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Tang K, Lin W, Wang D, Hu X, Chen Z, Chen J, Liang B, Zhang L, Qin P, Wu D. Potential Role of MAP3K14 in Hepatocellular Carcinoma: A Study Based on Comprehensive Bioinformatical Analysis and Validation. J Cancer 2024; 15:2731-2745. [PMID: 38577603 PMCID: PMC10988307 DOI: 10.7150/jca.95322] [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: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
According to reports, MAP3K14 is considered an oncogene and is aberrantly expressed in various types of tumor cells. Its abnormal expression is closely associated with the occurrence and progression of various cancers. MAP3K14 also plays a significant role in the development of non-alcoholic steatohepatitis (NASH)-related hepatocellular carcinoma and its connection to tumor stem cells. The prognostic value of MAP3K14 in HCC, as well as its potential functions and roles, requires further elucidation. We evaluated the potential role of MAP3K14 in HCC based on data mining from a range of public databases. The bioinformatics analysis of TCGA, GEO, TIMER, cBioportal, Kaplan-Meier plotter, MethSurv, ENCORI and CellMiner databases was carried out. The expression of MAP3K14 protein in HCC was detected by immunohistochemical method. The mRNA and protein expression levels of MAP3K14 in tumor tissues were higher than those in normal tissues (p < 0.05). The expression of MAP3K14 was correlated with Pathologic T stage (p=0.026), Pathologic stage (p=0.032), Tumor status (p=0.024) and AFP (p=0.002). HCC patients with high expression of MAP3K14 had poor overall survival (OS), progression free survival (PFS) and recurrence free survival (RFS). Multivariate Cox regression analysis showed that the Pathologic stage (p < 0.001) and MAP3K14 expression levels (p < 0.05) is an independent prognostic factor affecting the survival of patients with liver cancer. GO/KEGG analysis suggested that key biological processes (PI3K-Akt signaling pathway) may be the mechanism promoting HCC development. In addition, MAP3K14 was significantly correlated with the infiltrating levels of B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells (p < 0.05). MAP3K14 is up-regulated in HCC and is closely related to the prognosis of HCC patients. MAP3K14 may serve as a potential biomarker for poor prognosis of HCC.
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Affiliation(s)
- Ke Tang
- School of Public Health, Guangdong Medical University, Dongguan City, 523808, China
- Guangzhou Center for Disease Control and Prevention, Guangzhou City, 510440, China
| | - Weiquan Lin
- Guangzhou Center for Disease Control and Prevention, Guangzhou City, 510440, China
| | - Dedong Wang
- Guangzhou Center for Disease Control and Prevention, Guangzhou City, 510440, China
| | - Xiangzhi Hu
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou City, 510632, China
| | - Zhitao Chen
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou City, 510632, China
| | - Jinbin Chen
- Guangzhou key laboratory for clinical rapid diagnosis and early warning of infectious diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou City, 510180, China
| | - Boheng Liang
- Guangzhou Center for Disease Control and Prevention, Guangzhou City, 510440, China
| | - Lin Zhang
- Guangzhou Center for Disease Control and Prevention, Guangzhou City, 510440, China
| | - Pengzhe Qin
- Guangzhou Center for Disease Control and Prevention, Guangzhou City, 510440, China
| | - Di Wu
- School of Public Health, Guangdong Medical University, Dongguan City, 523808, China
- Guangzhou Center for Disease Control and Prevention, Guangzhou City, 510440, China
- The State Key Lab of Respiratory Disease, School of Public Health, Guangzhou Medical University, Xinzao Town, Panyu District, Guangzhou, 511436, China
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Salido-Guadarrama I, Romero-Cordoba SL, Rueda-Zarazua B. Multi-Omics Mining of lncRNAs with Biological and Clinical Relevance in Cancer. Int J Mol Sci 2023; 24:16600. [PMID: 38068923 PMCID: PMC10706612 DOI: 10.3390/ijms242316600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
In this review, we provide a general overview of the current panorama of mining strategies for multi-omics data to investigate lncRNAs with an actual or potential role as biological markers in cancer. Several multi-omics studies focusing on lncRNAs have been performed in the past with varying scopes. Nevertheless, many questions remain regarding the pragmatic application of different molecular technologies and bioinformatics algorithms for mining multi-omics data. Here, we attempt to address some of the less discussed aspects of the practical applications using different study designs for incorporating bioinformatics and statistical analyses of multi-omics data. Finally, we discuss the potential improvements and new paradigms aimed at unraveling the role and utility of lncRNAs in cancer and their potential use as molecular markers for cancer diagnosis and outcome prediction.
