Gene expression profile of EGFRwt/KRASwt/ALKwt lung adenocarcinoma (“pan-driver-gene-negative” LUAD) and developing a prognostic signature for “pan-driver-gene-negative” LUAD. Gene expression profile of EGFRwt/KRASwt/ALKwt lung adenocarcinoma (“pan-driver-gene-negative” LUAD) and developing a prognostic signature for “pan-driver-gene-negative” LUAD

For developing a accurate prognostic signature for “pan-driver-gene-negative” LUAD, we employed whole genome microarray expression profiling as a discovery platform to identify candidate genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis based on whole-genome microarrays indicated that the Wnt/β-catenin pathway was activated in “pan-driver-gene-negative” LUAD. Furthermore, the Wnt/β-catenin-pathway-based gene expression profiles revealed 39 transcripts differentially expressed by diagnostic status, with 30 genes being upregulated and 9 downregulated. Finally, a Wnt/β-catenin-pathway-based signature (CSDW) comprising 4 genes (β-catenin, Wnt2b, DVL3 and SOX9) was developed to classify patients into high-risk and low-risk groups in the training cohort. Patients with high-risk scores in the training cohort had shorter overall survival (hazard ratio [HR] 10·42, 6·46–16·79; p<0·001) than patients with low-risk scores. The CSDW performance was further validated in an internal cohort and two external cohorts. The protein expression levels of several hub genes, including β-catenin, SOX9, DVL3 and Wnt2b, were strongly correlated with lymphatic metastasis and distant organ metastasis. Furthermore, a nomogram comprising CSDW and other variables was generated to predict progression-free survival and overall survival in the training cohort and performed well in the three independent validation cohorts (C-index: 0·725, 0·697 and 0·693, respectively). For developing a accurate prognostic signature for “pan-driver-gene-negative” LUAD, we employed whole genome microarray expression profiling as a discovery platform to identify candidate genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis based on whole-genome microarrays indicated that the Wnt/β-catenin pathway was activated in “pan-driver-gene-negative” LUAD. Furthermore, the Wnt/β-catenin-pathway-based gene expression profiles revealed 39 transcripts differentially expressed by diagnostic status, with 30 genes being upregulated and 9 downregulated. Finally, a Wnt/β-catenin-pathway-based signature (CSDW) comprising 4 genes (β-catenin, Wnt2b, DVL3 and SOX9) was developed to classify patients into high-risk and low-risk groups in the training cohort. Patients with high-risk scores in the training cohort had shorter overall survival (hazard ratio [HR] 10·42, 6·46–16·79; p<0·001) than patients with low-risk scores. The CSDW performance was further validated in an internal cohort and two external cohorts. The protein expression levels of several hub genes, including β-catenin, SOX9, DVL3 and Wnt2b, were strongly correlated with lymphatic metastasis and distant organ metastasis. Furthermore, a nomogram comprising CSDW and other variables was generated to predict progression-free survival and overall survival in the training cohort and performed well in the three independent validation cohorts (C-index: 0·725, 0·697 and 0·693, respectively). Overall design: In this multicenter analysis, we collected 626 “pan-driver-gene-negative” LUAD samples from three independent hospitals. In the discovery phase, we profiled the mRNA expression of each candidate gene using genome-wide microarrays in 52 paired LUAD and adjacent normal tissues. In the training phase, tissue microarrays (TMAs) and LASSO Cox regression analysis were applied to further screen candidate molecules in 189 patients (SYSUFH set). In the validation phase, one internal cohort (SYSUFH set, n=182) and two external cohorts (Sun Yat-sen University Cancer Center (SYSUCC) set, n=152; WUHAN set, n=103) were used to validate our novel prognostic signature.

为开发针对泛驱动基因阴性肺腺癌（LUAD）的精准预后特征，本研究以全基因组微阵列表达谱作为发现平台以筛选候选基因。基于全基因组微阵列的京都基因与基因组百科全书（KEGG）通路富集分析显示，Wnt/β-连环蛋白通路在泛驱动基因阴性肺腺癌中被激活。进一步基于Wnt/β-连环蛋白通路的基因表达谱分析发现，39个转录本的表达水平随诊断状态呈现显著差异，其中30个基因上调、9个基因下调。最终，本研究构建了一种基于Wnt/β-连环蛋白通路的预后特征（CSDW），包含4个核心基因（β-连环蛋白、Wnt2b、DVL3及SOX9），可在训练队列中将患者划分为高风险组与低风险组。训练队列中高风险评分患者的总生存期显著短于低风险评分患者（风险比[HR]=10.42，95%置信区间6.46~16.79；p<0.001）。CSDW的预后效能随后在1个内部队列与2个外部队列中得到验证。包括β-连环蛋白、SOX9、DVL3及Wnt2b在内的多个核心枢纽基因的蛋白表达水平与淋巴结转移及远处器官转移显著相关。此外，本研究还构建了包含CSDW及其他临床变量的列线图，用于预测训练队列患者的无进展生存期与总生存期，且该列线图在3个独立验证队列中均表现出良好的预测效能（一致性指数[C-index]分别为0.725、0.697及0.693）。
为开发针对泛驱动基因阴性肺腺癌（LUAD）的精准预后特征，本研究以全基因组微阵列表达谱作为发现平台以筛选候选基因。基于全基因组微阵列的京都基因与基因组百科全书（KEGG）通路富集分析显示，Wnt/β-连环蛋白通路在泛驱动基因阴性肺腺癌中被激活。进一步基于Wnt/β-连环蛋白通路的基因表达谱分析发现，39个转录本的表达水平随诊断状态呈现显著差异，其中30个基因上调、9个基因下调。最终，本研究构建了一种基于Wnt/β-连环蛋白通路的预后特征（CSDW），包含4个核心基因（β-连环蛋白、Wnt2b、DVL3及SOX9），可在训练队列中将患者划分为高风险组与低风险组。训练队列中高风险评分患者的总生存期显著短于低风险评分患者（风险比[HR]=10.42，95%置信区间6.46~16.79；p<0.001）。CSDW的预后效能随后在1个内部队列与2个外部队列中得到验证。包括β-连环蛋白、SOX9、DVL3及Wnt2b在内的多个核心枢纽基因的蛋白表达水平与淋巴结转移及远处器官转移显著相关。此外，本研究还构建了包含CSDW及其他临床变量的列线图，用于预测训练队列患者的无进展生存期与总生存期，且该列线图在3个独立验证队列中均表现出良好的预测效能（一致性指数[C-index]分别为0.725、0.697及0.693）。
研究设计：本多中心分析共纳入来自3家独立医院的626例泛驱动基因阴性肺腺癌样本。发现阶段：采用全基因组微阵列对52例配对肺腺癌及癌旁正常组织的候选基因mRNA表达谱进行检测；训练阶段：对189例患者（SYSUFH队列）采用组织微阵列（TMAs）及最小绝对收缩和选择算子-考克斯（LASSO Cox）回归分析进一步筛选候选分子；验证阶段：采用1个内部队列（SYSUFH队列，n=182）及2个外部队列（中山大学肿瘤防治中心[SYSUCC]队列，n=152；武汉队列，n=103）对本研究构建的新型预后特征进行验证。