interaction models showed that there was no interaction between the three selected SNPs and smoking status in lung cancer. CONCLUSIONS There may be an association between lung adenocarcinoma and rs1948915 polymorphism in the Chinese northeast population, while rs7013433 and rs6983267 might have no association. There was no interaction between the three selected SNPs and smoking status.
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Affiliation(s)
- Yangtao Ji
- Department of Laboratory Medicine, National Clinical Research Center for Laboratory MedicineThe First Affiliated Hospital of China Medical UniversityShenyangLiaoningPeople's Republic of China
| | - Yue Yang
- Department of Laboratory MedicineThe First Affiliated Hospital of China Medical UniversityShenyangLiaoningPeople's Republic of China
| | - Zhihua Yin
- Department of EpidemiologySchool of Public Health, China Medical UniversityShenyangLiaoningPeople's Republic of China
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Multi-Run Concrete Autoencoder to Identify Prognostic lncRNAs for 12 Cancers. Int J Mol Sci 2021; 22:ijms222111919. [PMID: 34769351 PMCID: PMC8584911 DOI: 10.3390/ijms222111919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/28/2021] [Accepted: 10/30/2021] [Indexed: 12/13/2022] Open
Abstract
Background: Long non-coding RNA plays a vital role in changing the expression profiles of various target genes that lead to cancer development. Thus, identifying prognostic lncRNAs related to different cancers might help in developing cancer therapy. Method: To discover the critical lncRNAs that can identify the origin of different cancers, we propose the use of the state-of-the-art deep learning algorithm concrete autoencoder (CAE) in an unsupervised setting, which efficiently identifies a subset of the most informative features. However, CAE does not identify reproducible features in different runs due to its stochastic nature. We thus propose a multi-run CAE (mrCAE) to identify a stable set of features to address this issue. The assumption is that a feature appearing in multiple runs carries more meaningful information about the data under consideration. The genome-wide lncRNA expression profiles of 12 different types of cancers, with a total of 4768 samples available in The Cancer Genome Atlas (TCGA), were analyzed to discover the key lncRNAs. The lncRNAs identified by multiple runs of CAE were added to a final list of key lncRNAs that are capable of identifying 12 different cancers. Results: Our results showed that mrCAE performs better in feature selection than single-run CAE, standard autoencoder (AE), and other state-of-the-art feature selection techniques. This study revealed a set of top-ranking 128 lncRNAs that could identify the origin of 12 different cancers with an accuracy of 95%. Survival analysis showed that 76 of 128 lncRNAs have the prognostic capability to differentiate high- and low-risk groups of patients with different cancers. Conclusion: The proposed mrCAE, which selects actual features, outperformed the AE even though it selects the latent or pseudo-features. By selecting actual features instead of pseudo-features, mrCAE can be valuable for precision medicine. The identified prognostic lncRNAs can be further studied to develop therapies for different cancers.
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Liu B, Liu Y, Zou J, Zou M, Cheng Z. Smoking is Associated with Lung Adenocarcinoma and Lung Squamous Cell Carcinoma Progression through Inducing Distinguishing lncRNA Alterations in Different Genders. Anticancer Agents Med Chem 2021; 22:1541-1550. [PMID: 34315392 DOI: 10.2174/1871520621666210727115147] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/08/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Smoking participates in pathogenesis of lung cancer. Long non-coding RNAs (lncRNAs) play some specific roles during development of lung cancers. OBJECTIVE To investigate effects of smoking on lncRNA alterations in lung cancer. METHODS There are 522 lung adenocarcinoma (LUAD) and 504 lung squamous cell carcinoma (LUSC) participants. Clinical and lncRNA genetic data were downloaded from The Cancer Genome Atlas (TCGA) database. LncRNA alterations were analyzed in lung cancer patients. Smoking category and packs were evaluated. Correlations between smoking and LncRNA alterations were analyzed. Kaplan-Meier analysis was performed to determine overall survival and disease free survival. RESULTS There are more non-smokers in LUSC than in LUAD. In both LUAD and LUSC, smoking could increase total mutation counts and fraction of copy number alterations. Smoking index positively correlated with total mutations in LUAD, but not in LUSC. Smoking could trigger lncRNA alterations both in LUAD and LUSC. Smoking regulated different lncRNA between male and female. EXOC3-AS1 and LINC00603 alterations were positively correlated with smoking index in male LUAD smokers. In female LUAD smokers, smoking index was positively correlated with SNHG15, TP53TG1 and LINC01600 and negatively with LINC00609 and PTCSC3. In both male and female LUSC patients, smoking increased or decreased several lncRNA alterations. DGCR5 alteration increased in male LUSC than in female LUSC patients. In female LUSC patients, LOH12CR2 alteration was positively correlated with smoking index. CONCLUSIONS Smoking promoted LUAD and LUSC development by affecting different lncRNA alterations in different genders.
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Affiliation(s)
- Bing Liu
- Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yuan Liu
- Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jingfeng Zou
- Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Menglin Zou
- Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Zhenshun Cheng
- Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
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Daulatabad SV, Srivastava R, Janga SC. Lantern: an integrative repository of functional annotations for lncRNAs in the human genome. BMC Bioinformatics 2021; 22:279. [PMID: 34039271 PMCID: PMC8157669 DOI: 10.1186/s12859-021-04207-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/18/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, there are a plethora of resources for annotating genes, despite the extensive corpus of lncRNA literature, the available resources with lncRNA ontology annotations are rare. RESULTS We present a lncRNA annotation extractor and repository (Lantern), developed using PubMed's abstract retrieval engine and NCBO's recommender annotation system. Lantern's annotations were benchmarked against lncRNAdb's manually curated free text. Benchmarking analysis suggested that Lantern has a recall of 0.62 against lncRNAdb for 182 lncRNAs and precision of 0.8. Additionally, we also annotated lncRNAs with multiple omics annotations, including predicted cis-regulatory TFs, interactions with RBPs, tissue-specific expression profiles, protein co-expression networks, coding potential, sub-cellular localization, and SNPs for ~ 11,000 lncRNAs in the human genome, providing a one-stop dynamic visualization platform. CONCLUSIONS Lantern integrates a novel, accurate semi-automatic ontology annotation engine derived annotations combined with a variety of multi-omics annotations for lncRNAs, to provide a central web resource for dissecting the functional dynamics of long non-coding RNAs and to facilitate future hypothesis-driven experiments. The annotation pipeline and a web resource with current annotations for human lncRNAs are freely available on sysbio.lab.iupui.edu/lantern.
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Affiliation(s)
- Swapna Vidhur Daulatabad
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Informatics and Communications Technology Complex, 535 W Michigan St., IT 475H, Indianapolis, IN, 46202, USA
| | - Rajneesh Srivastava
- Department of Surgery, Indiana Center for Regenerative Medicine and Engineering (ICRME), Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Informatics and Communications Technology Complex, 535 W Michigan St., IT 475H, Indianapolis, IN, 46202, USA.