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Affiliation(s)
- Ivan Salido-Guadarrama
- Departamento de Bioinformatìca y Análisis Estadísticos, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City 11000, Mexico
| | - Sandra L. Romero-Cordoba
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
- Biochemistry Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico
| | - Bertha Rueda-Zarazua
- Posgrado en Ciencias Biológicas, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
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Xu J, Pang B, Lan Y, Dou R, Wang S, Kang S, Zhang W, Liu Y, Zhang Y, Ping Y. Identifying the personalized driver gene sets maximally contributing to abnormality of transcriptome phenotype in glioblastoma multiforme individuals. Mol Oncol 2023; 17:2472-2490. [PMID: 37491836 PMCID: PMC10620122 DOI: 10.1002/1878-0261.13499] [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: 12/02/2022] [Revised: 06/21/2023] [Accepted: 07/24/2023] [Indexed: 07/27/2023] Open
Abstract
High heterogeneity in genome and phenotype of cancer populations made it difficult to apply population-based common driver genes to the diagnosis and treatment of cancer individuals. Characterizing and identifying the personalized driver mechanism for glioblastoma multiforme (GBM) individuals were pivotal for the realization of precision medicine. We proposed an integrative method to identify the personalized driver gene sets by integrating the profiles of gene expression and genetic alterations in cancer individuals. This method coupled genetic algorithm and random walk to identify the optimal gene sets that could explain abnormality of transcriptome phenotype to the maximum extent. The personalized driver gene sets were identified for 99 GBM individuals using our method. We found that genomic alterations in between one and seven driver genes could maximally and cumulatively explain the dysfunction of cancer hallmarks across GBM individuals. The driver gene sets were distinct even in GBM individuals with significantly similar transcriptomic phenotypes. Our method identified MCM4 with rare genetic alterations as previously unknown oncogenic genes, the high expression of which were significantly associated with poor GBM prognosis. The functional experiments confirmed that knockdown of MCM4 could significantly inhibit proliferation, invasion, migration, and clone formation of the GBM cell lines U251 and U118MG, and overexpression of MCM4 significantly promoted the proliferation, invasion, migration, and clone formation of the GBM cell line U87MG. Our method could dissect the personalized driver genetic alteration sets that are pivotal for developing targeted therapy strategies and precision medicine. Our method could be extended to identify key drivers from other levels and could be applied to more cancer types.
