Peer Review #1 of "Tumor microenvironment related novel signature predict lung adenocarcinoma survival (v0.1)"

Background:Lung adenocarcinoma (LUAD) is the most common histological type of lung cancers, which is the primary cause of cancer-related mortality worldwide.Growing evidence has suggested that tumor microenvironment (TME) plays a pivotal role in tumorigenesis and progression.Hence, we investigate the correlation of TME related genes with LUAD prognosis.Method:The information of LUAD gene expression data was obtained from The Cancer Genome Atla(TCGA).According to their immune/stromal scores calculated by the ESTIMATE algorithm, differentially expressed genes(DEGs) were identified.Then, we performed univariate Cox regression analysis on DEGs to obtain genes that are apparently bound up with LUAD survival (SurGenes).Functional annotation and protein-protein interaction (PPI) was also conducted on SurGenes.By validating the SurGenes with another data sets of lung cancer from Gene Expression Omnibus (GEO), 106 TME related SurGenes were generated.Further, intersection analysis was executed between the 106 TME related SurGenes and hub genes from PPI network, PTPRC and CD19 were obtained.And Gene Set Enrichment Analysis and CIBERSORT analysis were performed on PTPRC and CD19.Based on the TCGA LUAD dataset, we conducted factor analysis and Step-wise multivariate Cox regression analysis for 106 TME related SurGenes to construct the prognostic model for LUAD survival prediction.LUAD dataset in GEO (GSE68465) was used as the testing dataset to confirm the prognostic model.Multivariate Cox regression analysis was used between risk score from the prognostic model and clinical parameters.Result:106 TME related genes were collected in our research totally, which were markablely correlated with the overall survival(OS) of LUAD patient.Bioinformatics analysis suggest them mainly concentrated on immune response, cell adhesion, and extracellular matrix.More importantly, among 106 TME related SurGenes, PTPRC and CD19 were highly interconnected nodes among PPI network and correlated with immune activity, exhibiting significant prognostic potential.The prognostic model was a weighted linear combination of the 106 genes, by which the low-OS LUAD samples could be separated from the high-OS samples with success.This model was also able to rebustly predict the situation of survival (training set: p-value<0.0001,areaunder the curve (AUC) =0.649; testing set: p-value=0.0009,AUC=0.617).By combining with clinical parameters, the prognostic model was optimized.The AUC achieved 0.716 for 3 year and 0.699 for 5 year. Conclusion:A series of TME-related prognostic genes were acquired in this research, which could reflect immune disorders within tumor microenvironment, and PTPRC and CD19 show the potential to be an indicator for LUAD prognosis and tumor microenvironment modulation.The prognostic model constructed base on those prognostic genes presented a high predictive ability, and may have clinical implications in the overall survival prediction of LUAD.

Topic: Ferroptosis and cancer prognosis
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences