Identifcation Of Key Genes Controlling Colon Cancer Stem Cell Characteristics Based On The Stemness Index Via Bioinformatics Analysis

Objective:Colorectal cancer(Colorectal Cancer,CRC)is currently one of the most common and deadly cancers,and Colon Adenocarcinoma(COAD)is the most common pathological type of CRC.As many as 83%of colorectal cancer patients in my country are already in the middle and advanced stages when they are first diagnosed.It is not difficult to see that the diagnosis and treatment of colorectal cancer is full of many challenges.At the same time,the occurrence and development of colon cancer is also a very complicated process,involving a variety of cell activities and various signaling pathways.With the gradual disclosure of tumor heterogeneity,cancer stem cells(CSCs)are being considered to be the initial component of tumorigenesis.However,the growth and maintenance mechanism of COAD stem cells is still unclear.In order to better describe the characteristics of CSCs,Malta et al.published in CELL in 2018 based on the genetic map of tumor cells and embryonic stem cells in TCGA,using a type of logistic regression(OCLR)based on the dedifferentiation characteristics of tumors.The new index-stemness index(m RNA Expression Based Stemness Index,m RNAsi).This study uses bioinformatics big data analysis combined with stemness index to explore key genes related to COAD stemness characteristics,which will help to continue to explore the molecular mechanism of COAD stem cells and provide some references for COAD diagnosis and treatment in the futureMethods:Download COAD's RNA sequencing(RNA-Seq)expression data and corresponding clinical information from the TCGA database.The stemness index m RNAsi data of COAD cases in TCGA were obtained from previous studies,and the correlation between m RNAsi and tumor stage or tumor grade and the prognostic value of m RNAsi were studied.Log₂was used to transform the original expression RNA-Seq data of COAD,and the Limma package in R language was used to analyze differentially expressed genes(DEG_S).The criteria for selecting DEG_Sare:|log₂FC|>1,P<0.01,FDR<0.05;use the WGCNA package in R to construct a co-expression network for DEGS and identify the key modules and genes in it.Then,use the clustering analyzer in the R language to perform gene ontology(GO)function annotation and Kyoto Encyclopedia of Genes and Genome(KEGG)analysis on the selected key genes related to stemness to explore the biological processes and signal pathways that they participate in..The online STRING database was used to obtain the protein-protein interaction network(PPI network interaction map)of the key stemness-related genes,and the corrplot package in R was used to verify the Pearson correlation at the transcription level of the key stemness-related genes.Results:1.DEGs between COAD organization and normal organization.In this study,the m RNAsi of COAD cases in TCGA was obtained from the attachment of Tathiane M.Malta's article,and the corresponding clinical information of 452 COAD cases was downloaded from the TCGA database.The difference analysis found that the m RNAsi in COAD cancer tissue was significantly higher than that in normal tissue.Download the COAD RNA-Seq data from the TCGA database,including 41 normal samples and 473 COAD samples,and screen the DEG_Sbetween COAD tissues and normal tissues.Through the difference analysis,we obtained 6478 DEG_S,of which4562 were up-regulated.,1916 downgrades.2.Identify m RNAsi-related modules and genes through WGCNA.A DEG_Sco-expression network was constructed using WGCNA to obtain biological gene modules,and the green modules with the largest positive correlation coefficient were selected.The selection criteria were defined as cor.MM>0.8 and cor.GS>0.5 to screen for key genes related to dryness.,Screened and got 5 key genes related to stemness CHEK1,BUB1,KIF18A,TTK and PLK4.The specific expression values??of each key gene related to stemness were extracted,and heat maps and box plots were drawn.The results showed that these five key stemness-related genes were obviously overexpressed in COAD tissues.3.Use the PPI network to study the correlation between key genes related to dryness and protein levels.Correlation analysis of 5 key genes related to stemness revealed that there is a strong and statistically significant correlation between the key genes related to stemness.The STRING online tool was used to analyze the protein interaction relationship between the key genes related to stemness and the edge number of each node gene in the PPI network.The result showed that the edge number of each gene was equal.4.Use GO and KEGG analysis to perform functional annotation and pathway analysis on key genes related to stemness.GO annotations show that the biological processes(BP)in which the key genes related to stemness participate together mainly focus on the regulation of organelle fission,nuclear fission,mitosis,nuclear division,and cell cycle phase transitions;the participating cell composition(CC)is related to chromosome regions,etc.;The molecular function(MF)involved is related to protein serine/threonine kinase activity,etc.KEGG enrichment analysis showed that key genes related to stemness are involved in signaling pathways such as organelle fission,nuclear fission,mitosis,nuclear division,and cell cycle phase transition.Conclusion:After screening,CHEK1,BUB1,KIF18A,TTK,and PLK4 are the five genes closely related to the dryness characteristics of COAD.After gene function enrichment,the most important signal pathway related to COAD stem cells is the cell cycle pathway.