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Affiliation(s)
- Jinyuan Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Bo Pang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Yujia Lan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Renjie Dou
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Shuai Wang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Shaobo Kang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Wanmei Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Yuanyuan Liu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Yijing Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
| | - Yanyan Ping
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityChina
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4
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Yang G, Chen X, Quan Z, Liu M, Guo Y, Tang Y, Peng L, Wang L, Wu Y, Wu X, Liu J, Zheng Y. Comprehensive analysis of the FOXA1-related ceRNA network and identification of the MAGI2-AS3/DUSP2 axis as a prognostic biomarker in prostate cancer. Front Oncol 2023; 13:1048521. [PMID: 36998469 PMCID: PMC10043306 DOI: 10.3389/fonc.2023.1048521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
BackgroundProstate cancer (PCa) is the second most common cause of cancer-related deaths in American men. Even though increasing evidence has disclosed the competitive endogenous RNA (ceRNA) regulatory networks among cancers, the complexity and behavior characteristics of the ceRNA network in PCa remain unclear. Our study aimed to investigate the forkhead box A1 (FOXA1)-related ceRNA regulatory network and ascertain potential prognostic markers associated with PCa.MethodsRNA sequence profiles downloaded from The Cancer Genome Atlas (TCGA) were analyzed to recognize differentially expressed genes (DEGs) derived from tumor and non-tumor adjacent samples as well as FOXA1low and FOXA1high tumor samples. The enrichment analysis was conducted for the dysregulated mRNAs. The network for the differentially expressed long non-coding RNA (lncRNA)-associated ceRNAs was then established. Survival analysis and univariate Cox regression analysis were executed to determine independent prognostic RNAs associated with PCa. The correlation between DUSP2 and immune cell infiltration level was analyzed. Tissue and blood samples were collected to verify our network. Molecular experiments were performed to explore whether DUSP2 is involved in the development of PCa.ResultsA ceRNA network related to FOXA1 was constructed and comprised 18 lncRNAs, 5 miRNAs, and 44 mRNAs. The MAGI2-AS3~has-mir-106a/has-mir-204~DUSP2 ceRNA regulatory network relevant to the prognosis of PCa was obtained by analysis. We markedly distinguished the MAGI2-AS3/DUSP2 axis in the ceRNA. It will most likely become a clinical prognostic model and impact the changes in the tumor immune microenvironment of PCa. The abnormal MAGI2-AS3 expression level from the patients’ blood manifested that it would be a novel potential diagnostic biomarker for PCa. Moreover, down-expressed DUSP2 suppressed the proliferation and migration of PCa cells.ConclusionsOur findings provide pivotal clues to understanding the role of the FOXA1-concerned ceRNA network in PCa. Simultaneously, this MAGI2-AS3/DUSP2 axis might be a new significant prognostic factor associated with the diagnosis and prognosis of PCa.
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Affiliation(s)
- Guo Yang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiong Chen
- Department of Urology, The Ninth People’s Hospital of Chongqing, Chongqing, China
| | - Zhen Quan
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Miao Liu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuan Guo
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yangbin Tang
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lang Peng
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Leilei Wang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yingying Wu
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xiaohou Wu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiayu Liu
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Yongbo Zheng, ; Jiayu Liu,
| | - Yongbo Zheng
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Yongbo Zheng, ; Jiayu Liu,
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Zhu X, Song J, Wang M, Wang X, Lv L. Dysregulated ceRNA network modulated by copy number variation-driven lncRNAs in breast cancer: A comprehensive analysis. J Gene Med 2023; 25:e3471. [PMID: 36525372 DOI: 10.1002/jgm.3471] [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: 08/10/2022] [Revised: 11/09/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
Breast cancer is a malignancy harmful to physical and mental health in women, with quite high mortality. Copy number variations (CNVs) are vital factors affecting the progression of breast cancer. Detecting CNVs in breast cancer to predict the prognosis of patients has become a promising approach to accurate treatment in recent years. The differential analysis was performed on CNVs of long noncoding RNAs (lncRNAs) as well as the expression of lncRNAs, microRNAs (miRNAs) and mRNAs in normal tissue and breast tumor tissue based on The Cancer Genome Atlas (TCGA) database. The CNV-driven lncRNAs were identified by the Kruskal-Wallis test. Meanwhile, a competitive endogenous RNA (ceRNA) network regulated by CNV-driven lncRNA was constructed. As the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed, the mRNAs in the dysregulated ceRNA network were mainly enriched in the biological functions and signaling pathways, including the Focal Adhesion-PI3K-Akt-mTOR-signaling pathway, the neuronal system, metapathway biotransformation Phase I and II and blood circulation, etc. The relationship between the CNVs of five lncRNAs and their gene expression in the ceRNA network was analyzed via a chi-square test, which confirmed that except for LINC00243, the expression of four lncRNAs was notably correlated with the CNVs. The survival analysis revealed that only the copy number gain of LINC00536 was evidently related to the poor prognosis of patients. The CIBERSORT algorithm showed that five lncRNAs were correlated with the abundance of immune cell infiltration and immune checkpoints. In a word, by analyzing CNV-driven lncRNAs and the ceRNA network regulated by these lncRNAs, this study explored the mechanism of breast cancer and provided novel insights into new biomarkers.
