Construction of the prediction model and evaluation of predicted outcome.

<p>(A) Schematic overview of the strategy used for constructing prediction models and evaluating the predicted outcomes based on gene expression signatures. Kaplan-Meier plots of the overall survival (OS) of the 2predicted groups of lung adenocarcinoma patients in the (B) HM, (C) MGH, (D) Duke, (E) and ACC cohorts. The differences between groups were significant, as indicated by the log-rank test. The + symbols in panels B–E indicate censored data.</p

Clinical and Pathological Features of Lung Adenocarcinoma Cancer Patients.

<p>Abbreviations: TM, Toronto and Memorial Sloan-Kettering Cancer Center; HM, H. Lee Moffit Cancer Center and University of Michigan; MGH, Massachusetts General Hospital; ACC, Aichi Cancer Center; NA, Not available.</p

Development and Validation of a Prognostic Gene-Expression Signature for Lung Adenocarcinoma

<div><p>Although several prognostic signatures have been developed in lung cancer, their application in clinical practice has been limited because they have not been validated in multiple independent data sets. Moreover, the lack of common genes between the signatures makes it difficult to know what biological process may be reflected or measured by the signature. By using classical data exploration approach with gene expression data from patients with lung adenocarcinoma (n = 186), we uncovered two distinct subgroups of lung adenocarcinoma and identified prognostic 193-gene gene expression signature associated with two subgroups. The signature was validated in 4 independent lung adenocarcinoma cohorts, including 556 patients. In multivariate analysis, the signature was an independent predictor of overall survival (hazard ratio, 2.4; 95% confidence interval, 1.2 to 4.8; <em>p</em> = 0.01). An integrated analysis of the signature revealed that <em>E2F1</em> plays key roles in regulating genes in the signature. Subset analysis demonstrated that the gene signature could identify high-risk patients in early stage (stage I disease), and patients who would have benefit of adjuvant chemotherapy. Thus, our study provided evidence for molecular basis of clinically relevant two distinct two subtypes of lung adenocarcinoma.</p> </div

Univariate and Multivariate Cox Proportional Hazard Regression Analyses of Overall Survival in the ACC Cohort (n = 117).

<p>Abbreviations: CI, confidence interval; M, male; F (sex), female; WT, wild-type; F (gene signature), fast-growing; S, slow-growing.</p

Hierarchical clustering analysis of gene expression data from the discovery cohort.

<p>(A) Hierarchical clustering of gene-expression data from 186 patients with lung adenocarcinoma in the discovery (Toronto/Canada and Memorial Sloan-Kettering Cancer Center [TM]) cohort. Genes with an expression level that was at least 2-fold different from the median value across tissues in at least 20 tissues were selected for hierarchical clustering analysis (3036 gene features). The data are presented in matrix format, where each row represents an individual gene and each column represents a tissue. Each cell in the matrix represents the expression level of a gene feature in an individual tissue. The red and green color in the cells reflects the genes’ relatively high and low expression levels, respectively, as indicated in the scale bar (a log2-transformed scale). Kaplan-Meier plots of the (B) overall survival (OS) and (C) recurrence-free survival (RFS) of patients with lung adenocarcinoma in the TM cohort. Patients were stratified according to gene-expression patterns (creating two clusters, C1 and C2). RFS data are currently not available from 20 patients.</p

Significant association of the 2 gene-expression signature subtypes with adjuvant chemotherapy.

<p>(A) Kaplan-Meier plots of the overall survival (OS) of adenocarcinoma patients in the TM and HM cohorts. The data were plotted according to the prognostic gene-expression signature (subgroups F and S). Kaplan-Meier plots of patients in (B) subgroup F or (C) subgroup S with stage III disease. Data were plotted according to whether patients were treated with or without adjuvant chemotherapy (CTX).</p

Cross comparison of gene lists from 4 independent cohorts of lung adenocarcinoma patients.

<p>(A) Venn diagram of genes whose expression is significantly different between subgroups F and S. a univariate test (2-sample t-test) with multivariate permutation test (10,000 random permutations) was applied. In each comparison, we applied a cut-off P-value of less than 0.001 to retain genes whose expression was significantly different between the 2 groups of tissues examined. (B) Expression patterns of selected genes shared in 4 lung adenocarcinoma cohorts. The expression of 470 genes is commonly up- or down-regulated in all 4 cohorts. Colored bars at the top of the heat map represent samples as indicated.</p

Kaplan–Meier Plots of DFS rates of all patients grouped by AJCC stage.

<p>Patients were stratified by risk level according to the five predictors (A to E). <i>P</i> values are based on the log-rank test.</p

CONSORT flow diagram for selection of prediction models.

<p>CONSORT flow diagram for selection of prediction models.</p

Kaplan–Meier survival plots of the DFS rates of VI patients stratified by risk level according to the five genomic predictors (A to E).

<p><i>P</i> values are based on the log-rank test. Int, intermediate.</p