Screening For Genes Related To Methylation In Lusc Based On TCGA Database And Methylation Of SOX15 Gene Promoter

Objective: To study the RNA sequencing data and DNA methylation data of LUSC in TCGA database by using bioinformatics method,and to screen the genes related to methylation in LUSC.Methods: 1.RNA sequence(RNAseq)data,DNA methylation data and corresponding clinical information of 376 patients with LUSC were downloaded from the TCGA(The Cancer Genome Atlas)database using the R language RTCGA Tool box package,and use the DESeq2 and minfi software package respectively to select differentially expressed genes(|log FC|> 2.0,P <0.001)and differential methylation sites(|??|> 0.2,P <0.001);2.Screening candidate genes using correlation analysis(r>0.6)between m RNA expression data and DNA methylation data;3.Analysis of the pathways involved in the target gene by GO and KEGG,combined with the literature to screen the final target gene.Results: 1.2581 differentially expressed genes and 28793 differential methylation sites were screened in the TCGA database;2.Six candidate genes(SOX15,PRAME,KIF15,KCTD1,SLC6A8,OTX1)were screened;3.GO KEGG analysis showed that the gene SOX15 is involved in metabolism,multicellular biological development,immune system and other processes,and the gene SOX15 participates in P53 pathway,PI3 kinase pathway,Ras pathway,VEGF signaling pathway,TGF-? signaling pathway,FGF signaling pathway,etc.Conclusion: The target gene SOX15 was screened,and the SOX15 gene was highly expressed in LUSC.SOX15 gene may be related to the occurrence and development of LUSC.Objective: To verify the expression of SOX15 m RNA in LUSC by LUSC and normal lung tissues.Methods: Collecting the 41 cases of LUSC and normal lung tissues,The expression of SOX15 m RNA was verified by q RT-PCR and its clinicopathological significance was analyzed.Results: Further q RT-PCR experiments showed that the expression of the gene SOX15 m RNA in LUSC was significantly higher than that in normal lung tissues(p<0.01),and the expression of the gene SOX15 m RNA was associated with clinical stage and lymph node metastasis.Conclusion: SOX15 m RNA is highly expressed in LUSC,and the expression of SOX15 m RNA was associated with clinical stage and lymph node metastasis.Objective: To analyze the methylation level of the promoter region of SOX15 gene and explore its clinical significance.Methods: Differential methylation sites in 338 LUSC and 38 normal lung tissues from the Illumina humanmethylation 450 platform in the TCGA database were analyzed.The relationship between SOX15 gene and methylation in LUSC was analyzed.Explore its clinical significance.Results: The methylation level of two points(cg01029592,cg13159929)in the promoter region of the gene SOX15 was significantly lower in LUSC(P<0.001),and negatively correlated with the gene SOX15 m RNA expression(r=-0.76,P<0.001;r=-0.77,P<0.001).Survival analysis showed that the level of methylation of the gene SOX15 was correlated with prognosis(P<0.05).Using the expression data of the gene SOX15 in LUSC,the tumor specificity was analyzed by ROC curve,and it was found that the area under the curve AUC=91.036%.Conclusion: By analyzing the methylation data of SOX15 DNA in the TCGA database,the results showed that the methylation level of methylation site in the promoter region of SOX15 gene was significantly lower in LUSC.The hypomethylation of the gene SOX15 promoter region may lead to high m RNA expression and is associated with the prognosis of LUSC.The gene SOX15 is expected to be a tumor-specific marker for LUSC.