Analysis Of Key Candidate Genes And Pathways And Construction Of A Nomogram Predicting The Overall Survival Of Patients With Osteosarcoma

Objective Analysis of Osteosarcoma(OS)gene expression profiling using bioinformatics.Key candidate genes and pathways of osteosarcoma were screened and analyzed,to explore the pathogenesis of OS at the molecular level.Nomogram was constructed to predict the Overall Survival of OS patients more accurately and individually,to provide prognosis information for patients and assist doctors in the formulation of treatment plans.Methods (1)The raw data of the OS microarray dataset was downloaded from the Gene Expression Omnibus(GEO)database,differentially expressed genes(DEGs)were screened using bioinformatics methods,and Gene Ontology(GO)was performed using the R language enrichplot package for differential genes.And pathway enrichment analysis(KEGG),through the STRING online software,Cytoscape and its plug-in cytoHubba,NetworkAnalyzer of OS significant differences in genes protein-protein interaction network analysis(PPI analysis),looking for the key(Hub)gene.(2)Another raw Data of OS patients was obtained from the SEER database.And factors related to OS prognosis were obtained based on univariate COX regression analysis.Furthermore,multivariate COX regression analysis was performed to obtain independent prognostic factors of OS.The prognostic normogram was constructed based on COX analysis.The Concordance index(C-index)and the Area Under Curve(AUC)of the Receiver Operator Characteristic curve(ROC)were used to quantify the recognition.In addition,we also plotted the K-M survival curve.Results (1)(1)A total of 408 DEGs(OS group / normal control group)were screened,including 274 up-regulated genes and 134 down-regulated DEGs,showing significant differences in gene expression between the two groups.(2)GO analysiswas performed on 408 DEGs,and the first eight functional enrichment categories were selected.DEGs is mainly involved in mitotic nuclear division,sister chromatid separation,chromosome separation,mitotic microtubule cytoskeletal tissue,organelle fission and other biological processes.The molecular functions involved histone kinase-active chemokine receptor-binding microtubules motor tubulin binding chemokine active RAGE receptor binding.DEGs were mainly concentrated in spindle microtubules centromeric region.KEGG pathway enrichment analysis showed that DEGs was mainly involved in classical signaling pathways such as the pi3k-akt signaling pathway,chemokine signaling pathway,T-cell receptor signaling pathway,Toll-like receptor signaling pathway,TNF signaling pathway,p53 signaling pathway and NF-?B signaling pathway.(3)In this study,408 significantly different genes were put into the STRING tool to find the hub genes.According to the MCC method,the top 10 hub genes were CDC6,FEN1,OIP5,GINS2,RFC3,TRIP13,MCM10,AURKA,TIPIN,DTYMK.(2)(1)Univariate COX analysis showed that OS was associated with diagnostic age,Grade,SEER stage,AJCC TNM stage,tumor sized,surgery,lymphadenectomy,and radiotherapy.Multivariate COX analysis showed that diagnostic age,Grade,SEER stage,tumor size,and surgery were independent risk factor for OS.(2)Normogram validation was performed.The training cohort showed that the C-index value for nomogram predictions of OS was 0.766(95%CI,0.742-0.790).Similarly,the C-index values corresponding to the validation cohort is0.760(95%CI,0.729-0.791).Furthermore,by analyzing the AUC(area of ROC curve),the results showed that the actual survival time of the two groups of subjects were very consistent with the nomogram prediction results.In the training cohort,the AUC of 1,3 and 5 years were 0.859,0.785 and 0.748,while in the validation cohort the AUC at 1,3 and 5 years were 0.853,0.748 and 0.737,respectively.These data suggest that the normogram we constructed is an effective predictor of survival in patients with osteosarcoma.(3)In K-M survival curve,the high-risk group of training cohort in the 5 years of survival rate is 41.8%(95% CI,37.5%-46.7%),low-risk group is 75.7%(98% CI,71.7%-79.9%).Meanwhile,the inspection of high-risk group of validation cohort 5 years of survival rate is 37.8%(95% CI,31.8.7 %-45.0%),low-risk group is 78.1%(98% CI,74.0%-82.4%).Conclusion (1)This study adopts the method of bioinformatics to OS gene chip data for further mining,found 408 DEGs and its related pathways.DEGs of OS are involved in multiple biological processes and molecular functions,including nuclearfission,microtubule cytoskeletal tissue,histone kinase activity,microtubule movement,etc..And DEGs participate in PI3K-Akt signaling pathway,chemokine signaling pathway,p53 signaling pathway,NF-?B signaling pathway and other classical signaling pathways.The high expression of CDC6,FEN1,OIP5,GINS2,and RFC3 in OS may play important roles in its occurrence and development,providing new ideas for exploring the molecular mechanism of OS and finding new therapeutic targets.(2)In this study,a normogram was constructed to predict the overall survival of patients with osteosarcoma based on 5 variables.The C-index and ROC curve were well validated for nomogram.This predictive model has the potential to provide individualized survival and prognosis assessment for patients with osteosarcoma and assist clinicians to make personalized clinical decisions.