[1]张和平,王敬敏,任萍.基于加权基因共表达网络分析方法筛选并鉴定结直肠癌的驱动基因[J].新乡医学院学报,2023,40(5):462-467.[doi:10.7683/xxyxyxb.2023.05.012]
　ZHANG Heping,WANG Jingmin,REN Ping.Screening and identification of driving genes for colorectal cancer based on weighted gene coexpression network analysis method[J].Journal of Xinxiang Medical University,2023,40(5):462-467.[doi:10.7683/xxyxyxb.2023.05.012]
点击复制

基于加权基因共表达网络分析方法筛选并鉴定结直肠癌的驱动基因
分享到：

《新乡医学院学报》[ISSN:1004-7239/CN:41-1186/R]

卷:
40卷
期数:
2023年5
页码:
462-467
栏目:
临床研究
出版日期:
2023-05-05

文章信息/Info

Title:
Screening and identification of driving genes for colorectal cancer based on weighted gene coexpression network analysis method
作者:
张和平1; 王敬敏2; 任萍3
（1.焦作市人民医院肛肠科，河南　焦作　454000；2.焦作市人民医院不孕不育门诊，河南　焦作　454000；3.焦作市人民医院耳鼻喉科，河南　焦作　454000）
Author(s):
ZHANG Heping1; WANG Jingmin2; REN Ping3
(1.Department of Anorectal,People′s Hospital of Jiaozuo,Jiaozuo 454000,Henan Province,China;2.Infertility Clinic,People′s Hospital of Jiaozuo,Jiaozuo 454000,Henan Province,China;3.Department of Otorhinolaryngologics,People′s Hospital of Jiaozuo,Jiaozuo 454000,Henan Province,China)
关键词:
加权基因共表达网络分析; 结直肠癌; 驱动基因; CYTH1基因
Keywords:
weighted gene co-expression network analysis; colorectal cancer; driving gene; CYTH1 gene
分类号:
R735
DOI:
10.7683/xxyxyxb.2023.05.012
文献标志码:
A
摘要:
目的　基于加权基因共表达网络分析(WGCNA)方法筛选并鉴定结直肠癌（CRC）的驱动基因，探讨核心驱动基因在CRC发生发展、诊断和治疗中的作用。
方法　通过NCBI基因表达综合数据库(GEO)收集CRC相关的数据，数据集为GSE21510，芯片平台为GPL570；使用GEO2R工具对差异基因进行分析，根据P值和基因表达fold-change对差异基因进行排序，选择前2 000个样本进行进一步分析。使用WGCNA算法进行模块构建，分析模块与临床特征的相关性，鉴定出与临床表型高度相关的模块，提取与临床性状相关性最高的模块内基因，将基因导入Cytoscape，分析核心基因，选择核心基因CYTH1进一步研究。基于Oncomine数据库分析CYTH1在结直肠癌组织与对照结直肠组织中的差异表达。取对数生长期LOVO、SW620、HCT116、SW480、RKO、CaCo2和NCM460细胞，应用实时荧光定量-聚合酶链式反应(RT-qPCR)法检测CYTH1在各种细胞中的表达；取对数生长期HCT116和SW480细胞，转染CYTH1基因干扰片段，采用细胞计数试剂盒-8法检测细胞增殖情况，Transwell实验检测细胞迁移能力。
结果　WGCNA结果显示，turquoise模块与CRC临床转移特征有相关性。分析turquoise模块的权重基因，使用Cytoscape软件将turquoise" 模块的权重基因构建共表达网络图，筛选出核心基因CYTH1。基于Oncomine数据库检索结果，与正常结直肠组织相比，CRC组织中CYTH1 mRNA表达水平下调约75%。RT-qPCR 检测结果显示，LOVO、SW620、HCT116、SW480、RKO和CaCo2细胞中CYTH1相对表达量显著低于NCM460（t=31.080、21.262、51.963、3.093、114.344、216.340，P<0.001）。干预1、2、3、4 d，si-NC-HCT116细胞与si-CYTH1-HCT116细胞增殖率比较差异无统计学意义（t=0.321、-0.474、-0.711、1.011，P>0.05），si-NC-SW480细胞与si-CYTH1-SW480细胞增殖率比较差异无统计学意义（t= 0.148、-0.254、0.040、0.157，P>0.05）。培养24 h后，si-CYTH1-HCT116细胞迁移数显著高于si-NC-HCT116细胞（t= -17.318，P<0.001）；si-CYTH1-SW480细胞迁移数显著高于si-NC-SW480细胞（t=-7.876，P<0.001）。
结论　CYTH1在CRC组织和细胞中表达下调，可抑制CRC细胞的迁移能力，在CRC中发挥抑癌作用，其有可能成为CRC有效的治疗靶点。
Abstract:
Objective　To screen and identify the driving genes in colorectal cancer (CRC) based on weighted gene co-expression network analysis(WGCNA) method,and explore the effect of core driving genes in the occurrence,development,diagnosis and treatment of CRC.