- Department of Medical and Molecular Genetics, Medical Research and Library Building, Indiana University School of Medicine, 975 West Walnut Street, Indianapolis, IN, 46202, USA.
- Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN, 46202, USA.
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Wang X, Wang X, Huang G, Chen Y. Lower expression of LINC00092 in lung adenocarcinoma might mean poorer prognosis: A study based on data mining and bioinformatics. Medicine (Baltimore) 2020; 99:e23012. [PMID: 33126385 PMCID: PMC7598869 DOI: 10.1097/md.0000000000023012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The mechanisms that underlie long non-coding RNA 00092 (LINC00092) in lung adenocarcinoma (LUAD) remain unclear. In this study, by mining the Cancer Genome Atlas and Gene Expression Omnibus databases and using bioinformatics tools, we try to elucidate the function of LINC00092 in LUAD.The the Cancer Genome Atlas and gene expression Omnibus microarray datasets were used to analyze and evaluate the expression of LINC00092 in LUAD and its clinical significance. Clinical samples were collected and the relative expression level of LINC00092 were identified by quantitative real time polymerase chain reaction. The LINC00092 related genes were identified by Multi Experiment Matrix, The Atlas of ncRNA in Cancer and the database of RNA-Binding Protein specificities. The predicted genes were then sent to the Gene Ontology enrichment and the Kyoto Encyclopedia of Genes and Genomes pathway analysis.The expression of LINC00092 was significantly decreased in LUAD tissues compared to non-tumor tissues (standard mean difference =-1.10, 95% confidence interval: -1.87 to -0.32, P < .001, random). Low expression of LINC00092 was associated with the poor overall survival (hazard ratio = 1.32, 95% confidence interval: 1.08-1.62, P < .05, fixed) and high pathological stage (P < .05). The relative expression level of LINC00092 in clinical samples were significantly lower in LUAD tissues compared with adjacent normal tissues. (P < 0.05) 61 LINC00092 related genes were identified; the Kyoto Encyclopedia of Genes and Genomes analysis showed that the most significant signaling pathways were: NF-κB, HIF-1 and ErbB signaling pathways.In this study, we found that the decrease of LINC00092 expression was involved in LUAD tumorigenesis and metastasis, and the depletion of LINC00092 was associated with a poor prognosis in patients with LUAD. The mechanisms that underlie LINC00092 in LUAD might be related to the NF-κB, HIF-1 and ErbB signaling pathways.
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Affiliation(s)
- Xin Wang
- Department of Respiratory Medicine
| | - Xianwei Wang
- Department of Pathology, People's Hospital of Deyang City, Deyang, Sichuan Province
| | - Guichuan Huang
- Department of Respiratory Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing , Peoples R China
| | - Yi Chen
- Department of Respiratory Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing , Peoples R China
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Tian Y, Cui L, Lin C, Wang Y, Liu Z, Miao X. LncRNA CDKN2B-AS1 relieved inflammation of ulcerative colitis via sponging miR-16 and miR-195. Int Immunopharmacol 2020; 88:106970. [PMID: 33182065 DOI: 10.1016/j.intimp.2020.106970] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/13/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND This study was aimed to explore the differential expression of lncRNA CDKN2B-AS1-miR-195-5p/miR-16-5p axis in ulcerative colitis (UC) and its role in regulating UC pathogenesis. METHODS One hundred and eighty-seven UC patients and one hundred and fifty-two healthy volunteers were recruited, and their blood samples were collected. Inflammatory cytokines in serum were determined with ELISA, and lncRNA CDKN2B-AS1, miR-195-5p and miR-16-5p levels were detected with RT-PCR. Then pcDNA3.1-CDKN2B-AS1, si-CDKN2B-AS1, miR-195-5p mimic, miR-195-5p inhibitor, miR-16-5p mimic and miR-16-5p inhibitor were transfected into HT29 cells, and proliferation and apoptosis of the cells were assessed. Dual-luciferase reporter gene assay was implemented to identify the sponging relationship between lncRNA CDKN2B-AS1 and miR-195-5p/miR-16-5p. RESULTS CDKN2B-AS1 level was negatively correlated with levels of inflammatory cytokines, including TNF-α, IL-6 and sIL-2R, yet miR-16-5p and miR-195-5p levels were negatively correlated with the CDKN2B-AS1 level. The CDKN2B-AS1 combined with miR-16-5p and miR-195-5p also achieved an optimum efficacy in differentiating between light and medium UC, light and severe UC, as well as medium and heavy UC. Furthermore, pcDNA3.1-CDKN2B-AS1 depressed expressions of IFN-γ, IL-8, IL-1β and TNF-α in HT29 cells (P < 0.05), and strengthened proliferation of the cells (P < 0.05). CDKN2B-AS1 also sponged and regulated miR-16-5p and miR-195-5p in HT29 cells, and miR-16-5p and miR-195-5p could reverse the effect of CDKN2B-AS1 on inflammatory cytokine production, barrier function and apoptosis of HT29 cells (P < 0.05). CONCLUSION LncRNA CDKN2B-AS1 regulated inflammation of UC by sponging miR-195-5p and miR-16-5p, providing an alternative for diagnosis and treatment of UC.
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Affiliation(s)
- Yuanyuan Tian
- Department of Gastroenterology, Hainan General Hospital & Hainan Affiliated Hospital of Hainan Medical University, Haikou City, Hainan Province 570311, China
| | - Lujia Cui
- Department of Gastroenterology, Hainan General Hospital & Hainan Affiliated Hospital of Hainan Medical University, Haikou City, Hainan Province 570311, China
| | - Cheng Lin
- Department of Gastroenterology, Hainan General Hospital & Hainan Affiliated Hospital of Hainan Medical University, Haikou City, Hainan Province 570311, China
| | - Yuxuan Wang
- Department of Gastroenterology, Hainan General Hospital & Hainan Affiliated Hospital of Hainan Medical University, Haikou City, Hainan Province 570311, China
| | - Zhanju Liu
- Department of Pathology, Haikou Hospital of Traditional Chinese Medicine, Haikou City, Hainan Province 570216, China
| | - Xinpu Miao
- Department of Gastroenterology, Hainan General Hospital & Hainan Affiliated Hospital of Hainan Medical University, Haikou City, Hainan Province 570311, China.
