[1]王俐勇,赵焕英,付文卓,等.加权共表达网络分析在肝癌环状RNA研究中的应用[J].医学信息,2023,36(04):1-6.[doi:10.3969/j.issn.1006-1959.2023.04.001]
　WANG Li-yong,ZHAO Huan-ying,FU Wen-zhuo,et al.Application of Weighted Gene Co-expression Network Analysis in the Study of Circular RNA in Liver Cancer[J].Journal of Medical Information,2023,36(04):1-6.[doi:10.3969/j.issn.1006-1959.2023.04.001]
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加权共表达网络分析在肝癌环状RNA研究中的应用()
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医学信息[ISSN:1006-1959/CN:61-1278/R]

卷:
36卷
期数:
2023年04期
页码:
1-6
栏目:
生物信息学
出版日期:
2023-02-15

文章信息/Info

Title:
Application of Weighted Gene Co-expression Network Analysis in the Study of Circular RNA in Liver Cancer
文章编号:
1006-1959（2023）04-0001-06
作者:
王俐勇; 赵焕英; 付文卓; 等
（首都医科大学中心实验室1，基础医学院2，北京 100069）
Author(s):
WANG Li-yong; ZHAO Huan-ying; FU Wen-zhuo; et al.
(Core of Facility1,College of Basic Medicine2,Capital Medical University,Beijing 100069,China)
关键词:
环状RNA; WGCNA; 肝癌
Keywords:
circRNA; WGCNA; Liver cancer
分类号:
R735.7
DOI:
10.3969/j.issn.1006-1959.2023.04.001
文献标志码:
A
摘要:
目的 应用加权基因共表达网络分析（WGCNA）研究肝癌组织中环状RNA，以期寻找合适的生物标志物作为肝癌临床诊断指标。方法 从GEO数据库下载肝癌数据，通过WGCNA方法深入挖掘分析得到与肝癌发展密切相关的环状RNA，并结合环状RNA-miRNA-mRNA互作数据库筛选靶向miRNA和基因，利用Kaplan-Meier plotter数据库库筛选出来circRNA靶向的microRNA进行生存分析验证，通过DAVID软件对靶向基因进行功能富集分析。结果 共检测到3032个circRNA分子；应用WGCNA方法共得到7个模块，其中Turquoise模块与肝癌组织呈正相关（P＜0.05）；Turquoise模块中circRNA表达量在肝癌组织中均表达上调，且经过在线数据库比对筛选得到2个环状RNA分子（hsa_circ_0064324和hsa_circ_0040827），Pathway富集分析显示，这些靶向基因富集在鞘磷脂信号通路、癌症蛋白聚糖、血小板活化通路、胰腺癌通路、神经胶质细胞瘤、FoxO信号通路、癌症中胆碱代谢通路等多个和癌症相关的通路上。肝癌细胞系中hsa_circ_0064324和hsa_circ_0040827均表达上调，且Kaplan-Meier生存分析发现，hsa-miR-146b-3p、hsa-miR-331-3p、hsa-miR-874-3p和hsa-miR-942-3p高表达与肝癌总体生存期呈负相关（P＜0.05）。结论 WGCNA方法筛选得到的环状RNA可能作为肝癌临床诊断生物标志物，有助于揭示肝癌发病机制，为研发药物和治疗诊断提供新依据。
Abstract:
Objective To study the circular RNA in liver cancer tissues by weighted gene co-expression network analysis (WGCNA), in order to find suitable biomarkers as clinical diagnostic indicators of liver cancer.Methods The data of liver cancer were downloaded from GEO database, and the circular RNA closely related to the development of liver cancer was obtained by WGCNA method. Combined with the circular RNA-miRNA-mRNA interaction database, the targeted miRNA and gene were screened. The circRNA-targeted microRNA was screened by Kaplan-Meier plotter database for survival analysis and verification, and the functional enrichment analysis of targeted genes was performed by DAVID software.Results A total of 3032 circRNA molecules were detected; a total of 7 modules were obtained by WGCNA method, among which Turquoise module was positively correlated with liver cancer tissues (P<0.05). The expression of circRNA in the Turquoise module was up-regulated in liver cancer tissues, and two circular RNA molecules (hsa_circ_0064324, hsa_circ_0040827) were screened by online database comparison. Pathway enrichment analysis showed that these targeted genes were enriched in sphingomyelin signaling pathway, proteoglycans in cancer, platelet activation pathway, pancreatic cancer pathway, glioma pathway, FoxO signaling pathway, choline metabolism in cancer pathway and other cancer-related pathways. The expression of hsa_circ_0064324 and hsa_circ_0040827 was up-regulated in hepatocellular carcinoma cell lines, and Kaplan-Meier survival analysis showed that the high expression of hsa-miR-146b-3p, hsa-miR-331-3p, hsa-miR-874-3p and hsa-miR-942-3p was negatively correlated with the overall survival of liver cancer (P<0.05).Conclusion The circular RNA screened by WGCNA method may be used as a biomarker for clinical diagnosis of liver cancer, which is helpful to reveal the pathogenesis of liver cancer and provide a new basis for the development of drugs and treatment diagnosis.

