Construction Of Multi-omics Prognostic Models Related To Autophagy In Renal Clear Cell Carcinoma

Part I Construction of a prognostic model of autophagy-related genes in patients with renal clear cell carcinomaObjective:To construct a central gene prognostic index of clear cell renal cell carcinoma(cc RCC)related to overall survival through the Cox regression model,and obtain clinical biomarkers and prognostic judgment models related to autophagy.Method:Download the cc RCC data set from the TCGA database to identify the expression of autophagy-related genes(ARGs)in cc RCC patients.Functional enrichment analysis GO and Kyoto Encyclopedia of Genes and Genomes KEGG analysis were constructed from the Metacape database.The central gene is provided by Cytoscape software.Then,a Cox proportional hazard regression model was used to identify the central gene cc RCC that is significantly related to overall survival(OS)in cc RCC.Then a prognostic index(PI)based on the central gene was constructed,and apply single factor,multi-factor COX and KM survival curve,multi-index ROC,etc.to verify.Results: PI was constructed based on genes related to OS,and cc RCC patients were divided into high-risk and low-risk groups based on the median value.There was a statistical difference between the two,and the survival time of the high-risk group was significantly reduced.PI is an independent predictor in multivariate analysis.Conclusion:1.The prognostic index we constructed has certain predictive value for the prognosis of patients with renal clear cell carcinoma.2.In the prognosis model we constructed,the risk factors are BECN1,ULK1,and the protective factors are PINK1,BNIP3,and ZFYVE1.3.Multi-factor COX analysis showed that the prognosis model developed based on 5 autophagy-related m RNAs(BECN1,PINK1,ULK1,BNIP3,and ZFYVE1)can be independent of the classic TNM staging,and may become a powerful supplement to clinical patient prognosis prediction methods.Part II Construction of autophagy-related lnc RNA prognostic model for patients with renal clear cell carcinomaObjective: To obtain lnc RNA related to renal clear cell autophagy through the combined application of Lasso and Random Forest algorithms,and use multi-factor COX to construct a prognostic regression model,and verify it in the training set and test set respectively,and finally draw a prognostic judgment nomogram and perform GSEA Related pathway analysis.Method:Download the cc RCC data set from the TCGA database,isolate the lnc RNA data and perform difference analysis.Identify the expression of autophagy-related genes(ARGs)in cc RCC patients.Calculate the lnc RNA co-expressed with ARGs as autophagy-related lnc RNA,combine the Lasso and Random Forest algorithm to obtain the prognostic-related renal clear cell autophagy lnc RNA,apply the multi-factor COX method to construct the prognosis model,and draw the mulberry chart.Then construct a prognostic index(PI)based on lnc RNA in the training set,verify it in the test set,and finally draw a prognostic judgment nomogram and GSEA related pathway analysis.Results: PI was constructed based on lnc RNA related to OS,and cc RCC patients were divided into high-risk and low-risk groups according to the median value.The survival time of the high-risk group was significantly reduced.PI is an independent predictor in multivariate analysis.Obtained 8 prognostic-related lnc NRA(CTD-2023M8.1,LINC00460,PROX1-AS1,RP11-19E11,RP11-191N8.2,AP000439.3,RP11-297L17.2,RP11-133F8.2).A nomogram related to prognosis was constructed.GSEA analysis results show that the prognostic model is related to PPAR,ERBB,TGF-?,RENAL CELL CARCINOMA pathway.Conclusion:1.We used TCGA-KIRC data to construct a prognostic model of lnc RNA related to autophagy in renal clear cell carcinoma.2.The model has a reliable predictive effect,and satisfactory results can be obtained in the training set and test set.It may be a powerful supplement to TNM staging and guide the judgment of clinical prognosis.3.Using this model,we obtained 2 types of 8 lnc RNAs,of which 5are risky lnc RNAs,namely: CTD-2023M8.1,LINC00460,PROX1-AS1,RP11-19E11,RP11-191N8.2,3 protective lnc RNAs,Respectively:AP000439.3,RP11-297L17.2,RP11-133F8.2.4.We have developed a nomogram for the prognosis of renal cancer autophagy-related lnc RNA,which can easily predict the prognosis of patients,and the calibration chart shows that the predicted survival rate basically coincides with the actual survival rate.Part III Verification of Autophagy-related lnc RNA in renal clear cell carcinomaPurpose: After constructing the autophagy-related lnc RNA prognosis model of clear cell renal cell carcinoma,we finally obtained 8lnc RNAs(AP000439.3,RP11-133F8.2,RP11-297L17.2,RP11-19E11.1,RP11-191N8.2,CTD-2023M8.1,PROX1.AS1,LINC00460).For the reliability of the results,TCGA-KIRC TNM data and laboratory verification were carried out.Methods:1.Draw 8 lnc RNA in the TCGA-KIRC data adjacent to cancer and between the different TNM stages of cancer expression graphs,analysis in the early stage(I,II)and late(III,IV),and the tumor and In normal control tissues,whether there are differential expressions of 8 lnc RNAs;2.Use q RT-PCR to detect the expression of 8 types of lnc RNA in renal clear cell carcinoma tissues and adjacent tissues to study whether there are differential expressions in the tissues;3.Use q RT-PCR to detect the expression of 8 kinds of lnc RNA in renal clear cell carcinoma cell lines 786-O,Caki-1,ACHN and immortalized human renal proximal tubule cells HK-2,and study whether they are in the cell line There is a differential expression.Results: TCGA-KIRC TNM data analysis showed that 8 types of lnc RNA are related to prognosis,and there are 5 types of risk lnc RNA:RP11-19E11.1,RP11-191N8.2,CTD-2023M8.1,PROX1.AS1,LINC00460.3 types Protective lnc RNA: AP000439.3,RP11-133F8.2,RP11-297L17.2.Except that RP11-297L17.2 expression is low in tissues and cell lines,the other lnc RNA analysis results are consistent with the TCGA-KIRC TNM analysis data.Conclusion:1.Through the combined analysis of TCGA-KIRC TNM staging and q RT-PCR verification of tissues and cell lines,7 lnc RNAs are closely related to the prognosis of renal clear cell carcinoma: Linc00460,CTD-2023M8.1,PROX1-AS1,RP11-19E11.1,RP11-191N8.2 and AP000439.3,RP11-133F8.2.2.Among them,Linc00460,CTD-2023M8.1,PROX1-AS1,RP11-19E11.1,and RP11-191N8.2 are disease risk factors,and AP000439.3 and RP11-133F8.2 are disease protection factors.3.The lnc RNA screened by our prognostic model has been well verified in the independent TNM data of TCGA-KIRC.4.The two newly screened lnc RNA CTD-2023M8.1 and RP11-19E11.1 have not been reported before,and may become new prognostic markers of renal clear cell carcinoma.