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Affiliation(s)
- Xiaotao Zhu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Jialu Song
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Mingzheng Wang
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xiaohui Wang
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Lin Lv
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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Zhu H, Tan J, Pan X, Ouyang H, Zhang Z, Li M, Zhao Y. HELLPAR/RRM2 axis related to HMMR as novel prognostic biomarker in gliomas. BMC Cancer 2023; 23:125. [PMID: 36750807 PMCID: PMC9903609 DOI: 10.1186/s12885-023-10596-w] [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: 09/03/2022] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Gliomas are the most frequent type of central nervous system tumor, accounting for more than 70% of all malignant CNS tumors. Recent research suggests that the hyaluronan-mediated motility receptor (HMMR) could be a novel potential tumor prognostic marker. Furthermore, mounting data has highlighted the important role of ceRNA regulatory networks in a variety of human malignancies. The complexity and behavioural characteristics of HMMR and the ceRNA network in gliomas, on the other hand, remained unknown. METHODS Transcriptomic expression data were collected from TCGA, GTEx, GEO, and CGGA database.The relationship between clinical variables and HMMR was analyzed with the univariate and multivariate Cox regression. Kaplan-Meier method was used to assess OS. TCGA data are analyzed and processed, and the correlation results obtained were used to perform GO, GSEA, and ssGSEA. Potentially interacting miRNAs and lncRNAs were predicted by miRWalk and StarBase. RESULTS HMMR was substantially expressed in gliomas tissues compared to normal tissues. Multivariate analysis revealed that high HMMR expression was an independent predictive predictor of OS in TCGA and CGGA. Functional enrichment analysis found that HMMR expression was associated with nuclear division and cell cycle. Base on ssGSEA analysis, The levels of HMMR expression in various types of immune cells differed significantly. Bioinformatics investigation revealed the HEELPAR-hsa-let-7i-5p-RRM2 ceRNA network, which was linked to gliomas prognosis. And through multiple analysis, the good predictive performance of HELLPAR/RRM2 axis for gliomas patients was confirmed. CONCLUSION This study provides multi-layered and multifaceted evidence for the importance of HMMR and establishes a HMMR-related ceRNA (HEELPAR-hsa-let-7i-5p-RRM2) overexpressed network related to the prognosis of gliomas.
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Affiliation(s)
- Huaxin Zhu
- grid.412604.50000 0004 1758 4073Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006 Jiangxi China
| | - Jiacong Tan
- grid.412604.50000 0004 1758 4073Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006 Jiangxi China
| | - Xinyi Pan
- grid.260463.50000 0001 2182 8825Huankui Academy, Nanchang University, Honggutan New District, Jiangxi 330006 Nanchang, China
| | - Hengyang Ouyang
- grid.260463.50000 0001 2182 8825Huankui Academy, Nanchang University, Honggutan New District, Jiangxi 330006 Nanchang, China
| | - Zhixiong Zhang
- grid.412604.50000 0004 1758 4073Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006 Jiangxi China
| | - Meihua Li
- Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi, China.
| | - Yeyu Zhao
- Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang, 330006, Jiangxi, China.
