Transcription Factor And Target Gene Prediction And Functional Analysis Of Hepatocellular Carcinoma Related LncRNA HAO2-IT1

Background and Objective(1)Using TCGA and GEO databases to screen Asian Hepatocellular carcinoma-specific lncRNA HAO2-IT1 through bioinformatics and predict its function.(2)Predictive analysis of downstream regulatory target genes and upstream transcription factors of HAO2-IT1,and correlation analysis of clinical characteristics.(3)Collect hepatocellular carcinoma tissue samples for verification by qRT-PCR experiments,and detect differential expression and correlation of the three genes.Materials and Methods(1)The TCGA and GEO databases were used to download the Asian HCC expression profile files and clinical information files,and Venn analysis and survival analysis were used to screen for common differences and survival-related lncRNAs after performing a difference analysis.(2)Use GSEA software to perform gene sets enrichment analysis on HAO2-IT1,and use R software to perform GO and KEGG analysis to predict the function of HAO2-IT1.(3)Co-expression analysis and transcription factor prediction analysis of HAO2-IT1 screen out target genes and transcription factors that have regulatory relationships between upstream and downstream.(4)qRT-PCR was used to verify the different expression of HAO2-IT1,HAO2 and LEF1 in tissue samples from HCC and analyze their correlation.Results(1)TCGA combined with GEO analysis found that there were 4 differential lncRNAs.HHIP-AS1,HAO2-IT1,and HAND2-AS1 were down-regulated in HCC,and ST8SIA6-AS1 was up-regulated in HCC.HAO2-IT1 and overall survival(OS)and Disease survival(DFS)was significantly related.GSEA,GO and KEGG enrichment analysis showed that HAO2-IT1 may be involved in regulating tumor metabolism and other processes.(2)HAO2-IT1 has a significant correlation with the downstream target gene HAO2 and has a cis-regulatory relationship.HAO2-IT1 has a good correlation with the transcription factor LEF1 and has a high predicted score.HAO2 is down-regulated in HCC and LEF1 is up-regulated in HCC.Clinical analysis shows that high expression of HAO2-IT1 indicates lower stage,and higher expression of HAO2 also indicates lower stage and grade of HCC,but higher expression of LEF1 indicates higher stage of HCC.The Oncomine database further demonstrates the differential expression of HAO2 and LEF1 in HCC.CPTAC database analysis suggested that HAO2 was differentially expressed in HBV-associated hepatocellular carcinoma and adjacent tumors.(3)qRT-PCR results showed that HAO2-IT1 and HAO2 were down-regulated in tumors,and LEF1 was up-regulated in tumors.Coexpression analysis showed that the correlation between HAO2-IT1 and HAO2 was 0.89,and the correlation between LEF1 and HAO2-IT1 was-0.78.ConclusionsBioinformatics analysis found that HAO2-IT1 is down-regulated in HCC,which may be involved in tumor metabolism as a tumor suppressor gene,and predicted its upstream transcription factor LEF1 and cis-regulated downstream HAO2 gene.Clinical analysis shows that high expression of HAO2-IT1 indicates a lower stage of HCC,and high expression of HAO2 also indicates a lower stage and grade of HCC.However,the higher expression of LEF1,the higher stage of HCC.Using HCC tissue samples,qRT-PCR method was used to verify the results of biomarker analysis of LEF1,HAO2-IT1 and HAO2 genes.