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Abstract
Long noncoding RNAs (lncRNAs) have multiple functions in the regulation of cellular homeostasis. In recent years, numerous studies have shown that tumor-associated lncRNAs play key roles in promoting and maintaining tumor initiation and progression by shaping the tumor microenvironment through changing tumor cell intrinsic properties. Here, we focus on the roles of lncRNAs in cancer immunology. In the first part, we provide an overview of the roles played by lncRNAs and their deregulation in cancer at the cancer cell- and tumor microenvironment-associated immune cell levels. We go on to describe preclinical strategies for targeting lncRNAs, particularly highlighting the effects on tumor microenvironments. We then discuss the possibility of combining lncRNA targeting and tumor immune checkpoint inhibitor antibodies to treat cancer.
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Rajagopal T, Talluri S, Akshaya R, Dunna NR. HOTAIR LncRNA: A novel oncogenic propellant in human cancer. Clin Chim Acta 2020; 503:1-18. [DOI: 10.1016/j.cca.2019.12.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 12/27/2019] [Accepted: 12/30/2019] [Indexed: 02/08/2023]
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Gupta C, Su J, Zhan M, Stass SA, Jiang F. Sputum long non-coding RNA biomarkers for diagnosis of lung cancer. Cancer Biomark 2020; 26:219-227. [PMID: 31450489 DOI: 10.3233/cbm-190161] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Analysis of molecular changes in sputum may help diagnose lung cancer. Long non-coding RNAs (lncRNAs) play vital roles in various biological processes, and their dysregulations contribute to the development and progression of lung tumorigenesis. Herein, we determine whether aberrant lncRNAs could be used as potential sputum biomarkers for lung cancer. METHODS Using reverse transcription PCR, we measure expressions of lung cancer-associated lncRNAs in sputum of a discovery cohort of 67 lung cancer patients and 65 cancer-free smokers with benign diseases and a validation cohort of 59 lung cancer patients and 60 cancer-free smokers with benign diseases. RESULTS In the discovery cohort, four of the lncRNAs displayed a significantly different level in sputum of lung cancer patients vs.cancer-free smokers with benign diseases (all P< 0.001). From the four lncRNAs, three lncRNAs (SNHG1, H19, and HOTAIR) are identified as a biomarker panel, producing 82.09% sensitivity and 89.23% specificity for diagnosis of lung cancer. Furthermore, the biomarker panel has a higher sensitivity (82.09% vs. 52.24%, P= 0.02) and a similar specificity compared with sputum cytology (89.23% vs. 90.77%, P= 0.45). In addition, the lncRNA biomarker panel had a higher sensitivity (87.50% vs. 70.07%, p= 0.03) for diagnosis of squamous cell carcinoma compared with adenocarcinoma of the lung, while maintaining the same specificity (89.23%). The potential of the sputum lncRNA biomarkers for lung cancer detection is confirmed in the validation cohort. CONCLUSION We have for the first time shown that the analysis of lncRNAs in sputum might be a noninvasive approach for diagnosis of lung cancer.
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Affiliation(s)
- Chhavi Gupta
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jian Su
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Min Zhan
- Departments of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sanford A Stass
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Feng Jiang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
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Kuang P, Chen P, Wang L, Li W, Chen B, Liu Y, Xu Y, Wang H, Zhao S, Ye L, Yu F, Ji H, He Y. RNA sequencing analysis of small cell lung cancer reveals candidate chemotherapy insensitivity long noncoding RNAs and microRNAs. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:121. [PMID: 32175414 PMCID: PMC7049041 DOI: 10.21037/atm.2020.01.75] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 01/13/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND The further progression of credible expression profiling analysis of genes continues to expand our understanding of the biological characteristics in lung cancer. In this study, RNA sequencing (RNA-Seq) was used to contrast the transcriptomics profiling of small cell lung cancer (SCLC) that acquired partial response (PR) and stable disease (SD)/progressive disease (PD) after first-line chemotherapy. We aimed to illuminate the underlying mechanisms of long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) in the efficacy of SCLC first-line chemotherapy. METHODS Six male patients (mean age, 64.2 years) with SCLC were enrolled in this study. RNA-Seq was executed on the tumor tissues from 3 patients with PR outcome and 3 patients with SD or PD therapeutic effect after first-line chemotherapy. RESULTS RNA-Seq generated 26.67×106 (±8.7×106) reads in SCLC tissues [mean (±standard deviation)]. Analysis revealed that 64 lncRNAs had higher expression and 194 had lower expression in the PR group ≥2-fold (P<0.05). Three downregulated genes in the PR group [HOXA-AS3, cancer susceptibility 9 (CASC9), and KEGG] could have a role in the insensitivity of SCLC. A total of 1,303 differential miRNAs were defined between PR and the SD or PD SCLC group, while 520 miRNAs had higher expression, and 783 had lower expression in the PR group. Two lower expressed miRNAs in the PR group (miRNA 601 and miRNA 596) might be the key genes in SCLC chemotherapy insensitivity. CONCLUSIONS The expression of 3 gene (HOXA-AS3, CASC9, and KEGG) and 2 miRNAs (miRNA 601 and miRNA 596) were markedly decreased in SCLC patients who achieved PR. They thus might be the promising candidate genes in SCLC chemotherapy insensitivity.
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Affiliation(s)
- Peng Kuang
- Department of Medical Oncology, The First Affiliated Hospital Of Nanchang University, Nanchang 330006, China
| | - Peixin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Tongji University, Shanghai 200433, China
| | - Lei Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Wei Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Bin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Yu Liu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Tongji University, Shanghai 200433, China
| | - Yi Xu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Tongji University, Shanghai 200433, China
| | - Hao Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
- Tongji University, Shanghai 200433, China
| | - Sha Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Lingyun Ye
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Feng Yu
- Department of Medical Oncology, The First Affiliated Hospital Of Nanchang University, Nanchang 330006, China
| | - Hongbin Ji
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
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14
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Wang S, Jiang W, Zhang X, Lu Z, Geng Q, Wang W, Li N, Cai X. LINC-PINT alleviates lung cancer progression via sponging miR-543 and inducing PTEN. Cancer Med 2020; 9:1999-2009. [PMID: 31981466 PMCID: PMC7064031 DOI: 10.1002/cam4.2822] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/18/2019] [Accepted: 12/23/2019] [Indexed: 12/11/2022] Open
Abstract
Long intergenic nonprotein coding RNA p53‐induced transcript (LINC‐PINT) has been reported to participate in various cancers. Here, we investigated the effects of LINC‐PINT on lung cancer progression. Firstly, in our study, we implied that LINC‐PINT was obviously decreased in NSCLC. Thereafter, in A549 and H1299 cells, LINC‐PINT was upregulated via transfecting LV‐LINC‐PINT. As exhibited, LINC‐PINT repressed cell proliferation and cell colony formation of A549 and H1299 cells. Subsequently, flow cytometry evidenced that A549 and H1299 cell apoptosis was obviously triggered and the cell cycle was arrested in G1 phase. Then, migration and transwell invasion experiments were carried out to detect the cell migration and invasion capacity. We found A549 and H1299 cell migration and invasion capacity were restrained by the upregulation of LINC‐PINT. Meanwhile, we predicted that miR‐543 could function as the target of LINC‐PINT and the association was verified. Moreover, we exhibited that miR‐543 was remarkably increased in lung cancer, which could be regulated by LINC‐PINT negatively. Furthermore, PTEN could act as the downstream target of miR‐543 and upregulation of miR‐543 repressed PTEN, which was reversed by LV‐PINT in A549 and H1299 cells. Finally, xenografts were utilized to confirm the function of LINC‐PINT on lung cancer. All these findings concluded that LINC‐PINT exerted crucial biological roles in NSCLC through sponging miR‐543 and inducing PTEN.