参考文献/References:

[1]Yin L,Cai ZH,Zhu BA,et al.Identification of key pathways and genes in the dynamic progression of HCC based on WGCNA[J].Genes (Basel),2018,9(2):92.[2]Cho HJ,Cheong JY.Role of immune cells in patients with hepatitis B virus-related hepatocellular carcinoma[J].Int J Mol Sci,2021,22(15):8011.[3]Chaabane M,Andreeva K,Hwang JY,et al.seekCRIT: Detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data[J].PLoS Comput Biol,2020,16(10):e1008338.[4]Zhang Y,Qian LL,Liu YY,et al.CircRNA-ceRNA network revealing the potential regulatory roles of CircRNA in alzheimer’s disease involved the cGMP-PKG signal pathway[J].Front Mol Neurosci,2021,14:665788.[5]Tian ZL,He WX,Tang JN,et al.Identification of important modules and biomarkers in breast cancer based on WGCNA[J].Onco Targets Ther,2020,13:6805-6817.[6]Vo JN,Cieslik M,Zhang YJ,et al.The landscape of circular RNA in cancer[J].Cell 2019,176(4):869-881.e13.[7]Liu ZG,Yu YQ,Huang ZB,et al.CircRNA-5692 inhibits the progression of hepatocellular carcinoma by sponging miR-328-5p to enhance DAB2IP expression[J].Cell Death Dis,2019,10(12):900.[8]Huang ZY,Xia HM,Liu SQ,et al.The mechanism and clinical significance of circular RNAs in hepatocellular carcinoma[J].Front Oncol,2021,11:714665.[9]Huang XY,Huang ZL,Huang J,et al.Exosomal circRNA-100338 promotes hepatocellular carcinoma metastasis via enhancing invasiveness and angiogenesis[J].J Exp Clin Cancer Res,2020,39(1):20.[10]Huang XY,Huang ZL,Zhang PB,et al.CircRNA-100338 is associated with mTOR signaling pathway and poor prognosis in hepatocellular carcinoma[J].Front Oncol,2019,9:392.[11]Huang GQ,Liang M,Liu HY,et al.CircRNA hsa_circRNA_104348 promotes hepatocellular carcinoma progression through modulating miR-187-3p/RTKN2 axis and activating Wnt/β-catenin pathway[J].Cell Death Dis,2020,11(12):1065.[12]Deldar Abad Paskeh M,Mirzaei S,Ashrafizadeh M,et al.Wnt/β-catenin signaling as a driver of hepatocellular carcinoma progression: an emphasis on molecular pathways[J].J Hepatocell Carcinoma,2021,8:1415-1444.[13]Liang WW,Sun FF,Zhao YM,et al.Identification of susceptibility modules and genes for cardiovascular disease in diabetic patients using WGCNA analysis[J].J Diabetes Res,2020,2020:4178639.[14]Hou J,Ye XF,Feng WX,et al.Distance correlation application to gene co-expression network analysis[J].BMC Bioinformatics,2022,23(1):81.[15]Yang HY,Wang YK,Zhang ZY,et al.Identification of KIF18B as a hub candidate gene in the metastasis of clear cell renal cell carcinoma by weighted gene Co-expression network analysis[J].Front Genet,2020,11:905.[16]Bian YY,Huang JT,Zeng ZL,et al.Construction of survival-related co-expression modules and identification of potential prognostic biomarkers of osteosarcoma using WGCNA[J].Ann Transl Med,2022,10(6):296.[17]Jiramongkol Y,Lam EW.FOXO transcription factor family in cancer and metastasis[J].Cancer Metastasis Rev,2020,39(3):681-709.[18]Li C,Miao RC,Liu SS,et al.Down-regulation of miR-146b-5p by long noncoding RNA MALAT1 in hepatocellular carcinoma promotes cancer growth and metastasis[J].Oncotarget,2017,8(17):28683-28695.[19]Zhang QF,Zhu BL,Qian JP,et al.MiR-942 promotes proliferation and metastasis of hepatocellular carcinoma cells by inhibiting RRM2B[J].Onco Targets Ther,2019,12:8367-8378.

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更新日期/Last Update: 1900-01-01