Methods　The data of CRC were collected through the NCBI gene expression omnibu (GEO) database,the data set was GSE21510,and the chip platform was GPL570.The differential genes was analyzed by GEO2R tool.The differential genes were sequenced according to P value and gene expression fold-change,and the first 2 000 samples were selected for further analysis.The modules was constructed by the WGCNA algorithm,the correlation between the modules and clinical characteristics was analyzed,and the modules highly correlated with clinical phenotypes was identified,the genes within the module that were most correlated with clinical traits was extracted,the genes was imported into Cytoscape,the core genes was analyzed,and the core gene CYTH1 was selected for further research.The differential expression of CYTH1 in CRC and control colorectal tissues was analyzed based on Oncomine database.The LOVO,SW620,HCT116,SW480,RKO,CaCo2 and NCM460 cells at logarithmic growth phase were collected,and the expression of CYTH1 in these cells was detected by real-time fluorescence quantification-polymerase chain reaction (RT-qPCR).The HCT116 and SW480 cells at logarithmic growth phase were transfected with the CYTH1 gene interference fragment,and the cell proliferation was detected by cell counting kit-8 assay,the migration of the cells were detected by Transwell assay.
Results　The results of WGCNA showed that the turquoise module was correlated with the characteristics of CRC clinical metastasis.The weight genes of the turquoise module were analyzed,the co-expression network diagram of the weight genes in the turquoise module was constructed by Cytoscape software,and the core gene CYTH1 was screened out.Based on the retrieval results from the Oncomine database,the expression level of CYTH1 mRNA in CRC tissues was down-regulated by about 75% compared with that in normal colorectal tissues.The results of RT-qPCR showed that the relative expression level of CYTH1 in LOVO,SW620,HCT116,SW480,RKO and CaCo2 cells was significantly lower than that in NCM460 (t=31.080,21.262,51.963,3.093,114.344,216.340;P<0.001).At 1,2,3 and 4 days of intervention,there was no significant difference in the proliferation rate between si-NC-HCT116 cells and si-CYTH1-HCT116 cells (t=0.321,-0.474,-0.711,1.011;P>0.05);and there was no significant difference in the proliferation rate between si-NC-SW480 cells and si-CYTH1-SW480 cells (t=0.148,-0.254,0.040,0.157;P>0.05).At 24 hours of culture,the migration number of si-CYTH1-HCT116 cells was significantly higher than that of si-NC-HCT116 cells (t=-17.318,P<0.001);and the migration number of si-CYTH1-SW480 cells was significantly higher than that of si-NC-SW480 cells (t=-7.876,P<0.001).
Conclusion　CYTH1 is downregulated in CRC tissues and cells,which can inhibit "the migration ability of CRC cells and play an inhibitory role in CRC,and it may become an effective therapeutic target for CRC.