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Affiliation(s)
- Shu Wang
- Department of Gerontology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wenyang Jiang
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xinghua Zhang
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zilong Lu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qing Geng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wei Wang
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Nan Li
- Department of Cardiology, Shangrao People's Hospital, Shangrao, China
| | - Xinyong Cai
- Department of Cardiology, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, China
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15
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Wang D, Chen F, Zeng T, Tang Q, Chen B, Chen L, Dong Y, Li X. Comprehensive biological function analysis of lncRNAs in hepatocellular carcinoma. Genes Dis 2020; 8:157-167. [PMID: 33997162 PMCID: PMC8099694 DOI: 10.1016/j.gendis.2019.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/16/2019] [Accepted: 12/31/2019] [Indexed: 12/19/2022] Open
Abstract
Thousands of long non-coding RNAs (lncRNAs) have been discovered in human genomes by gene chip, next-generation sequencing, and/or other methods in recent years, which represent a significant subset of the universal genes involved in a wide range of biological functions. An abnormal expression of lncRNAs is associated with the growth, invasion, and metastasis of various types of human cancers, including hepatocellular carcinoma (HCC), which is an aggressive, highly malignant, and invasive tumor, and a poor prognosis in China. With a more in-depth understanding of lncRNA research for HCC and the emergence of new molecular-targeted therapies, the diagnosis, treatment, and prognosis of HCC will be considerably improved. Therefore, this review is expected to provide recommendations and directions for future lncRNA research for HCC.
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Affiliation(s)
- Dan Wang
- Department of Clinical Laboratory, People's Hospital of Rongchang District, Chongqing, Rongchang 402460, PR China.,Key Laboratory of Molecular Biology of Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, PR China
| | - Fengjiao Chen
- Key Laboratory of Molecular Biology of Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, PR China
| | - Tao Zeng
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Sichuan Province, Chengdu, 611731, PR China
| | - Qingxia Tang
- Department of Clinical Laboratory, People's Hospital of Rongchang District, Chongqing, Rongchang 402460, PR China
| | - Bing Chen
- Department of Clinical Laboratory, People's Hospital of Rongchang District, Chongqing, Rongchang 402460, PR China
| | - Ling Chen
- Key Laboratory of Molecular Biology of Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yan Dong
- Clinical Molecular Medicine Testing Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China
| | - Xiaosong Li
- Clinical Molecular Medicine Testing Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China
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16
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Nakano Y, Isobe K, Kobayashi H, Kaburaki K, Isshiki T, Sakamoto S, Takai Y, Tochigi N, Mikami T, Iyoda A, Homma S, Kishi K. Clinical importance of long non‑coding RNA LINC00460 expression in EGFR‑mutant lung adenocarcinoma. Int J Oncol 2019; 56:243-257. [PMID: 31789388 PMCID: PMC6910175 DOI: 10.3892/ijo.2019.4919] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/08/2019] [Indexed: 12/26/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been reported to be involved in the physiological and pathological processes of tumor pathogenesis, including epithelial-mesenchymal transition (EMT). However, epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitor (TKI) resistance is a major challenge in the treatment of advanced and recurrent EGFR-mutant lung adenocarcinoma. An increased understanding of the underlying mechanisms would aid in the development of effective therapeutic strategies against EGFR-TKI resistance, strategies which are urgently required for clinical therapy. In this study, long non-coding RNA LINC00460 was identified as a novel marker of a poor response to EGFR-TKI and prognosis. In lung cancer cells, LINC00460 promoted EGFR-TKI resistance as a competitive decoy for miR-149-5p, thereby facilitating interleukin (IL)-6 expression and inducing EMT-like phenotypes. The knockdown or knockout of LINC00460 in gefitinib-resistant non-small cell lung cancer cells restored the response to EGFR-TKI. In addition, as compared with patients with a low LINC00460 expression in tumors, those with a high LINC00460 expression had a significantly shorter progression-free survival following gefitinib therapy, and a shorter overall survival. Therefore, LINC00460 may be a predictor of and potential therapeutic target for EGFR-TKI resistance.
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Affiliation(s)
- Yuta Nakano
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143‑8541, Japan
| | - Kazutoshi Isobe
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143‑8541, Japan
| | - Hiroshi Kobayashi
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143‑8541, Japan
| | - Kyohei Kaburaki
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143‑8541, Japan
| | - Takuma Isshiki
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143‑8541, Japan
| | - Susumu Sakamoto
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143‑8541, Japan
| | - Yujiro Takai
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143‑8541, Japan
| | - Naobumi Tochigi
- Department of Surgical Pathology, Toho University School of Medicine, Tokyo 143‑8541, Japan
| | - Tetsuo Mikami
- Department of Pathology, Toho University School of Medicine, Tokyo 143‑8541, Japan
| | - Akira Iyoda
- Department of Chest Surgery, Toho University School of Medicine, Tokyo 143‑8541, Japan
| | - Sakae Homma
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143‑8541, Japan
| | - Kazuma Kishi
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143‑8541, Japan
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17
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Chen L, Zhu J, Zhang LJ. Long non-coding RNA small nucleolar RNA host gene 7 is upregulated and promotes cell proliferation in thyroid cancer. Oncol Lett 2019; 18:4726-4734. [PMID: 31611982 PMCID: PMC6781492 DOI: 10.3892/ol.2019.10782] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 06/06/2019] [Indexed: 12/23/2022] Open
Abstract
Thyroid cancer (THCA) is one of the most common types of endocrine cancer worldwide. However, the mechanisms underlying THCA progression have not been fully elucidated. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are dysregulated in human diseases, and are involved in regulating various biological processes. Furthermore, several reports have indicated that lncRNAs serve important roles in THCA. In the present study, a dataset from The Cancer Genome Atlas was used to analyze the expression levels and the clinical information of small nucleolar RNA host gene 7 (SNHG7) in THCA. Starbase was used to construct the competing endogenous RNA network. The Molecule Annotation System was used to analyze the data from Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. Furthermore, cell proliferation and cell cycle assays were used to detect the functions of SNHG7 in THCA. The present study revealed for the first time, to the best of our knowledge, that SNHG7 is markedly upregulated in THCA samples following analysis of The Cancer Genome Atlas datasets. SNHG7 expression was higher in advanced stage compared with early stage THCA samples. In addition, high expression levels of SNHG7 were associated with shorter survival times in THCA patients compared with low expression levels. Bioinformatics analysis revealed that SNHG7 was associated with the processes of ‘protein translation’, ‘viral life cycle’, ‘RNA processing’, ‘mRNA splicing’, ‘histone ubiquitination’, ‘endoplasmic reticulum-to-Golgi vesicle-mediated transport’, ‘sister chromatid cohesion’, ‘DNA damage checkpoint regulation’, ‘translation’ and ‘the spliceosome’. Additionally, knockdown of SNHG7 significantly inhibited thyroid cancer cell proliferation and cell cycle progression in vitro. Taken together, the results obtained in the present study suggested that SNHG7 may serve as a novel therapeutic and prognostic target for THCA.
