目的通过对基因表达数据库(GEO)中变应性鼻炎(allergicrhinitis,AR)相关的基因芯片进行生物信息学分析,获得AR的生物标志物。方法2018年6月至2019年12月,从可公开获得的GEO(http://www.ncbi.nlm.nih.gov/geo)中下载包括3名健康对照者和6...目的通过对基因表达数据库(GEO)中变应性鼻炎(allergicrhinitis,AR)相关的基因芯片进行生物信息学分析,获得AR的生物标志物。方法2018年6月至2019年12月,从可公开获得的GEO(http://www.ncbi.nlm.nih.gov/geo)中下载包括3名健康对照者和6例AR患者的数据(GSE46171)。使用GEO2R在线工具在AR和正常组织之间进行筛查。然后使用生物信息学方法,包括基因本体(geneontology,GO)富集分析,京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)信号通路分析和蛋白质-蛋白质相互作用(PPI)网络构建,以鉴定AR中的关键基因。同期,武汉大学人民医院耳鼻咽喉头颈外科在手术中收集15例AR患者和15名健康对照者的下鼻甲黏膜组织,用于进一步验证重要的基因和途径,进行实时定量聚合酶链反应。采用SPSS 9.0统计学软件对测量结果进行统计学分析。结果共选择217个差异基因(differentially expressed genes,DEG),其中112个是下调基因,105个是上调基因。其中表达差异最大的5个上调基因依次为:KLK7、TMPRSS11A、SPRR2C、TPSAB1及TXLNGY;表达差异最大的5个下调基因依次为:XIST、CTAG1A、PRB1、CXCL11及PRB2。通过在217个DEG之间构建PPI网络,获得的15个hub基因依次为IFIH1、CCR2、CD80、TLR7、EIF1AY、DDX3Y、RSAD2、RPS4Y2、RPS4Y1、XAF1、KDM5D、ZFY、NLGN4Y、IFIT5和DDX60L,这些基因位于基因网络中的枢纽上。以15例AR患者和15名健康对照者的下鼻甲黏膜组织对这15个基因进行验证,结果显示AR患者的IFIH1、CCR2、CD80、TLR7、RSAD2、XAF1、IFIT5和DDX60L表达低于健康对照者,EIF1AY、DDX3Y、RPS4Y2、RPS4Y1、KDM5D、ZFY和NLGN4Y表达高于健康对照者,差异均有统计学意义(P值均<0.05)。结论本研究共发现了217个AR密切相关基因,并通过PPI网络获得15个hub基因,这些基因可能参与了AR的发病过程,有望成为AR新的生物标志物。展开更多
BACKGROUND Gastric signet ring cell carcinoma(GSRCC)is one of the most malignant tumors.It has the features of high invasiveness,rapid progression,and resistance to chemotherapy.However,systematic analyses of mRNAs ha...BACKGROUND Gastric signet ring cell carcinoma(GSRCC)is one of the most malignant tumors.It has the features of high invasiveness,rapid progression,and resistance to chemotherapy.However,systematic analyses of mRNAs have not yet been performed for GSRCC.AIM To identify key mRNAs and signaling pathways in GSRCC.METHODS A transcriptome analysis of two GSRCC and two non-GSRCC samples was performed in this study.Differentially expressed mRNAs and pathways were identified based on the KEGG and PANTHER pathway annotations.The interactive relationships among the differential genes were mapped with the STRING database.Quantitative real-time polymerase chain reaction was used to validate the key gene expression in GSRCC.RESULTS About 1162 differential genes(using a 2-fold cutoff,P<0.05)were identified in GSRCC compared with non-GSRCC.The enriched KEGG and PANTHER pathways for the differential genes included immune response pathways,metabolic pathways,and metastasis-associated pathways.Ten genes(MAGEA2,MAGEA2B,MAGEA3,MAGEA4,MAGEA6,MUC13,GUCA2A,FFAR4,REG1A,and REG1B)were identified as hub genes in the protein-protein interaction network.The expression levels of five genes(MAGEA2,MAGEA3,MAGEA4,MAGEA6,and REG1B)showed potential clinical value.CONCLUSION We have identified the potential key genes and pathways in GSRCC,and these hub genes and pathways could be diagnostic markers and therapeutic targets for GSRCC.展开更多
