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Five Hub Genes Can Be The Potential DNA Methylation Biomarkers For Cholangiocarcinoma Using Bioinformatics Analysis.
Onco Targets Ther 2019; 12:8355-8365OT

Abstract

Background

Cholangiocarcinoma (CCA) is a subtype of highly malignant hepatic tumor, which has low 5-year survival rate and poor clinical outcome. Only a few patients can be detected early and accepted with the surgery. Most of CCA patients are diagnosed in advanced stage, and the treatments are limited. As for the inoperable, advanced CCA patients, chemotherapy is the main treatment, due to lacking molecular targets, therapeutic effect is limited.

Materials and methods

To explore potential therapeutic targets for CCA, we analyzed three microarray datasets derived from the Gene Expression Omnibus (GEO) database. Then, we used GEO2R tools of NCBI to discover the differentially expressed genes (DEGs) from the CCA and normal liver tumor microarrays (TMA). Subsequently, we used the Database for Annotation, Visualization and Integrated Discovery (DAVID GO) to perform the Gene Ontology function (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Then, we carried out the Cytoscape software to search for the hub genes downregulated in CCA and identify the protein-protein interaction (PPI) of these genes. Besides, we used the GEPIA tool to evaluate the differential expressions of hub genes in CCA patients. Then, we also used MEXPRESS database to detect the promoter methylation levels of hub genes in CCA and normal tissue samples. In addition, we evaluated the expression of these genes in CCA lines and normal bile tract cells after 5-AZA (DNA methyltransferase inhibitor) treatment.

Results

A total of 115 downregulated DEGs were identified. Among them, 10 hub genes with a high degree of connectivity were picked out. Among these 10 hub genes, F2, AHSG, ALDH8A1, SERPIND1 and AGXT showed higher DNA methylation levels of promoter in CCA compared with normal liver tissues. Therefore, these 5 genes may be the potential DNA methylation biomarkers and therapeutic targets in CCA.

Authors+Show Affiliations

Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, People's Republic of China. Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou 310003, Zhejiang, People's Republic of China. Key Laboratory of Organ Transplantation, Hangzhou 310003, Zhejiang, People's Republic of China. Institute of Immunology, School of Medicine, Zhejiang University, Hangzhou 310058, Zhejiang, People's Republic of China.Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, People's Republic of China. Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou 310003, Zhejiang, People's Republic of China. Key Laboratory of Organ Transplantation, Hangzhou 310003, Zhejiang, People's Republic of China.Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, People's Republic of China. Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou 310003, Zhejiang, People's Republic of China. Key Laboratory of Organ Transplantation, Hangzhou 310003, Zhejiang, People's Republic of China.Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, People's Republic of China. Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou 310003, Zhejiang, People's Republic of China. Key Laboratory of Organ Transplantation, Hangzhou 310003, Zhejiang, People's Republic of China.Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, People's Republic of China. Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou 310003, Zhejiang, People's Republic of China. Key Laboratory of Organ Transplantation, Hangzhou 310003, Zhejiang, People's Republic of China.Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, People's Republic of China. Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou 310003, Zhejiang, People's Republic of China. Key Laboratory of Organ Transplantation, Hangzhou 310003, Zhejiang, People's Republic of China.Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, People's Republic of China. Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou 310003, Zhejiang, People's Republic of China. Key Laboratory of Organ Transplantation, Hangzhou 310003, Zhejiang, People's Republic of China.Institute of Immunology, School of Medicine, Zhejiang University, Hangzhou 310058, Zhejiang, People's Republic of China.Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, People's Republic of China. Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Hangzhou 310003, Zhejiang, People's Republic of China.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31632083

Citation

Chen, Diyu, et al. "Five Hub Genes Can Be the Potential DNA Methylation Biomarkers for Cholangiocarcinoma Using Bioinformatics Analysis." OncoTargets and Therapy, vol. 12, 2019, pp. 8355-8365.
Chen D, Wu H, He B, et al. Five Hub Genes Can Be The Potential DNA Methylation Biomarkers For Cholangiocarcinoma Using Bioinformatics Analysis. Onco Targets Ther. 2019;12:8355-8365.
Chen, D., Wu, H., He, B., Lu, Y., Wu, W., Liu, H., ... Wu, J. (2019). Five Hub Genes Can Be The Potential DNA Methylation Biomarkers For Cholangiocarcinoma Using Bioinformatics Analysis. OncoTargets and Therapy, 12, pp. 8355-8365. doi:10.2147/OTT.S203342.
Chen D, et al. Five Hub Genes Can Be the Potential DNA Methylation Biomarkers for Cholangiocarcinoma Using Bioinformatics Analysis. Onco Targets Ther. 2019;12:8355-8365. PubMed PMID: 31632083.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Five Hub Genes Can Be The Potential DNA Methylation Biomarkers For Cholangiocarcinoma Using Bioinformatics Analysis. AU - Chen,Diyu, AU - Wu,Hao, AU - He,Bin, AU - Lu,Yuejie, AU - Wu,Wenxuan, AU - Liu,Hua, AU - Feng,Xiaode, AU - Chen,Jianzhong, AU - Wu,Jian, Y1 - 2019/10/11/ PY - 2019/01/29/received PY - 2019/09/20/accepted PY - 2019/10/22/entrez PY - 2019/10/22/pubmed PY - 2019/10/22/medline KW - cholangiocarcinoma KW - expression profiling data KW - hub genes KW - methylation SP - 8355 EP - 8365 JF - OncoTargets and therapy JO - Onco Targets Ther VL - 12 N2 - Background: Cholangiocarcinoma (CCA) is a subtype of highly malignant hepatic tumor, which has low 5-year survival rate and poor clinical outcome. Only a few patients can be detected early and accepted with the surgery. Most of CCA patients are diagnosed in advanced stage, and the treatments are limited. As for the inoperable, advanced CCA patients, chemotherapy is the main treatment, due to lacking molecular targets, therapeutic effect is limited. Materials and methods: To explore potential therapeutic targets for CCA, we analyzed three microarray datasets derived from the Gene Expression Omnibus (GEO) database. Then, we used GEO2R tools of NCBI to discover the differentially expressed genes (DEGs) from the CCA and normal liver tumor microarrays (TMA). Subsequently, we used the Database for Annotation, Visualization and Integrated Discovery (DAVID GO) to perform the Gene Ontology function (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Then, we carried out the Cytoscape software to search for the hub genes downregulated in CCA and identify the protein-protein interaction (PPI) of these genes. Besides, we used the GEPIA tool to evaluate the differential expressions of hub genes in CCA patients. Then, we also used MEXPRESS database to detect the promoter methylation levels of hub genes in CCA and normal tissue samples. In addition, we evaluated the expression of these genes in CCA lines and normal bile tract cells after 5-AZA (DNA methyltransferase inhibitor) treatment. Results: A total of 115 downregulated DEGs were identified. Among them, 10 hub genes with a high degree of connectivity were picked out. Among these 10 hub genes, F2, AHSG, ALDH8A1, SERPIND1 and AGXT showed higher DNA methylation levels of promoter in CCA compared with normal liver tissues. Therefore, these 5 genes may be the potential DNA methylation biomarkers and therapeutic targets in CCA. SN - 1178-6930 UR - https://www.unboundmedicine.com/medline/citation/31632083/Five_Hub_Genes_Can_Be_The_Potential_DNA_Methylation_Biomarkers_For_Cholangiocarcinoma_Using_Bioinformatics_Analysis L2 - https://dx.doi.org/10.2147/OTT.S203342 DB - PRIME DP - Unbound Medicine ER -