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Affiliation(s)
- Li Chen
- Department of Endocrinology, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, Hubei 434020, P.R. China
| | - Jing Zhu
- Department of Clinical Laboratory, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, Hubei 434020, P.R. China
| | - Ling-Jie Zhang
- Department of Anesthesiology, Hubei Provincial Hospital of Integrated Chinese and Western Medicine, Wuhan, Hubei 430015, P.R. China
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18
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Gong W, Yang L, Wang Y, Xian J, Qiu F, Liu L, Lin M, Feng Y, Zhou Y, Lu J. Analysis of Survival-Related lncRNA Landscape Identifies A Role for LINC01537 in Energy Metabolism and Lung Cancer Progression. Int J Mol Sci 2019; 20:ijms20153713. [PMID: 31374807 PMCID: PMC6696180 DOI: 10.3390/ijms20153713] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023] Open
Abstract
Many long non-coding RNAs (lncRNAs) have emerged as good biomarkers and potential therapeutic targets for various cancers. We aimed to get a detailed understanding of the lncRNA landscape that is associated with lung cancer survival. A comparative analysis between our RNA sequencing (RNA-seq) data and TCGA datasets was conducted to reveal lncRNAs with significant correlations with lung cancer survival and then the association of the most promising lncRNA was validated in a cohort of 243 lung cancer patients. Comparing RNA-seq data with TCGA ones, 84 dysregulated lncRNAs were identified in lung cancer tissues, among which 10 lncRNAs were significantly associated with lung cancer survival. LINC01537 was the most significant one (p = 2.95 × 10−6). Validation analysis confirmed the downregulation of LINC01537 in lung cancer. LINC01537 was observed to inhibit tumor growth and metastasis. It also increased cellular sensitivity to nilotinib. PDE2A (phosphodiesterase 2A) was further identified to be a target of LINC01537 and it was seen that LINC01537 promoted PDE2A expression via RNA–RNA interaction to stabilize PDE2A mRNA and thus echoed effects of PDE2A on energy metabolism including both Warburg effect and mitochondrial respiration. Other regulators of tumor energy metabolism were also affected by LINC01537. These results elucidate a suppressed role of LINC01537 in lung cancer development involving tumor metabolic reprogramming, and we believe that it might be a biomarker for cancer survival prediction and therapy.
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Affiliation(s)
- Wei Gong
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Lei Yang
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China.
| | - Yuanyuan Wang
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Jianfeng Xian
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Fuman Qiu
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Li Liu
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Mingzhu Lin
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Yingyi Feng
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Yifeng Zhou
- Department of Genetics, Medical College of Soochow University, 1 Shizi Road, Suzhou 215123, China
| | - Jiachun Lu
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China.
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19
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PILAR1, a novel prognostic LncRNA, reveals the presence of a unique subtype of lung adenocarcinoma patients with KEAP1 mutations. Gene 2019; 691:167-175. [DOI: 10.1016/j.gene.2018.12.060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 12/27/2018] [Indexed: 02/06/2023]
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20
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Li JY, Luo ZQ. LCAL1 enhances lung cancer survival via inhibiting AMPK-related antitumor functions. Mol Cell Biochem 2019; 457:11-20. [DOI: 10.1007/s11010-019-03507-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/01/2019] [Indexed: 12/25/2022]
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21
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Yang L, Sun K, Chu J, Qu Y, Zhao X, Yin H, Ming L, Wan J, He F. Long non-coding RNA FTH1P3 regulated metastasis and invasion of esophageal squamous cell carcinoma through SP1/NF-kB pathway. Biomed Pharmacother 2018; 106:1570-1577. [PMID: 30119232 DOI: 10.1016/j.biopha.2018.07.129] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 07/18/2018] [Accepted: 07/24/2018] [Indexed: 01/28/2023] Open
Abstract
AIMS:: Recent research showed that Long non-protein coding RNA ferritin heavy chain 1 pseudogene 3 (FTH1P3) plays a crucial role in the course of tumor formation. The present study was aimed to explore its role in esophageal squamous cell carcinoma (ESCC). MAIN METHODS Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) was used to examine the expression levels of FTH1P3, mRNA SP1 and NF-kB in ESCC samples and cell lines. The impact of FTH1P3 knockdown was evaluated by WST-1 assays, colony formation assays, scratch wound assays, migration and invasion assays. KEY FINDINGS FTH1P3 was significantly upregulated in ESCC tissues and cells (P < 0.001). Knockdown of FTH1P3 notably decreased the proliferation, migration, and invasion capacity of ESCC cells. Silencing of FTH1P3 decreased the expression of specificity protein 1 (Sp1) and NF-kB (p65) in EC9706 and EC1. SIGNIFICANCE FTH1P3 plays a crucial role in ESCC tumorigenesis, and can be used as a potential therapeutic target for ESCC.
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Affiliation(s)
- Lijun Yang
- Department of Medical Laboratory, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Kaiyan Sun
- Department of Medical Laboratory, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Jie Chu
- Department of Medical Laboratory, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Yunhui Qu
- Department of Medical Laboratory, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Xue Zhao
- Institute of Medical and Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Huiqing Yin
- Department of Medical Laboratory, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Liang Ming
- Department of Medical Laboratory, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Junhu Wan
- Department of Medical Laboratory, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Fucheng He
- Department of Medical Laboratory, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan Province, China.