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Wang Y, Wang Z, Li K, Xiang W, Chen B, Jin L, Hao K. lncRNAs Functioned as ceRNA to Sponge miR-15a-5p Affects the Prognosis of Pancreatic Adenocarcinoma and Correlates With Tumor Immune Infiltration. Front Genet 2022; 13:874667. [PMID: 35899199 PMCID: PMC9312832 DOI: 10.3389/fgene.2022.874667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
Pancreatic adenocarcinoma (PAAD) is one of the most common malignant tumors with poor prognosis worldwide. Mounting evidence suggests that the expression of lncRNAs and the infiltration of immune cells have prognostic value for patients with PAAD. We used Gene Expression Omnibus (GEO) database and identified six genes (COL1A2, ITGA2, ITGB6, LAMA3, LAMB3, and LAMC2) that could affect the survival rate of pancreatic adenocarcinoma patients. Based on a series of in silico analyses for reverse prediction of target genes associated with the prognosis of PAAD, a ceRNA network of mRNA (COL1A2, ITGA2, LAMA3, LAMB3, and LAMC2)–microRNA (miR-15a-5p)–long non-coding RNA (LINC00511, LINC01578, PVT1, and TNFRSF14-AS1) was constructed. We used the algorithm “CIBERSORT” to assess the proportion of immune cells and found three overall survival (OS)–associated immune cells (monocytes, M1 macrophages, and resting mast cell). Moreover, the OS-associated gene level was significantly positively associated with immune checkpoint expression and biomarkers of immune cells. In summary, our results clarified that ncRNA-mediated upregulation of OS-associated genes and tumor-infiltration immune cells (monocytes, M1 macrophages M1, and resting mast cell resting) correlated with poor prognosis in PAAD.
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Affiliation(s)
- Yu Wang
- Laboratory Medicine Center, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, China
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhen Wang
- Laboratory Medicine Center, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - KaiQiang Li
- Laboratory Medicine Center, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - WeiLing Xiang
- Laboratory Medicine Center, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - BinYu Chen
- Laboratory Medicine Center, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - LiQin Jin
- Laboratory Medicine Center, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, China
- Department of Scientific Research, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
- *Correspondence: LiQin Jin, ; Ke Hao,
| | - Ke Hao
- Laboratory Medicine Center, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, China
- *Correspondence: LiQin Jin, ; Ke Hao,
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Dong X, Jin C, Chen D, Chen Y, Ye ZQ, Zhang X, Huang X, Zhang W, Gu DN. Genomic Instability-Related LncRNA Signature Predicts the Prognosis and Highlights LINC01614 Is a Tumor Microenvironment-Related Oncogenic lncRNA of Papillary Thyroid Carcinoma. Front Oncol 2021; 11:737867. [PMID: 34604079 PMCID: PMC8481916 DOI: 10.3389/fonc.2021.737867] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/30/2021] [Indexed: 12/20/2022] Open
Abstract
Background Genomic instability (GI) is among the top ten characteristics of malignancy. Long non-coding RNAs (lncRNAs) are promising cancer biomarkers that are reportedly involved in GI. So far, the clinical value of GI-related lncRNAs (GIlncs) in papillary thyroid cancer (PTC) has not been clarified. Methods Integrative analysis of lncRNA expression and somatic mutation profiles was performed to identify GIlncs. Analysis of differentially expressed lncRNAs in the group with high- and low- cumulative number of somatic mutations revealed significant GIlncs in PTC. Univariate and multivariate Cox proportional hazard regression analyses were performed to identify hub-GIlncs. Results A computational model based on four lncRNAs (FOXD2-AS1, LINC01614, AC073257.2, and AC005082.1) was identified as a quantitative index using an in-silicon discovery cohort. GILS score was significantly associated with poor prognosis, as validated in the TCGA dataset and further tested in our local RNA-Seq cohort. Moreover, a combination of clinical characteristics and the composite GILS-clinical prognostic nomogram demonstrates satisfactory discrimination and calibration. Furthermore, the GILS score and FOXD2-AS1, LINC01614, AC073257.2, and AC005082.1 were also associated with driver mutations and multiple clinical-pathological variables, respectively. Moreover, RNA-Seq confirmed the expression patterns of FOXD2-AS1, LINC01614, AC073257.2, and AC005082.1 in PTC and normal thyroid tissues. Biological experiments demonstrated that downregulated or overexpressed LINC01614 affect PTC cell proliferation, migration, and invasion in vitro. Activation of the stromal and immune cell infiltration was also observed in the high LINC01614 group in the PTC microenvironment. Conclusion In summary, we identified a signature for clinical outcome prediction in PTC comprising four lncRNAs associated with GI. A better understanding of the GI providing an alternative evaluation of the progression risk of PTC. Our study also demonstrated LINC01614 as a novel oncogenic lncRNA and verified its phenotype in PTC.
