Systematic profiling of invasion‐related gene signature predicts prognostic features of lung adenocarcinoma

Abstract

Due to the high heterogeneity of lung adenocarcinoma (LUAD), molecular subtype based on gene expression profiles is of great significance for diagnosis and prognosis prediction in patients with LUAD. Invasion‐related genes were obtained from the CancerSEA database, and LUAD expression profiles were downloaded from The Cancer Genome Atlas. The ConsensusClusterPlus was used to obtain molecular subtypes based on invasion‐related genes. The limma software package was used to identify differentially expressed genes (DEGs). A multi‐gene risk model was constructed by Lasso‐Cox analysis. A nomogram was also constructed based on risk scores and meaningful clinical features. 3 subtypes (C1, C2 and C3) based on the expression of 97 invasion‐related genes were obtained. C3 had the worst prognosis. A total of 669 DEGs were identified among the subtypes. Pathway enrichment analysis results showed that the DEGs were mainly enriched in the cell cycle, DNA replication, the p53 signalling pathway and other tumour‐related pathways. A 5‐gene signature (KRT6A, MELTF, IRX5, MS4A1 and CRTAC1) was identified by using Lasso‐Cox analysis. The training, validation and external independent cohorts proved that the model was robust and had better prediction ability than other lung cancer models. The gene expression results showed that the expression levels of MS4A1 and KRT6A in tumour tissues were higher than in normal tissues, while CRTAC1 expression in tumour tissues was lower than in normal tissues. The 5‐gene signature prognostic stratification system based on invasion‐related genes could be used to assess prognostic risk in patients with LUAD.

Gene Expression Profiles of Multiple Synchronous Lesions in Lung Adenocarcinoma

“…Furthermore, with the DEGs that overlapped with the PanCancer Immune Panel, the enriched GO categories indicated that the up-regulated DEGs were enriched in chemokines, B cell functions, and cytokine signaling in the immune system, and the down-regulated DEGs were enriched in interleukins, leukocyte functions, and NK cell functions. The overexpression of the genes in B cell functions in lung cancer has been reported [ 42 , 43 , 44 ]. Increased expression levels of BLK [ 42 ] and MS4A1 [ 43 ] have been reported in lung adenocarcinoma, and BLK and CD19 [ 44 ] have been reported to be significantly correlated with the overall survival in patients with lung adenocarcinoma.…”

“…The overexpression of the genes in B cell functions in lung cancer has been reported [ 42 , 43 , 44 ]. Increased expression levels of BLK [ 42 ] and MS4A1 [ 43 ] have been reported in lung adenocarcinoma, and BLK and CD19 [ 44 ] have been reported to be significantly correlated with the overall survival in patients with lung adenocarcinoma. Some studies have reported decreased expressions of the genes in NK cell functions in lung cancer.…”

“…In summary, this study presents a comprehensive analysis of the gene [ 43 ] expression profiles for lung adenocarcinoma with synchronous AAH. We also validated sequentially up-regulated genes ( ACSL5 and SERINC2 ) across AAH to ADC and identified differential immune cell profiles in AAH.…”

A DNA methylation profile of long non-coding RNAs can predict OS in prostate cancer

“…Univariate Cox regression analysis was performed to calculate the correlation between methylation level of CpG sites filtered in the above step and patient’s OS, and the p-value < 0.05 was considered in this study. Next, a Least Absolute Shrinkage and Selection Operator (LASSO) regression model was performed to screen the most useful prediction CpG sites, and a methylation-based classifier was constructed for predicting OS based on the sum of CpG site methylation levels weighted by the coefficients [ 12 ]. LASSO regression is a variable selection and shrinkage method for the regression models to identify the variables and relevant regression coefficients, which are established to minimize the prediction error.…”

Risk stratification of lung adenocarcinoma using a nomogram combined with ferroptosis-related LncRNAs and subgroup analysis with immune and N6-methyladenosine modification

“…Lung adenocarcinoma (LUAD) is the subtype of lung cancer with the highest prevalence [ 3 , 4 ]. Despite advancements in surgery, radiotherapy, chemotherapy, and other advanced therapeutics, the prognosis remains poor due to the high heterogeneity of LUAD [ 5 , 6 ]. As such, research into the molecular mechanisms and pathogenesis of LUAD requires further research to develop promising therapies.…”