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22
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Zhao B, Xu H, Ai X, Adalat Y, Tong Y, Zhang J, Yang S. Expression profiles of long noncoding RNAs in lung adenocarcinoma. Onco Targets Ther 2018; 11:5383-5390. [PMID: 30233202 PMCID: PMC6134945 DOI: 10.2147/ott.s167633] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Purpose This study aimed to analyze expression profiles of long noncoding RNAs (lncRNAs) in lung adenocarcinoma. Methods lncRNA microarray technology was employed to detect lncRNA profiles of 3 pairs of lung adenocarcinoma tissues and adjacent tissues. Results We found 134 upregulated lncRNAs and 460 downregulated lncRNAs in lung adenocarcinoma tissues compared to adjacent tissues. Among them, LINC00152, LINC00691, and LINC00578 showed the most significant changes of upregulation, while LINC00668, LINC00710, and LINC00607 showed the most significant changes of downregulation. Fluorescent quantitative polymerase chain reaction (PCR) analysis of tissue samples from an additional 90 patients with lung adenocarcinoma showed significantly increased levels of LINC00152, LINC00691, and LINC00578 and decreased levels of LINC00668, LINC00710, and LINC00607 in lung adenocarcinoma tissues. In addition, LINC00578 was closely associated with the existence of metastasis of lung adenocarcinoma, but the other 5 lncRNAs showed no significant correlation with clinicopathologic characteristics such as age, gender, tumor stage, and the existence of metastasis. Further follow-up study showed that LINC00578 expression was closely associated with the survival of patients with lung adenocarcinoma. Conclusion We revealed the expression profiles of lncRNAs in lung adenocarcinoma and identified LINC00578 as a promising biomarker and therapeutic target for lung adenocarcinoma.
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Affiliation(s)
- Bing Zhao
- Department of Day Oncology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Hang Xu
- Intensive Care Unit, The Sixth Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang, People's Republic of China
| | - Xiaoye Ai
- Department of Day Oncology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Yasheng Adalat
- Department of Day Oncology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Ying Tong
- Department of Day Oncology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Jiazhennan Zhang
- Department of Day Oncology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Shune Yang
- Department of Breast Cancer and Lymphoma, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, People's Republic of China,
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23
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Li J, Li H, Lv X, Yang Z, Gao M, Bi Y, Zhang Z, Wang S, Cui Z, Zhou B, Yin Z. Polymorphism in lncRNA AC016683.6 and its interaction with smoking exposure on the susceptibility of lung cancer. Cancer Cell Int 2018; 18:91. [PMID: 29997452 PMCID: PMC6031149 DOI: 10.1186/s12935-018-0591-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/26/2018] [Indexed: 01/03/2023] Open
Abstract
Background Long non-coding RNAs play pivotal roles in the carcinogenesis of multiple types of cancers. This study is firstly to evaluate influence of rs4848320 and rs1110839 polymorphisms in long non-coding RNA AC016683.6 on the susceptibility of lung cancer. Methods The present study was a hospital-based case–control study with 434 lung cancer patients and 593 cancer-free controls. Genotyping of the two SNPs detected by Taqman® allelic discrimination method. Results There were no statistically significant associations between rs4848320 and rs1110839 polymorphisms in AC016683.6 and risk of lung cancer in overall population. However, in the smoking population, rs4848320 and rs1110839 polymorphisms significantly increased the risk of lung cancer in dominant and homozygous models (Rs4848320: P = 0.029; Rs1110839: P = 0.034), respectively. In male population, rs1110839 genetic variant was related to the risk of lung cancer in all genetic models (GG vs. TT: P = 0.008; Dominant model: P = 0.029; Recessive model: P = 0.027) rather than heterozygous model. The crossover analyses provided rs4848320 and rs1110839 risk genotypes carriers combined with smoking exposure 2.218-fold, 1.755-fold increased risk of lung cancer (Rs4848320: P = 0.005; Rs1110839: P = 0.017). Additionally, there were significantly positive multiplicative interaction of rs4848320 polymorphism with smoking status, with adjusted OR of 2.244 (1.162–4.334), but rs1110839 polymorphism did not exist. Conclusions Rs4848320 and rs1110839 polymorphisms may be associated with lung cancer susceptibility. Interaction of rs4848320 risk genotypes with smoking exposure may strengthen the risk effect on lung cancer.
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Affiliation(s)
- Juan Li
- 1Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China
| | - Hang Li
- 1Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China
| | - Xiaoting Lv
- 1Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China
| | - Zitai Yang
- 1Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China
| | - Min Gao
- 1Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China
| | - Yanhong Bi
- 1Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China
| | - Ziwei Zhang
- 1Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China
| | - Shengli Wang
- 1Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China
| | - Zhigang Cui
- 3School of Nursing, China Medical University, Shenyang, 110122 China
| | - Baosen Zhou
- 1Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China
| | - Zhihua Yin
- 1Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110122 People's Republic of China.,2Key Laboratory of Cancer Etiology and Intervention, University of Liaoning Province, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122 People's Republic of China
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24
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Huang Q, Liu Y, Dong S. Emerging roles of long non-coding RNAs in the toxicology of environmental chemicals. J Appl Toxicol 2018; 38:934-943. [PMID: 29388697 DOI: 10.1002/jat.3595] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/27/2017] [Accepted: 12/27/2017] [Indexed: 12/12/2022]
Abstract
Environmental chemicals (ECs) are drawing great attention to their effects on health and their toxicological mechanisms are being investigated. Long non-coding RNA (lncRNA) is a class of RNA with more than 200 nucleotides and does not have protein coding potential. Recently, it is emerging as a star molecule that participates in a wide range of physiological and pathological processes. It has been reported to be abnormally expressed in diseases. As an epigenetic factor, lncRNAs play an important role in the response of organisms to environmental stress. Their roles in the toxicity of ECs are being identified. Altered expression profiles of lncRNAs have been explored after exposure to ECs. Various kinds of ECs are reported to disturb the expression of lncRNAs in vitro and in vivo. Then, dysregulated lncRNAs can affect the expression of target genes directly or indirectly via regulating the level of microRNAs. The network among lncRNAs, microRNAs and mRNAs can initiate or impede specific signaling pathway and lead to adverse outcome upon exposure to ECs. Recovery of the lncRNAs level by overexpression or knockdown technology diminished the effect induced by ECs. In the review, biological roles of lncRNAs are depicted. The lncRNAs involved in the toxicology are summarized. Types of ECs that have been reported to affect the expression of lncRNAs are categorized. The interaction between various types of ECs and lncRNAs is discussed.
