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Xu L, Xiao T, Xu L, Yao W. Identification of therapeutic targets and prognostic biomarkers in cholangiocarcinoma via WGCNA. Front Oncol 2022; 12:977992. [PMID: 36591499 PMCID: PMC9795187 DOI: 10.3389/fonc.2022.977992] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022] Open
Abstract
Background Cholangiocarcinoma (CCA) is a highly aggressive malignant tumor for which limited treatment methods and prognostic signatures are available. This study aims to identify potential therapeutic targets and prognostic biomarkers for CCA. Methods Based on differentially expressed genes (DEGs) identified from The Cancer Genome Atlas (TCGA) data, our study identified key gene modules correlated with CCA patient survival by weighted gene coexpression network analysis (WGCNA). Cox regression analysis identified survival-related genes in the key gene modules. The biological properties of the survival-related genes were evaluated by CCK-8 and transwell assays. Then, these genes were used to construct a prognostic signature that was internally and externally validated. Additionally, by combining clinical characteristics with the gene-based prognostic signature, a nomogram for survival prediction was built. Results WGCNA divided the 1531 DEGs into four gene modules, and the yellow gene module was significantly associated with overall survival (OS) and histologic neoplasm grade. Our study identified the lncRNA AGAP2-AS1 and a novel gene, GOLGA7B, that are closely related to survival. GOLGA7B downregulation promoted the invasion, migration and proliferation of CCA cells, but AGAP2-AS1 had the opposite effect. AGAP2-AS1 and GOLGA7B were integrated into a gene-based prognostic signature, and both internal and external validation studies confirmed that this two-gene prognostic signature and nomogram could accurately predict CCA patient prognosis. Conclusion AGAP2-AS1 and GOLGA7B are potential therapeutic targets and prognostic biomarkers for CCA.
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Affiliation(s)
- Lei Xu
- Department of Pediatrics Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ting Xiao
- Department of Ultrasonography Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ling Xu
- Department of Nursing Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Yao
- Department of Oncology Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China,*Correspondence: Wei Yao,
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Liu Y, Khan S, Li L, ten Hagen TL, Falahati M. Molecular mechanisms of thyroid cancer: A competing endogenous RNA (ceRNA) point of view. Biomed Pharmacother 2022; 146:112251. [DOI: 10.1016/j.biopha.2021.112251] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/23/2021] [Accepted: 09/26/2021] [Indexed: 12/25/2022] Open
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Dai C, Liu B, Li S, Hong Y, Si J, Xiong Y, Wu N, Ma Y. Construction of a circRNA-miRNA-mRNA Regulated Pathway Involved in EGFR-TKI Lung Adenocarcinoma Resistance. Technol Cancer Res Treat 2021; 20:15330338211056809. [PMID: 34825849 PMCID: PMC8647233 DOI: 10.1177/15330338211056809] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Objectives: Epidermal growth factor receptor-tyrosine kinase
inhibitors are widely used for lung epidermal growth factor receptor-positive
lung adenocarcinomas, but acquired resistance is inevitable. Although non-coding
RNAs, such as circular RNA and microRNA, are known to play vital roles in
epidermal growth factor receptor-tyrosine kinase inhibitor resistance,
comprehensive analysis is lacking. Thus, this study aimed to explore the
circular RNA-microRNA-messenger RNA regulatory network involved in epidermal
growth factor receptor-tyrosine kinase inhibitor resistance.
Methods: To identify differentially expressed genes between the
epidermal growth factor receptor-tyrosine kinase inhibitor sensitive cell line
PC9 and resistant cell line PC9/ epidermal growth factor receptor-tyrosine
kinase inhibitor resistance(PC9/ER), circular RNA, microRNA and messenger RNA
microarrays were performed. Candidates were then identified to construct a
circular RNA-microRNA-messenger RNA network using bioinformatics. Additionally,
Gene Oncology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were
conducted to evaluate the network messenger RNA, setting up a protein-protein
interaction network for hub-gene identification. Afterwards, RNA
immunoprecipitation was performed to enrich microRNA, and quantitative real-time
PCR was used to estimated gene expression levels. Results: In
total, 603, 377, and 1863 differentially expressed circular RNA, microRNA,
messenger RNAs, respectively, were identified using microarray analysis,
constructing a circular RNA-microRNA-messenger RNA network containing 18
circular RNAs, 17 microRNAs and 175 messenger RNAs. Moreover, Gene Oncology and
Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that the most
enriched biological process terms and pathways were related to epidermal growth
factor receptor-tyrosine kinase inhibitor resistance, including Wnt and Hippo
signaling pathways. Based on the competing endogenous RNA and protein-protein
interaction network, circ-0007312 was showed to interact with miR-764 and both
circ-0003748 and circ-0001398 were shown to interact with miR-628; both these
microRNAs targeted MAPK1. Furthermore, circ-0007312, circ-0003748, circ-0001398,
and MAPK1 were up-regulated, whereas miR-764 and miR-628 were downregulated in
PC9/ER cells as compared to parental PC9 cells. We also found that circ-0007312
and miR-764 were positively expressed in plasma. Conclusions: Our
original study associated with mechanism of target therapy in lung cancer
provided a systematic and comprehensive regulation of circular RNA, microRNA and
messenger RNA in epidermal growth factor receptor-tyrosine kinase inhibitor
resistance. It was found that circ-0007312- miR-764-MAPK1,
circ-0003748-miR-628-MAPK1, and circ-0001398-miR-628-MAPK1 axis may play key
roles in epidermal growth factor receptor-tyrosine kinase inhibitor
resistance.