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Affiliation(s)
- Xubin Dong
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Cong Jin
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Danxiang Chen
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yizuo Chen
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhi-Qiang Ye
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaohua Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaoli Huang
- Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wei Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dian-Na Gu
- Department of Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Zhou Y, Wang S, Yan H, Pang B, Zhang X, Pang L, Wang Y, Xu J, Hu J, Lan Y, Ping Y. Identifying Key Somatic Copy Number Alterations Driving Dysregulation of Cancer Hallmarks in Lower-Grade Glioma. Front Genet 2021; 12:654736. [PMID: 34163522 PMCID: PMC8215700 DOI: 10.3389/fgene.2021.654736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/26/2021] [Indexed: 01/17/2023] Open
Abstract
Somatic copy-number alterations (SCNAs) are major contributors to cancer development that are pervasive and highly heterogeneous in human cancers. However, the driver roles of SCNAs in cancer are insufficiently characterized. We combined network propagation and linear regression models to design an integrative strategy to identify driver SCNAs and dissect the functional roles of SCNAs by integrating profiles of copy number and gene expression in lower-grade glioma (LGG). We applied our strategy to 511 LGG patients and identified 98 driver genes that dysregulated 29 cancer hallmark signatures, forming 143 active gene-hallmark pairs. We found that these active gene-hallmark pairs could stratify LGG patients into four subtypes with significantly different survival times. The two new subtypes with similar poorest prognoses were driven by two different gene sets (one including EGFR, CDKN2A, CDKN2B, INFA8, and INFA5, and the other including CDK4, AVIL, and DTX3), respectively. The SCNAs of the two gene sets could disorder the same cancer hallmark signature in a mutually exclusive manner (including E2F_TARGETS and G2M_CHECKPOINT). Compared with previous methods, our strategy could not only capture the known cancer genes and directly dissect the functional roles of their SCNAs in LGG, but also discover the functions of new driver genes in LGG, such as IFNA5, IFNA8, and DTX3. Additionally, our method can be applied to a variety of cancer types to explore the pathogenesis of driver SCNAs and improve the treatment and diagnosis of cancer.
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Affiliation(s)
- Yao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuai Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haoteng Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Bo Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yihan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jinyuan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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10
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Zhang DD, Shi Y, Liu JB, Yang XL, Xin R, Wang HM, Wang PY, Jia CY, Zhang WJ, Ma YS, Fu D. Construction of a Myc-associated ceRNA network reveals a prognostic signature in hepatocellular carcinoma. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:1033-1050. [PMID: 34141458 PMCID: PMC8167205 DOI: 10.1016/j.omtn.2021.04.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/28/2021] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) remains an extremely lethal disease worldwide. High-throughput methods have revealed global transcriptome dysregulation; however, a comprehensive investigation of the complexity and behavioral characteristics of the competing endogenous RNA (ceRNA) network in HCC is lacking. In this study, we extracted the transcriptome (RNA) sequencing data of 371 HCC patients from The Cancer Genome Atlas platform. With the comparison of the high Myc expression (Mychigh) tumor and low Myc expression (Myclow) tumor groups in HCC, we identified 1,125 differentially expressed (DE) mRNAs, 589 long non-coding RNAs (lncRNAs), and 93 microRNAs (miRNAs). DE RNAs predicted the interactions necessary to construct an associated Myc ceRNA network, including 19 DE lncRNAs, 5 miRNAs, and 72 mRNAs. We identified a significant signature (long intergenic non-protein-coding [LINC] RNA 2691 [LINC02691] and LINC02499) that effectively predicted overall survival and had protective effects. The target genes of microRNA (miR)-212-3p predicted to intersect with DE mRNAs included SEC14-like protein 2 (SEC14L2) and solute carrier family 6 member 1 (SLC6A1), which were strongly correlated with survival and prognosis. With the use of the lncRNA-miRNA-mRNA axis, we constructed a ceRNA network containing four lncRNAs (LINC02691, LINC02499, LINC01354, and NAV2 antisense RNA 4), one miRNA (miR-212-3p), and two mRNAs (SEC14L2 and SLC6A1). Overall, we successfully constructed a mutually regulated ceRNA network and identified potential precision-targeted therapies and prognostic biomarkers.
