Zhimin Zheng1, Weijie Deng1, Jiansheng Yang2. 1. Department of Thoracic Surgery, Jinjiang Municipal Hospital, Quanzhou, Fujian Province 362200, China. 2. Department of Thoracic Surgery, The Second Clinical College of Fujian Medical University, Quanzhou, Fujian Province 362000, China.
Abstract
BACKGROUND: The acquisition of invasive tumor cell behavior is considered to be the cornerstone of the metastasis cascade. Thus, genetic markers associated with invasiveness can be stratified according to patient prognosis. In this study, we aimed to identify an invasive genetic trait and study its biological relevance in lung adenocarcinoma. METHODS: 250 TCGA patients with lung adenocarcinoma were used as the training set, and the remaining 250 TCGA patients, 500 ALL TCGA patients, 226 patients with GSE31210, 83 patients with GSE30219, and 127 patients with GSE50081 were used as the verification data sets. Subtype classification of all TCGA lung adenocarcinoma samples was based on invasion-associated genes using the R package ConsensusClusterPlus. Kaplan-Meier curves, LASSO (least absolute contraction and selection operator) method, and univariate and multivariate Cox analysis were used to develop a molecular model for predicting survival. RESULTS: As a consequence, two molecular subtypes for LUAD were first identified from all TCGA all data sets which were significant on survival time. C1 subtype with poor prognosis has higher clinical characteristics of malignancy, higher mutation frequency of KRAS and TP53, and a lower expression of immune regulatory molecules. 2463 differentially expressed invasion genes between C1 and C2 subtypes were obtained, including 580 upregulation genes and 1883 downregulation genes. Functional enrichment analysis found that upregulated genes were associated with the development of tumor pathways, while downregulated genes were more associated with immunity. Furthermore, 5-invasion gene signature was constructed based on 2463 genes, which was validated in four data sets. This signature divided patients into high-risk and low-risk groups, and the LUDA survival rate of the high-risk group is significantly lower than that of the low-risk group. Multivariate Cox analysis revealed that this gene signature was an independent prognostic factor for LUDA. Compared with other existing models, our model has a higher AUC. CONCLUSION: In this study, two subtypes were identified. In addition, we developed a 5-gene signature prognostic risk model, which has a good AUC in the training set and independent validation set and is a model with independent clinical characteristics. Therefore, we recommend using this classifier as a molecular diagnostic test to assess the prognostic risk of patients with LUDA.
BACKGROUND: The acquisition of invasive tumor cell behavior is considered to be the cornerstone of the metastasis cascade. Thus, genetic markers associated with invasiveness can be stratified according to patient prognosis. In this study, we aimed to identify an invasive genetic trait and study its biological relevance in lung adenocarcinoma. METHODS: 250 TCGA patients with lung adenocarcinoma were used as the training set, and the remaining 250 TCGA patients, 500 ALL TCGA patients, 226 patients with GSE31210, 83 patients with GSE30219, and 127 patients with GSE50081 were used as the verification data sets. Subtype classification of all TCGA lung adenocarcinoma samples was based on invasion-associated genes using the R package ConsensusClusterPlus. Kaplan-Meier curves, LASSO (least absolute contraction and selection operator) method, and univariate and multivariate Cox analysis were used to develop a molecular model for predicting survival. RESULTS: As a consequence, two molecular subtypes for LUAD were first identified from all TCGA all data sets which were significant on survival time. C1 subtype with poor prognosis has higher clinical characteristics of malignancy, higher mutation frequency of KRAS and TP53, and a lower expression of immune regulatory molecules. 2463 differentially expressed invasion genes between C1 and C2 subtypes were obtained, including 580 upregulation genes and 1883 downregulation genes. Functional enrichment analysis found that upregulated genes were associated with the development of tumor pathways, while downregulated genes were more associated with immunity. Furthermore, 5-invasion gene signature was constructed based on 2463 genes, which was validated in four data sets. This signature divided patients into high-risk and low-risk groups, and the LUDA survival rate of the high-risk group is significantly lower than that of the low-risk group. Multivariate Cox analysis revealed that this gene signature was an independent prognostic factor for LUDA. Compared with other existing models, our model has a higher AUC. CONCLUSION: In this study, two subtypes were identified. In addition, we developed a 5-gene signature prognostic risk model, which has a good AUC in the training set and independent validation set and is a model with independent clinical characteristics. Therefore, we recommend using this classifier as a molecular diagnostic test to assess the prognostic risk of patients with LUDA.
Authors: A A Alizadeh; M B Eisen; R E Davis; C Ma; I S Lossos; A Rosenwald; J C Boldrick; H Sabet; T Tran; X Yu; J I Powell; L Yang; G E Marti; T Moore; J Hudson; L Lu; D B Lewis; R Tibshirani; G Sherlock; W C Chan; T C Greiner; D D Weisenburger; J O Armitage; R Warnke; R Levy; W Wilson; M R Grever; J C Byrd; D Botstein; P O Brown; L M Staudt Journal: Nature Date: 2000-02-03 Impact factor: 49.962
Authors: D Neil Hayes; Stefano Monti; Giovanni Parmigiani; C Blake Gilks; Katsuhiko Naoki; Arindam Bhattacharjee; Mark A Socinski; Charles Perou; Matthew Meyerson Journal: J Clin Oncol Date: 2006-11-01 Impact factor: 44.544