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Affiliation(s)
- Qiansheng Huang
- Chinese Academy of Sciences, Key Lab of Urban Environment and Health, Institute of Urban Environment, Xiamen, 361021, People's Republic of China
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China
| | - Yiyao Liu
- Chinese Academy of Sciences, Key Lab of Urban Environment and Health, Institute of Urban Environment, Xiamen, 361021, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Sijun Dong
- Chinese Academy of Sciences, Key Lab of Urban Environment and Health, Institute of Urban Environment, Xiamen, 361021, People's Republic of China
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China
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25
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Peng L, Yuan XQ, Zhang CY, Peng JY, Zhang YQ, Pan X, Li GC. The emergence of long non-coding RNAs in hepatocellular carcinoma: an update. J Cancer 2018; 9:2549-2558. [PMID: 30026854 PMCID: PMC6036883 DOI: 10.7150/jca.24560] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 03/31/2018] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) accounting for roughly 90% of all primary liver neoplasms is the sixth most frequent neoplasm and the second prominent reason of tumor fatality worldwide. As regulators of diverse biological processes, long non-coding RNAs (lncRNAs) are involved in onset and development of neoplasms. With the continuous booming of well-featured lncRNAs in HCC from 2016 to now, we reviewed the newly-presented comprehension about the relationship between lncRNAs and HCC in this study. To be specific, we summarized the overview function and study tools of lncRNAs, elaborated the roles of lncRNAs in HCC, and sketched the molecule mechanisms of lncRNAs in HCC. In addition, the application of lncRNAs serving as biomarkers in early diagnosis and outcome prediction of HCC patients was highlighted.
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Affiliation(s)
- Li Peng
- Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, P.R. China; Cancer Research Institute, Central South University, Changsha 410078, P.R. China
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China
| | - Xiao-Qing Yuan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, China
| | - Chao-Yang Zhang
- Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, P.R. China; Cancer Research Institute, Central South University, Changsha 410078, P.R. China
| | - Jiang-Yun Peng
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P.R. China
| | - Ya-Qin Zhang
- Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, P.R. China; Cancer Research Institute, Central South University, Changsha 410078, P.R. China
| | - Xi Pan
- Department of Oncology, the third Xiangya Hospital, Central South University, Changsha 410013, P.R. China
| | - Guan-Cheng Li
- Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha 410078, P.R. China; Cancer Research Institute, Central South University, Changsha 410078, P.R. China
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26
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YAP and TAZ in Lung Cancer: Oncogenic Role and Clinical Targeting. Cancers (Basel) 2018; 10:cancers10050137. [PMID: 29734788 PMCID: PMC5977110 DOI: 10.3390/cancers10050137] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 12/17/2022] Open
Abstract
Lung cancer is the leading cause of cancer death in the world and there is no current treatment able to efficiently treat the disease as the tumor is often diagnosed at an advanced stage. Moreover, cancer cells are often resistant or acquire resistance to the treatment. Further knowledge of the mechanisms driving lung tumorigenesis, aggressiveness, metastasization, and resistance to treatments could provide new tools for detecting the disease at an earlier stage and for a better response to therapy. In this scenario, Yes Associated Protein (YAP) and Trascriptional Coactivator with PDZ-binding motif (TAZ), the final effectors of the Hippo signaling transduction pathway, are emerging as promising therapeutic targets. Here, we will discuss the most recent advances made in YAP and TAZ biology in lung cancer and, more importantly, on the newly discovered mechanisms of YAP and TAZ inhibition in lung cancer as well as their clinical implications.
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27
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Yuan S, Liu Q, Hu Z, Zhou Z, Wang G, Li C, Xie W, Meng G, Xiang Y, Wu N, Wu L, Yu Z, Bai L, Li Y. Long non-coding RNA MUC5B-AS1 promotes metastasis through mutually regulating MUC5B expression in lung adenocarcinoma. Cell Death Dis 2018; 9:450. [PMID: 29670111 PMCID: PMC5906460 DOI: 10.1038/s41419-018-0472-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 02/09/2018] [Accepted: 03/06/2018] [Indexed: 12/12/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been involved in the process of cancer occurrence, progression, and treatment. Lung cancer-related lncRNAs are still an emerging field, thus we sought to identify novel functional lncRNAs as candidate targets in lung cancer. Here, we identified one novel lncRNA, MUC5B-AS1 (Ensembl: ENST00000532061.2). MUC5B-AS1 was upregulated in lung adenocarcinoma tissues compared with normal lung tissues. Moreover, MUC5B-AS1 promoted lung cancer cell migration and invasion in vitro and promoted lung cancer cell metastasis in vivo. MUC5B-AS1 and its cognate sense transcript MUC5B were highly co-expressed and mutually regulated in lung adenocarcinoma. Mechanistically, MUC5B-AS1 promoted cell migration and invasion by forming an RNA–RNA duplex with MUC5B, thereby increasing MUC5B expression levels in lung adenocarcinoma. The high expression of MUC5B was significantly associated with poor outcomes in lung adenocarcinoma. Our findings highlight MUC5B-AS1 functions as an oncogenic lncRNA in tumor metastasis and implicate MUC5B-AS1 as an attractive candidate target for lung adenocarcinoma treatment.
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Affiliation(s)
- Shuai Yuan
- Department of Epidemiology, College of Preventive Medicine, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Qingyun Liu
- Department of Epidemiology, College of Preventive Medicine, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Zeyao Hu
- Department of Epidemiology, College of Preventive Medicine, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Zhengyu Zhou
- Department of Epidemiology, College of Preventive Medicine, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Guilu Wang
- Department of Epidemiology, College of Preventive Medicine, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Chengying Li
- Department of Epidemiology, College of Preventive Medicine, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Weijia Xie
- Department of Epidemiology, College of Preventive Medicine, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Gang Meng
- Department of Pathology, Southwest Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Ying Xiang
- Department of Epidemiology, College of Preventive Medicine, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Na Wu
- Department of Epidemiology, College of Preventive Medicine, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Long Wu
- Department of Epidemiology, College of Preventive Medicine, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Zubin Yu
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Li Bai
- Department of Respiratory Disease, Xinqiao Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Yafei Li
- Department of Epidemiology, College of Preventive Medicine, Army Medical University (Third Military Medical University), 400038, Chongqing, China.