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Affiliation(s)
- Dan-Dan Zhang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China.,Department of Pathology, Shihezi University School of Medicine, Shihezi, Xinjiang 832002, China
| | - Yi Shi
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China
| | - Ji-Bin Liu
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China
| | - Xiao-Li Yang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Rui Xin
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Hui-Min Wang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China
| | - Pei-Yao Wang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Cheng-You Jia
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Wen-Jie Zhang
- Department of Pathology, Shihezi University School of Medicine, Shihezi, Xinjiang 832002, China.,The Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang 832002, China
| | - Yu-Shui Ma
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, National Center for Liver Cancer, the Second Military Medical University, Shanghai 200433, China
| | - Da Fu
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
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11
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Shi Y, Zhang DD, Liu JB, Yang XL, Xin R, Jia CY, Wang HM, Lu GX, Wang PY, Liu Y, Li ZJ, Deng J, Lin QL, Ma L, Feng SS, Chen XQ, Zheng XM, Zhou YF, Hu YJ, Yin HQ, Tian LL, Gu LP, Lv ZW, Yu F, Li W, Ma YS, Da F. Comprehensive analysis to identify DLEU2L/TAOK1 axis as a prognostic biomarker in hepatocellular carcinoma. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:702-718. [PMID: 33575116 PMCID: PMC7851426 DOI: 10.1016/j.omtn.2020.12.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/19/2020] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the deadliest malignant tumors that are harmful to human health. Increasing evidence has underscored the critical role of the competitive endogenous RNA (ceRNA) regulatory networks among various human cancers. However, the complexity and behavior characteristics of the ceRNA network in HCC were still unclear. In this study, we aimed to clarify a phosphatase and tensin homolog (PTEN)-related ceRNA regulatory network and identify potential prognostic markers associated with HCC. The expression profiles of three RNAs (long non-coding RNAs [lncRNAs], microRNAs [miRNAs], and mRNAs) were extracted from The Cancer Genome Atlas (TCGA) database. The DLEU2L-hsa-miR-100-5p/ hsa-miR-99a-5p-TAOK1 ceRNA network related to the prognosis of HCC was obtained by performing bioinformatics analysis. Importantly, we identified the DLEU2L/TAOK1 axis in the ceRNA by using correlation analysis, and it appeared to become a clinical prognostic model by Cox regression analysis. Furthermore, methylation analyses suggested that the abnormal upregulation of the DLEU2L/TAOK1 axis likely resulted from hypomethylation, and immune infiltration analysis showed that the DLEU2L/TAOK1 axis may have an impact on the changes in the tumor immune microenvironment and the development of HCC. In summary, the current study constructing a ceRNA-based DLEU2L/TAOK1 axis might be a novel important prognostic factor associated with the diagnosis and prognosis of HCC.