参考文献/References:

［1］　ZAVORAL M,SUCHANEK S,MAJEK O,et al.Colorectal cancer screening:20 years of development and recent progress［J］.World J Gastroenterol,2014,20(14):3825-3834.
［2］　TODARO M,FRANCIPANE M G,MEDEMA J P,et al.Colon cancer stem cells:promise of targeted therapy［J］.Gastroenterology,2010,138(6):2151-2162.
［3］　XU Z,ZHOU Y,CAO Y,et al.Identification of candidate biomarkers and analysis of prognostic values in ovarian cancer by integrated bioinformatics analysis［J］.Med Oncol,2016,33(11):130.
［4］　NAVARRO G,MARTNEZ-PINILLA E,SNCHEZ-MELGAR A,et al.A genomics approach identifies selective effects of trans-resveratrol in cerebral cortex neuron and glia gene expression［J］.PLoS One,2017,12(4):e0176067.
［5］　LI X,HU W W,WANG L,et al.Co-expression analysis reveals key gene modules and pathways of oral squamous cell carcinoma［J］.Cancer Biomark,2018,22(4):763-771.
［6］　ZHANG J,LAN Q,LIN J.Identification of key gene modules for human osteosarcoma by co-expression analysis［J］.World J Surg Oncol,2018,16(1):89.
［7］　LIU X,HU A X,ZHAO J L,et al.Identification of key gene modules in human osteosarcoma by co-expression analysis weighted gene co-expression network analysis (WGCNA)［J］.J Cell Biochem,2017,118(11):3953-3959.
［8］　WAN Q,TANG J,HAN Y,et al.Co-expression modules construction by WGCNA and identify potential prognostic markers of uveal melanoma［J］.Exp Eye Res,2018,166:13-20.
［9］　ZHUANG D Y,JIANG L,HE Q Q,et al.Identification of hub subnetwork based on topological features of genes in breast cancer［J］.Int J Mol Med,2015,35(3):664-674.
［10］　LIANG K,ZHOU G,ZHANG Q,et al.Expression of hippo pathway in colorectal cancer［J］.Saudi J Gastroenterol,2014,20(3):188-194.
［11］　MANSOUR R N,ENDERAMI S E,ARDESHIRYLAJIMI A,et al.Evaluation of hypoxia inducible factor-1 alpha gene expression in colorectal cancer stages of Iranian patients［J］.J Cancer Res Ther,2016,12(4):1313-1317.
［12］　LANGFELDER P,HORVATH S.WGCNA:an R package for weighted correlation network analysis［J］.BMC Bioinform,2008,9:559.
［13］　XUE J,SCHMIDT S V,SANDER J,et al.Transcriptome-based network analysis reveals a spectrum model of human macrophage activation［J］.Immunity,2014,40(2):274-288.
［14］　孙宇晨,孙玄子,李静,等.通过WGCNA建立食管鳞癌放射敏感性的microRNA表达模型［J］.西安交通大学学报(医学版),2020,41(5):645-650,658.
SUN Y C,SUN X Z,LI J,et al.Validation of microRNAs radio-sensitivity biomarkers in esophageal squamous cell carcinoma based on WGCNA［J］.J Xi ′an Jiaotong Univ (Med Sci),2020,41(5):645-650,658.
［15］　李天客,张影,张素欣,等.基于加权基因共表达网络分析挖掘舌鳞状细胞癌的关键基因［J］.口腔医学研究,2020,36(5):423-427.
LI T K,ZHANG Y,ZHANG S X,et al.Identification of hub genes in tongue squamous cell carcinoma based on weighted gene co-expression network analysis［J］.J Oral Sci Res,2010,36(5):423-427.
［16］　邢林林.基于多基因互作信息的生物网络构建算法研究［D］.哈尔滨:哈尔滨工业大学,2018.
XING L L.Research on biological network construction Algorithm based on multi-gene interaction information［D］.Harbin:Harbin Institute of Technology,2018.
［17］　王攀.加权基因共表达网络分析（WGCNA）在食管鳞癌中的应用［D］.北京：北京协和医学院,2014.
WANG P.Application of weighted gene coexpression network analysis (WGCNA) in esophageal squamous cell carcinoma［D］.Beijing:Peking Union Medical College,2014.
［18］　陈超,童国俊,张建斌,等.利用加权基因共表达网络分析构建食管腺癌预后枢纽基因网络［J］.浙江医学,2019,41(20):2181-2184.
CHEN C,TONG G J,ZHANG J B,et al.Construction of prognostic hub gene network of esophageal adenocarcinoma by weighted gene co-expression network analysis［J］.Zhejiang Med J,2019,41(20):2181-2184.
［19］　RAK J,FOSTER K,POTRZEBOWSKA K,et al.Cytohesin 1 regulates homing and engraftment of human hematopoietic stem and progenitor cells［J］.Blood,2017,129(8):950-958.
［20］　QUAST T,TAPPERTZHOFEN B,SCHILD C,et al.Cytohesin-1 controls the activation of RhoA and modulates integrin-dependent adhesion and migration of dendritic cells［J］.Blood,2009,113(23):5801-5810.
［21］　GAMARA J,CHOUINARD F,DAVIS L,et al.Regulators and effectors of Arf GTPases in neutrophils［J］.J Immunol Res,2015,2015:235170.

