Screening And Preliminary Validation Of Colorectal Cancer-related Genes Based On TCGA Database

ObjectiveCancer has seriously endangered human health and reduced the quality of survival.Colorectal cancer is the third most common cancer in the world,and its high incidence and mortality rates have attracted widespread attention and research worldwide.With the development of genomics,microarray technology has been used to explore the genetic alterations of colorectal cancer,and to detect,accurately diagnose,accurately classify,intercept,and treat tumors at an early stage.In addition,based on bioinformatics analysis and related experimental studies,we can identify molecules and pathways that play an important role in tumorigenesis,some of which have been shown to be potential tumor markers or therapeutic targets.It is of great research significance to explore the potential molecular mechanisms associated with tumorigenesis and to screen factors associated with colorectal cancer,which can provide new therapeutic targets for colorectal cancer and improve the survival quality of patients.MethodsThe data of colorectal cancer samples from The Cancer Genome Atlas(TCGA)database were downloaded using R software.The statistical analysis was performed,|log FC|>1.2 and P<0.05 were set as the filtering condition to screen out genes differentially expressed in colorectal cancer,including PCP2,PLAC1,IL13RA2,PNCK,CT55,SAGE1,SLITRK2,MAGEA10,CSAG1,MAGEA12,PNMA5,MAGEA1,ATP2B3,DUSP9,PNCK,PDZD4,TKTL1 and CTAG2.And it was hypothesized that these genes with differential expression may be functional genes in colorectal cancer.We first performed expression validation analysis of the more significantly differentially expressed samples of PCP2,IL13RA2,and PNCK in TCGA through several database bioinformatics sites such as UALCAN and GEPIA2.0,and tested the prognostic value of survival using the Kaplan-Meier method.The immunohistochemistry staining on Tissue Microarray was used to confirm the expression of PCP2,IL13RA2,and PNCK.Finally,the correlation between PCP2,IL13RA2,and PNCK and immune cell infiltration in colorectal cancer was analyzed by TIMER2.0 database,respectively.ResultsThe expression of PCP2 was upregulated in 11 types of cancers including BLCA and BRCA.PCP2 played an important role in the prognosis of patients with multiple cancers such as DLBC and OV.The expression level of PCP2 in THYM was correlated most strongly with TMB,and that of PCP2 in THCA was correlated most strongly with MSI.The expression of PCP2 was correlated negatively with the immune score in BLCA and BRCA,and positively with the stromal score in multiple tumors such as BLCA and HNSC.TGCT was the tumor most susceptible to tumor microenvironment.The expression of PCP2 was significantly correlated with the level of immune infiltration of multiple immune cells.PCP2 expression was up-regulated in CRC.PCP2 expression in rectal cancer was statistically different from pathological stage and TNM stage,and the expression increased with increasing stage.PCP2 expression was statistically different from patient age and gender.PCP2 expression affected survival prognosis of CRC patients.PCP2 was hypermethylated in CRC.The results of KEGG pathway showed that in CRC,PCP2 was mainly negatively correlated with RIG-like receptor signaling pathway and TOLL-like receptor signaling pathway.Immunohistochemical results showed that PCP2 was positively expressed in CRC tissues.The expression of IL13RA2 was down-regulated in 10 types of tumors including BRCA and CHOL;up-regulated in 8 types of tumors including ESCA and GBM.The expression of IL13RA2 was correlated with survival prognosis in several tumors such as THCA and KIRP.IL13RA2 was highly expressed in CRC.The expression of IL13RA2 increased with pathological stage in rectal cancer II-IV.The expression of IL13RA2 was statistically different in patients’ age,gender,different subtypes of CRC,lymph node metastasis stage.The expression level of IL13RA2 was correlated with immune cell infiltration.KEGG channel results show that IL13RA2 in READ is mainly positively correlated with the JAK/STAT signaling pathway.Immunohistochemical results showed that IL13RA2 was positively expressed in CRC tissues.The expression of PNCK was upregulated in 10 types of tumors including CHOL and HNSC and downregulated in 7 types of tumors including BLCA and GBM.PNCK expression was correlated with survival prognosis in several tumors.PNCK was lowly expressed in colorectal cancer.The expression of PNCK increased with pathological stage in CRC.The expression of PNCK was statistically different in patient’s gender,age,CRC tissue subtypes.The expression of PNCK was hypermethylated in CRC.The expression level of PNCK was correlated with immune cell infiltration.KEGG pathway results showed that PNCK in COAD was mainly positively correlated with RIG-I receptor signaling pathway.Immunohistochemical results showed weakly positive expression of PNCK in CRC tissues and positive expression in paraneoplastic tissues.ConclusionPCP2,IL13RA2 and PNCK may be used as biomarkers of CRC in the future,participate in the occurrence and development of CRC,and play a role in tumor immunotherapy.