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Affiliation(s)
- Yi Shi
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.,Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China.,College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Dan-Dan Zhang
- Department of Pathology, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China.,Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Ji-Bin Liu
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China
| | - Xiao-Li Yang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Rui Xin
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Cheng-You Jia
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Hui-Min Wang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Gai-Xia Lu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Pei-Yao Wang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yu Liu
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.,College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Zi-Jin Li
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Jing Deng
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Qin-Lu Lin
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Liang Ma
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Shan-Shan Feng
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Xiao-Qi Chen
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Xiang-Min Zheng
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Ya-Fu Zhou
- Department of Cardiology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha 410005, Hunan, China
| | - Yong-Jun Hu
- Department of Cardiology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha 410005, Hunan, China
| | - Hua-Qun Yin
- School of Resource Processing and Bioengineering, Central South University, Changsha 410083, Hunan, China
| | - Lin-Lin Tian
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Li-Peng Gu
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Zhong-Wei Lv
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Fei Yu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Wen Li
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.,College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Yu-Shui Ma
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,Department of Pancreatic and Hepatobiliary Surgery, Cancer Hospital, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai 200032, China
| | - Fu Da
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China.,Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
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12
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Liu HW, Hu ZL, Li H, Tan QF, Tong J, Zhang YQ. Knockdown of lncRNA ANRIL suppresses the production of inflammatory cytokines and mucin 5AC in nasal epithelial cells via the miR-15a-5p/JAK2 axis. Mol Med Rep 2020; 23:145. [PMID: 33325534 PMCID: PMC7751488 DOI: 10.3892/mmr.2020.11784] [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: 06/10/2020] [Accepted: 10/08/2020] [Indexed: 12/13/2022] Open
Abstract
The incidence of allergic rhinitis (AR) is increasing worldwide. Human nasal epithelial cells (HNECs) are the key cells in the occurrence of AR. Antisense non-coding RNA in the INK4 locus (ANRIL) was discovered to be involved in the progression of AR. However, the mechanism by which ANRIL mediates the progression of AR remains to be determined. The present study aimed to further explore the mechanism by which ANRIL regulates AR. Thereby, HNECs were treated with IL-13 to mimic AR in vitro. The mRNA expression levels of ANRIL, microRNA (miR)-15a-5p, JAK2, mucin 5AC (MUC5AC), granulocyte-macrophage colony-stimulating factor (GM-CSF) and eotaxin-1, and protein expression levels of JAK2, STAT3 and phosphorylated-STAT3 in HNECs were analyzed using reverse transcription-quantitative PCR and western blotting, respectively. ELISAs were used to detect the secretory levels of inflammatory cytokines and mucin in cell supernatants. In addition, a dual luciferase reporter assay was used to confirm the downstream target of ANRIL and the target gene of miR-15a-5p. The results revealed that the secretory levels of eotaxin-1, GM-CSF and MUC5AC were significantly upregulated by IL-13 in the supernatant of HNECs. The expression levels of ANRIL and JAK2 were also upregulated in IL-13-induced HNECs, while the expression levels of miR-15a-5p were downregulated. In addition, ANRIL was identified to bind to miR-15a-5p. The IL-13-induced upregulation of eotaxin-1, GM-CSF and MUC5AC mRNA expression and secretory levels was significantly inhibited by the genetic knockdown of ANRIL, while the miR-15a-5p inhibitor effectively reversed this effect. JAK2 was also discovered to be directly targeted by miR-15a-5p. The overexpression of JAK2 significantly suppressed the therapeutic effect of miR-15a-5p mimics on IL-13-induced inflammation in vitro. In conclusion, the findings of the present study suggested that the genetic knockdown of ANRIL may suppress the production of inflammatory cytokines and mucin in IL-13-treated HNECs via regulation of the miR-15a-5p/JAK2 axis. Thus, ANRIL may serve as a novel target for AR treatment.
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Affiliation(s)
- Huo-Wang Liu
- Department of Otolaryngology-Head and Neck Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Zhong-Liang Hu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410007, P.R. China
| | - Hao Li
- Department of Otolaryngology-Head and Neck Surgery, The Fifth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830000, P.R. China
| | - Qi-Feng Tan
- Department of Otolaryngology-Head and Neck Surgery, The Fifth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830000, P.R. China
| | - Jing Tong
- Department of Otolaryngology-Head and Neck Surgery, The Fifth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830000, P.R. China
| | - Yong-Quan Zhang
- Department of Otolaryngology-Head and Neck Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
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