喉鳞状细胞癌的转录组数据分析及生物标志物筛选

Transcriptome data analyses and biomarker identification in laryngeal squamouscell carcinoma

目的通过数据挖掘分析长链非编码RNA(lncRNA)、微小RNA(miRNA)和信使RNA(mRNA)在喉鳞状细胞癌中的相互作用机制。方法从肿瘤基因图谱(TCGA)中获取喉鳞状细胞癌的lncRNA、miRNA、mRNA表达谱数据及相关临床数据,从TCGA和GEO数据库中获取喉鳞状细胞癌的DNA甲基化数据。进行蛋白相互作用(PPI)、基因文本(GO)、京都基因和基因组百科全书(KEGG)信号通路分析和Kaplan-Meier生存分析,构建竞争性内源RNA(ceRNA)网络和转录因子调控网络。结果LINC00278、LINC00689、MYHAS、miRNA-99a和miRNA-301a属于低风险基因(HR﹤1);MNX1-AS1、LINC02575、HOXB-AS4、LSAMP-AS1、LINC02086、IGFL2-AS1、LINC02253、CASC20、miRNA-383、miRNA-196a-2、miRNA-196a-1、miRNA-100和miRNA-4652属于高风险基因(HR﹥1)。ceRNA网络中有11个lncRNA(LINC02576、LINC02086、AC020659.1、LINC00528、LINC00689、HOXB-AS4、MNX1-AS1、LINC00278、AC010624.1、AC016773.1、MYHAS)、5个miRNA(has-miRNA-206、has-miRNA-573、has-miRNA-3662、has-miRNA-133b、has-miRNA-449a)和12个mRNA(STC2、PAX3、NETO2、EIF5A2、ADPRHL1、SYNM、ACTA1、GPR156、CLIC5、BMP3、HNF4A、FOXL2)。MYHAS的共表达mRNA(cor-mRNA)主要富集在钙信号通路、环磷酸鸟苷(cGMP)-cGMP依赖性蛋白激酶(PKG)信号通路和催产素信号通路等。转录因子网络中有9个转录因子(MYOD、RSRFC4、TAL1BETAITF2、YY1、P300、PAX3、PAX5、ZID和OLF1)。喉鳞状细胞癌DNA甲基化分析得到75个甲基化位点,对应高甲基化基因56个,低甲基化基因15个。结论ceRNA网络并不能完全阐释lncRNA、miRNA和mRNA在喉鳞状细胞癌发生中的作用机制,lncRNA、miRNA和mRNA在喉鳞状细胞癌发生过程中既相互联系又相互独立。筛选出的lncRNA、miRNA和mRNA为试验验证缩小了范围并提供了理论基础。MYHAS在喉鳞状细胞癌中发挥重要作用,是一个潜在的生物学靶点。

Objective To analyze the interaction mechanism of long noncoding RNA(lncRNA),microRNA(miRNA)and messenger RNA(mRNA)in laryngeal squamous cell carcinoma(LSCC)by using data mining.Method The transcriptome data of lncRNA,miRNA and mRNA in LSCC from TCGA database and related clinical data of were obtained;data of DNA methylation in LSCC was obtained from the TCGA and GEO database;the signaling pathway analysis of protein-protein interaction(PPI),gene ontology(GO),Kyoto Encyclopedia of Genes and Genomes(KEGG),and Kaplan-Meier survival analysis were performed to construct the competitive endogenous RNA(ceRNA)and transcription factor regulation network.Result LINC00278,LINC00689,MYHAS,miRNA-99a and miRNA-301a were low risk genes(HR<1);MNX1-AS1,LINC02575,HOXB-AS4,LSAMP-AS1,LINC02086,IGFL2-AS1,LINC02253,CASC20,miRNA-383,miRNA-196a-2,miRNA-196a-1,miRNA-100 and miRNA-4652 were high risk genes(HR>1).The ceRNA network included 11 lncRNA(LINC02576,LINC02086,AC020659.1,LINC00528,LINC00689,HOXB-AS4,MNX1-AS1,LINC00278,AC010624.1,AC016773.1 and MYHAS),5 miRNA(has-miRNA-206,has-miRNA-573,has-miRNA-3662,has-miRNA-133b and has-miRNA-449a)and 12 mRNA(STC2,PAX3,NETO2,EIF5A2,ADPRHL1,SYNM,ACTA1,GPR156,CLIC5,BMP3,HNF4A,FOXL2);the co-expression mRNA(cor-mRNA)of MYHAS was chiefly enriched in the calcium signaling pathway,cyclic guanosine monophosphate(cGMP)-cGMP-dependent protein kinase(PKG)signaling pathway and the oxytocin signaling pathway;there were 9 transcription factors in the transcription factor network(MYOD, RSRFC4, TAL1BETAITF2, YY1, P300, PAX3, PAX5, ZID and OLF1);a total of 75 methylation loci were obtainedfor the DNA methylation in LSCC, corresponding to 56 high methylation genes and 16 low methylation genes.Conclusion The ceRNA network cannot adequately explain the interaction mechanism of lncRNA, miRNA and mRNAin LSCC. The lncRNA, miRNA and mRNA are both interconnected and independent. The lncRNA, miRNA and mRNAscreened decrease the scope of testing identification and provide a theory basis. The MYHAS plays important role in theLSCC, which may be a potential biomarker.