文摘目的通过对基因表达数据库(GEO)中变应性鼻炎(allergicrhinitis,AR)相关的基因芯片进行生物信息学分析,获得AR的生物标志物。方法2018年6月至2019年12月,从可公开获得的GEO(http://www.ncbi.nlm.nih.gov/geo)中下载包括3名健康对照者和6例AR患者的数据(GSE46171)。使用GEO2R在线工具在AR和正常组织之间进行筛查。然后使用生物信息学方法,包括基因本体(geneontology,GO)富集分析,京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)信号通路分析和蛋白质-蛋白质相互作用(PPI)网络构建,以鉴定AR中的关键基因。同期,武汉大学人民医院耳鼻咽喉头颈外科在手术中收集15例AR患者和15名健康对照者的下鼻甲黏膜组织,用于进一步验证重要的基因和途径,进行实时定量聚合酶链反应。采用SPSS 9.0统计学软件对测量结果进行统计学分析。结果共选择217个差异基因(differentially expressed genes,DEG),其中112个是下调基因,105个是上调基因。其中表达差异最大的5个上调基因依次为:KLK7、TMPRSS11A、SPRR2C、TPSAB1及TXLNGY;表达差异最大的5个下调基因依次为:XIST、CTAG1A、PRB1、CXCL11及PRB2。通过在217个DEG之间构建PPI网络,获得的15个hub基因依次为IFIH1、CCR2、CD80、TLR7、EIF1AY、DDX3Y、RSAD2、RPS4Y2、RPS4Y1、XAF1、KDM5D、ZFY、NLGN4Y、IFIT5和DDX60L,这些基因位于基因网络中的枢纽上。以15例AR患者和15名健康对照者的下鼻甲黏膜组织对这15个基因进行验证,结果显示AR患者的IFIH1、CCR2、CD80、TLR7、RSAD2、XAF1、IFIT5和DDX60L表达低于健康对照者,EIF1AY、DDX3Y、RPS4Y2、RPS4Y1、KDM5D、ZFY和NLGN4Y表达高于健康对照者,差异均有统计学意义(P值均<0.05)。结论本研究共发现了217个AR密切相关基因,并通过PPI网络获得15个hub基因,这些基因可能参与了AR的发病过程,有望成为AR新的生物标志物。
基金Supported by National Key R&D Program of China,No.2018YFC1313101Wu Jieping Medical Foundation,No.320.6750.15276
文摘BACKGROUND Gastric signet ring cell carcinoma(GSRCC)is one of the most malignant tumors.It has the features of high invasiveness,rapid progression,and resistance to chemotherapy.However,systematic analyses of mRNAs have not yet been performed for GSRCC.AIM To identify key mRNAs and signaling pathways in GSRCC.METHODS A transcriptome analysis of two GSRCC and two non-GSRCC samples was performed in this study.Differentially expressed mRNAs and pathways were identified based on the KEGG and PANTHER pathway annotations.The interactive relationships among the differential genes were mapped with the STRING database.Quantitative real-time polymerase chain reaction was used to validate the key gene expression in GSRCC.RESULTS About 1162 differential genes(using a 2-fold cutoff,P<0.05)were identified in GSRCC compared with non-GSRCC.The enriched KEGG and PANTHER pathways for the differential genes included immune response pathways,metabolic pathways,and metastasis-associated pathways.Ten genes(MAGEA2,MAGEA2B,MAGEA3,MAGEA4,MAGEA6,MUC13,GUCA2A,FFAR4,REG1A,and REG1B)were identified as hub genes in the protein-protein interaction network.The expression levels of five genes(MAGEA2,MAGEA3,MAGEA4,MAGEA6,and REG1B)showed potential clinical value.CONCLUSION We have identified the potential key genes and pathways in GSRCC,and these hub genes and pathways could be diagnostic markers and therapeutic targets for GSRCC.
