年轻女性乳腺癌潜在核心基因的生物信息学分析

陶然; 赵卫红; 秦博宇; 焦顺昌

doi:10.3969/j.issn.2095-5227.2020.04.017

年轻女性乳腺癌潜在核心基因的生物信息学分析

Identification of potential core genes of breast cancer in young women based on bioinformatics

摘要

摘要: 目的利用生物信息学方法对年轻女性乳腺癌肿瘤组织及正常乳腺组织的差异表达基因进行筛选及分析,初步探索其相关分子机制。方法从癌症基因组图谱数据库(TCGA)下载年轻女性乳腺癌(≤35岁)相关转录组数据,其中包括29例乳腺肿瘤组织样本和3例正常乳腺组织样本。利用R语言Limma程序包筛选差异表达基因,进一步通过蛋白质相互作用数据库(STRING)构建差异表达基因编码蛋白质相互作用网络,着重对表达上调的核心基因进行生物学功能及信号通路分析。结果共筛选出720个差异表达基因,其中上调基因173个,下调基因547个。通过蛋白质相互作用分析得到的核心基因包括NCAPG、NCAPH、MELK、PBK、CDCA5、CDCA8、CCNB2、CCNA2、SPC25、SKA1、NPY1R、CXCL9、CXCL10、GALR2、CCR8、CXCL2、CXCL3、CXCL5、PPBP、CCL16。其中NCAPG、NCAPH、MELK、PBK、CDCA5、CDCA8、CCNB2、CCNA2、SPC25、SKA1、NPY1R、CXCL9、CXCL10、GALR2、CCR8在年轻女性乳腺癌中表达上调,同时发现CXCL2、CXCL3、CXCL5、PPBP、CCL16在癌组织中表达下调且既往研究报道较少。对上调核心基因进行GO分析显示:有丝分裂、细胞增殖正向调控和免疫应答等生物学过程与其相关性较大,同时上调核心基因与趋化因子信号通路以及神经活性配体-受体相互作用等KEGG信号通路关系密切。结论本研究筛选出与年轻女性乳腺癌显著相关的20个潜在核心基因,上调的核心基因与趋化因子信号通路有关。

Abstract: Objective To screen and analyze the differentially expressed genes of breast cancer and normal breast tissues in young women using bioinformatics method,and explore their related molecular mechanisms. Methods The transcriptome data of young women (≤35 years old) with breast cancer were downloaded from TCGA Database,including 29 breast tumor tissue samples and 3 normal breast tissue samples.Then the differentially expressed genes were screened by Limma package in R language,the protein interaction network of differentially expressed genes coding was constructed through STRING Database,and the biological functions and signal pathways of up-regulated core genes were mainly analyzed. Results A total of 720 differentially expressed genes were screened out,including 173 up-regulated genes and 547 down-regulated genes.The core genes obtained through the protein interaction analysis included NCAPG,NCAPH,MELK,PBK,CDCA5,CDCA8,CCNB2,CCNA2,SPC25,SKA1,NPY1R,CXCL9,CXCL10,GALR2,CCR8,CXCL2,CXCL3,CXCL5,PPBP,and CCL16.Among them,15 core genes with up-regulated expression in breast cancer of young women were NCAPG,NCAPH,MELK,PBK,CDCA5,CDCA8,CCNB2,CCNA2,SPC25,SKA1,NPY1R,CXCL9,CXCL10,GALR2 and CCR8;5 core down-regulated genes were CXCL2,CXCL3,CXCL5,PPBP and CCL16,and they were rarely reported in previous studies.The GO analysis showed that up-regulated core genes were highly correlated with biological processes such as mitosis,positive cell proliferation regulation,and immune response.Moreover,up-regulated core genes were closely correlated with KEGG signal pathways such as chemokine signal pathway and neuroactive ligand-receptor interaction. Conclusion This study has screened out 20 potential core genes of breast cancer in young women based on bioinformatics method,and analyzed the biological functions and signal pathways of up-regulated expression core genes.The findings contribute to a theoretical basis for the further understanding of the molecular mechanisms related to breast cancer in young women,and provide theoretical guidance to clinical diagnosis and treatment.

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