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28
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Zhang W, He W, Gao J, Wang Y, Zang W, Dong Z, Zhao G. RETRACTED: The long noncoding RNA CASC2 inhibits tumorigenesis through modulating the expression of PTEN by targeting miR-18a-5p in esophageal carcinoma. Exp Cell Res 2017; 361:30-38. [DOI: 10.1016/j.yexcr.2017.09.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/23/2017] [Accepted: 09/26/2017] [Indexed: 02/07/2023]
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29
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Fine particulate matter 2.5 exerted its toxicological effect by regulating a new layer, long non-coding RNA. Sci Rep 2017; 7:9392. [PMID: 28839203 PMCID: PMC5570922 DOI: 10.1038/s41598-017-09818-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 07/31/2017] [Indexed: 12/20/2022] Open
Abstract
Fine particulate matter (PM2.5) exposure, especially to its organic components, induces adverse health effects on the respiratory system. However, the molecular mechanisms have still not been fully elucidated. Long non-coding RNA (lncRNA) is involved in various physio-pathological processes. In this study, the roles of lncRNA were investigated to reveal the toxicology of PM2.5. Organic extracts of PM2.5 from Nanjing and Shanghai cities were adopted to treat human bronchial epithelial cell lines (BEAS-2B and A549). RNA sequencing showed that the lncRNA functioned as antisense RNA, intergenic RNA and pre-miRNA. The mRNA profiles were also altered after exposure. PM2.5 from Nanjing showed a more serious impact than that from Shanghai. In detail, higher expression of n405968 was positively related to the elevated mRNA levels of inflammatory factors (IL-6 and IL-8). Increasing levels of metastasis associated lung adenocarcinoma transcript 1 (MALAT1) were positively associated with the induced epithelial-mesenchymal transition (EMT) process. Similar response was observed between both cell lines. The higher content of polycyclic aromatic hydrocarbons (PAHs) is likely to contribute to higher toxicity of PM2.5 from Nanjing than that from Shanghai. Antagonism of aryl hydrocarbon receptor (AHR) or inhibition of CYP1A1 diminished the effects stimulated by PM2.5. Our results indicated that lncRNAs could be involved in the toxicology of PM2.5 through regulating the inflammation and EMT process.
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30
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Earl CC, Smith MT, Lease RA, Bundy BC. Polyvinylsulfonic acid: A Low-cost RNase inhibitor for enhanced RNA preservation and cell-free protein translation. Bioengineered 2017; 9:90-97. [PMID: 28662363 PMCID: PMC5972934 DOI: 10.1080/21655979.2017.1313648] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The effectiveness and economics of polyvinyl sulfonic acid (PVSA) as a ribonuclease inhibitor for in vitro systems is reported. PVSA was shown to inhibit RNA cleavage in the presence of RNase A as well as in the presence of Escherichia coli lysate, suggesting that PVSA can act as a broader ribonuclease inhibitor. In addition, PVSA was shown to improve the integrity of mRNA transcripts by up to 5-fold in vitro as measured by their translational viability. Improved preservation of mRNA transcripts in the presence of PVSA under common RNA storage conditions is also reported. A cost comparison with commercially available RNAse inhibitors indicates the economic practicality of PVSA which is approximately 1,700 times less expensive than commonly used ribonuclease inhibitors. PVSA can also be separated from RNA by alcohol precipitation for applications that may be sensitive to the presence of PVSA.
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Affiliation(s)
- Conner C Earl
- a Department of Chemical Engineering , Brigham Young University , Provo , UT , USA
| | - Mark T Smith
- a Department of Chemical Engineering , Brigham Young University , Provo , UT , USA
| | - Richard A Lease
- b Department of Chemical and Biomolecular Engineering , The Ohio State University , Columbus OH USA
| | - Bradley C Bundy
- a Department of Chemical Engineering , Brigham Young University , Provo , UT , USA
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31
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Malakar P, Shilo A, Mogilevsky A, Stein I, Pikarsky E, Nevo Y, Benyamini H, Elgavish S, Zong X, Prasanth KV, Karni R. Long Noncoding RNA MALAT1 Promotes Hepatocellular Carcinoma Development by SRSF1 Upregulation and mTOR Activation. Cancer Res 2017; 77:1155-1167. [PMID: 27993818 PMCID: PMC5334181 DOI: 10.1158/0008-5472.can-16-1508] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 11/26/2016] [Accepted: 12/06/2016] [Indexed: 12/30/2022]
Abstract
Several long noncoding RNAs (lncRNA) are abrogated in cancer but their precise contributions to oncogenesis are still emerging. Here we report that the lncRNA MALAT1 is upregulated in hepatocellular carcinoma and acts as a proto-oncogene through Wnt pathway activation and induction of the oncogenic splicing factor SRSF1. Induction of SRSF1 by MALAT1 modulates SRSF1 splicing targets, enhancing the production of antiapoptotic splicing isoforms and activating the mTOR pathway by modulating the alternative splicing of S6K1. Inhibition of SRSF1 expression or mTOR activity abolishes the oncogenic properties of MALAT1, suggesting that SRSF1 induction and mTOR activation are essential for MALAT1-induced transformation. Our results reveal a mechanism by which lncRNA MALAT1 acts as a proto-oncogene in hepatocellular carcinoma, modulating oncogenic alternative splicing through SRSF1 upregulation. Cancer Res; 77(5); 1155-67. ©2016 AACR.
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Affiliation(s)
- Pushkar Malakar
- Department of Biochemistry and Molecular Biology, Hebrew University-Hadassah Medical School, Ein Karem, Jerusalem, Israel
| | - Asaf Shilo
- Department of Biochemistry and Molecular Biology, Hebrew University-Hadassah Medical School, Ein Karem, Jerusalem, Israel
| | - Adi Mogilevsky
- Department of Biochemistry and Molecular Biology, Hebrew University-Hadassah Medical School, Ein Karem, Jerusalem, Israel
| | - Ilan Stein
- Department of Immunology and Cancer Research, Hebrew University-Hadassah Medical School, Ein Karem, Jerusalem, Israel
| | - Eli Pikarsky
- Department of Immunology and Cancer Research, Hebrew University-Hadassah Medical School, Ein Karem, Jerusalem, Israel
| | - Yuval Nevo
- Bioinformatics unit, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Ein Karem, Jerusalem, Israel
| | - Hadar Benyamini
- Bioinformatics unit, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Ein Karem, Jerusalem, Israel
| | - Sharona Elgavish
- Bioinformatics unit, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Ein Karem, Jerusalem, Israel
| | - Xinying Zong
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, Hebrew University-Hadassah Medical School, Ein Karem, Jerusalem, Israel.
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32
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ANRIL: a pivotal tumor suppressor long non-coding RNA in human cancers. Tumour Biol 2016; 37:5657-61. [PMID: 26753962 DOI: 10.1007/s13277-016-4808-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 01/06/2016] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a family of non-protein-coding RNAs with length more than 200 nucleotides. LncRNAs played important roles in many biological processes such as cell development, proliferation, invasion and migration. Deregulation of LncRNAs was found in multiple tumors where they can act as a tumor suppressor gene or oncogene. LncRNA ANRIL was identified as an oncogene involved in a number of tumors such as gastric cancer, lung cancer, hepatocellular carcinoma, and esophageal squamous cell carcinoma. Inhibition of ANRIL suppressed the cancer cell proliferation, migration and invasion. Increasing data has showed that ANRIL may act as a diagnostic and prognostic biomarker for some tumors. In our review, we summarize an overview of current knowledge concerning the expression and role of ANRIL in various cancers.
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