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Affiliation(s)
- Chenyue Dai
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Bing Liu
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Shaolei Li
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Yang Hong
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Jiahui Si
- Department of Anesthesiology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Ying Xiong
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Nan Wu
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Yuanyuan Ma
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), 12519Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
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Wang T, Mao P, Feng Y, Cui B, Zhang B, Chen C, Xu M, Gao K. Blocking hsa_circ_0006168 suppresses cell proliferation and motility of human glioblastoma cells by regulating hsa_circ_0006168/miR-628-5p/IGF1R ceRNA axis. Cell Cycle 2021; 20:1181-1194. [PMID: 34024251 PMCID: PMC8265815 DOI: 10.1080/15384101.2021.1930357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/30/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND hsa_circ_0006168 is an oncogenic circular RNA in esophageal cancer. However, its role remains unclarified in tumor progression of gliomas, especially in glioblastoma (GBM). METHODS Cell counting kit-8 assay, transwell assays, western blotting, and xenograft experiment, as well as colony formation assay and flow cytometry were performed to measure cell proliferation and motility. Expression of hsa_circ_0006168, microRNA (miR)-628-3p, insulin‑like growth factor 1 receptor (IGF1R), and Ras/extracellular signal regulated kinases (Erk)-related proteins were determined by quantitative real-time polymerase chain reaction and western blotting. The physical interaction was confirmed by dual-luciferase reporter assay and RNA pull-down assay. RESULTS hsa_circ_0006168 and IGF1R were upregulated, and miR-628-5p was downregulated in human GBM tissues and cells. Functionally, blocking hsa_circ_0006168 and overexpressing miR-628-5p suppressed cell proliferation, migration, invasion, and expression of Vimentin and Snail (mesenchymal markers) in A172 and LN229 cells, accompanied with increased E-cadherin (epithelial marker), decreased colony formation, and promoted apoptosis rate. Silencing miR-628-5p counteracted the suppression of hsa_circ_0006168 deficiency on these behaviors, and restoring IGF1R blocked miR-628-5p-mediated inhibition as well. More importantly, hsa_circ_0006168 knockdown could delay xenograft tumor growth in vivo and lower Ras and phosphorylated Erk1/2 expression in vitro and in vivo. Mechanically, hsa_circ_0006168 targeted and sponged miR-628-5p, and IFG1R was a novel target for miR-628-5p. Inhibiting miR-628-5p could abrogate in vitro role of hsa_circ_0006168 knockdown, and similarly IGF1R upregulation counteracted miR-628-5p role. CONCLUSION Silencing hsa_circ_0006168 might suppress GBM proliferation and motility via serving as competitive endogenous RNA for miR-628-5p and regulating IGF1R/Ras/Erk pathway.
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Affiliation(s)
- Tuo Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi, China
| | - Ping Mao
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi, China
| | - Yong Feng
- Department of Neurosurgery, The Hancheng People's Hospital, Weinan, Shannxi, China
| | - Bo Cui
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi, China
| | - Bin Zhang
- Department of Neurosurgery, Bao Ji Affiliated Hospital of Xi'an Medical University, Baoji, Shannxi, China
| | - Chen Chen
- Department of Neurosurgery, Mianxian Hospital, Mianxian, Shannxi, China
| | - Mingjie Xu
- Department of Neurosurgery, Traditional Chinese Medicine Hospital of Xixiang, Hanzhong, Shannxi, China
| | - Ke Gao
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi, China
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Bao Z, Zheng Q, Li L. Oncogenic roles and mechanisms of lncRNA AGAP2-AS1 in human solid tumors. Am J Transl Res 2021; 13:757-769. [PMID: 33594324 PMCID: PMC7868831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/26/2020] [Indexed: 06/12/2023]
Abstract
Cancer remains the second leading life-threatening disease worldwide. Increasing evidence indicates that long non-coding RNAs (lncRNAs) play an important role in multiple physiological and pathological processes, including gene amplification, mutation, rearrangement, and overexpression regulations. In this review, we comprehensively summarize the current knowledge of lncRNA AGAP2-AS1 from a cancer perspective. As a member of the lncRNA family, lncRNA AGAP2-AS1 is upregulated in solid tumor malignancies, functions as an oncogene, and plays a key role in tumorigenesis and tumor progression. AGAP2-AS1 expression is significantly increased in clinical cancer tissue samples, cell lines, and in vivo, and is closely related to an unfavorable prognosis in several cancers. Upregulated lncRNA AGAP2-AS1 binds with microRNAs (miRNAs) and promotes activation of downstream genes. This aberrant regulation induces carcinogenesis and tumorigenesis. Here we provide a comprehensive overview of AGAP2-AS1 in cancer progression that leads to an improved understanding of the effects of AGAP2-AS1 on early detection and therapeutic approaches. This information is essential for the future development of lncRNA AGAP2-AS1 as a potential therapy against these devastating cancers.
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Affiliation(s)
- Zhengyi Bao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University Hangzhou 310003, China
| | - Qiuxian Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University Hangzhou 310003, China
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