相似文献/References:

[1]朱武凌 范秉琳.青年与老年结直肠癌C—erbB一2不同表达与DNA倍体的关系[J].新乡医学院学报,2002,19(03):170.
[2]王璧,王战会,韩保卫,等.Runt相关转录因子3在结直肠癌组织中的表达及意义[J].新乡医学院学报,2022,39(12):1127.[doi:10.7683/xxyxyxb.2022.12.005]
　WANG Bi,WANG Zhanhui,HAN Baowei,et al.Expression and significance of Runt-related transcription factor 3 in colorectal cancer[J].Journal of Xinxiang Medical University,2022,39(5):1127.[doi:10.7683/xxyxyxb.2022.12.005]
[3]齐光照,李朵璐.细胞色素P450酶CYP2W1研究进展[J].新乡医学院学报,2019,36(7):698.[doi:10.7683/xxyxyxb.2019.07.025]
[4]李怡春,张　敏,杨晓煜,等.CD133在人结直肠癌组织中的表达及其与缺氧诱导因子1α和核心蛋白聚糖的相关性[J].新乡医学院学报,2019,36(11):1036.[doi:10.7683/xxyxyxb.2019.11.007]
　LI Yi-chun,ZHANG Min,YANG Xiao-yu,et al.Expression of CD133 in human colorectal cancer tissues and correlation with hypoxia-induced factor-1α and decorin[J].Journal of Xinxiang Medical University,2019,36(5):1036.[doi:10.7683/xxyxyxb.2019.11.007]
[5]平贯芳,熊万成,邓智建.长链非编码RNA 浆细胞瘤转化迁移基因1在结直肠癌组织和细胞中的表达及临床意义[J].新乡医学院学报,2019,36(10):949.[doi:10.7683/xxyxyxb.2019.10.011]
　PING Guan-fang,XIONG Wan-cheng,DENG Zhi-jian.Expression and clinical significance of long-chain non-coding RNA plasmacytoma variant translocation gene 1 in colorectal cancer tissues and cells[J].Journal of Xinxiang Medical University,2019,36(5):949.[doi:10.7683/xxyxyxb.2019.10.011]
[6]吕文豪,董　媛,魏子白.二甲双胍在结直肠癌治疗中的作用研究进展[J].新乡医学院学报,2021,38(7):692.[doi:10.7683/xxyxyxb.2021.07.020]
[7]姬颖华,杨晓煜,孟祥丽,等.盐酸安罗替尼联合信迪利单抗治疗标准治疗失败后微卫星稳定型结直肠癌疗效观察[J].新乡医学院学报,2021,38(8):719.[doi:10.7683/xxyxyxb.2021.08.004]
　JI Yinghua,YANG Xiaoyu,MENG Xiangli,et al.Clinical efficacy of Anlotinib hydrochloride combined with Sintilimab in the treatment of microsatellite stable colorectal cancer after the failure of standard treatment[J].Journal of Xinxiang Medical University,2021,38(5):719.[doi:10.7683/xxyxyxb.2021.08.004]
[8]马　晓,陈国荣,李君艳,等.外周血中性粒细胞与淋巴细胞比值及血清癌胚抗原、糖类抗原199联合检测对结直肠癌的诊断价值[J].新乡医学院学报,2021,38(1):062.[doi:10.7683/xxyxyxb.2021.01.013]
　MA Xiao,CHEN Guorong,LI Junyan,et al.Value of combined detection of neutrophil-lymphocyte ratio in peripheral blood,serum carcinoembryonic antigen and carbohydrate antigen 199 in the diagnosis of colorectal cancer[J].Journal of Xinxiang Medical University,2021,38(5):062.[doi:10.7683/xxyxyxb.2021.01.013]
[9]谢　阳,赵李红,杨昌建,等.不同肺复张策略治疗腹腔镜下结直肠癌根治术患者围手术期肺不张疗效观察[J].新乡医学院学报,2021,38(9):857.[doi:10.7683/xxyxyxb.2021.09.012]
　XIE Yang,ZHAO Lihong,YANG Changjian,et al.Effect of different lung recruitment strategies in treatment of perioperative atelectasis of patients undergoing laparoscopic radical resection of colorectal cancer[J].Journal of Xinxiang Medical University,2021,38(5):857.[doi:10.7683/xxyxyxb.2021.09.012]
[10]胡德升,高　磊,王　江,等.外周血胸苷酸合成酶基因表达与中晚期结直肠癌患者FOLFOX4化学治疗敏感性和预后的相关性[J].新乡医学院学报,2020,37(10):930.[doi:10.7683/xxyxyxb.2020.10.007]
　HU Desheng,GAO Lei,WANG Jiang,et al.Correlation between thymidylate synthase gene expression in peripheral blood and FOLFOX4 chemotherapy sensitivity and prognosis of patients with advanced colorectal cancer[J].Journal of Xinxiang Medical University,2020,37(5):930.[doi:10.7683/xxyxyxb.2020.10.007]

更新日期/Last Update: 2023-05-05