Abstract A13: Lung Adenocarcinoma Subtypes Based on the Expression of Airway Basal Cell Genes
Authors: Fukui Tomoya , Shaykhiev Renat , Hackett Neil R. , Downey Robert J. , Travis William D. , Crystal Ronald G. 
Published: March 2013

Abstract
Purpose: Lung adenocarcinoma, the most common subtype of lung cancer, is a heterogeneous disease. Biologic heterogeneity of cancer is determined, at least in part, by specific cell populations of the original tissue that contribute to the development of the particular tumor subtypes. Airway epithelium, the primary site of molecular changes leading to the development of lung cancer, is composed of various cell types, including ciliated, intermediate, secretory (mucus-producing and Clara), neuroendocrine, and basal cells (BC). The specific contribution of individual cell types of the airway epithelium to lung cancer heterogeneity to lung adenoCa is unclear. Based on the knowledge that airway BC are the stem/progenitor cells of the human airway epithelium and that molecular features of local stem/progenitor cells contribute to a distinct molecular subtype of various tumors, we hypothesized that a subset of lung adenoCa is characterized by activation of unique molecular features of airway BC linked to a distinct phenotype of lung adenoCa.
Methods: The normal human BC transcriptome was used to define an airway “BC signature” (Hackett et al., PLoS ONE 2011; 6:e18378). The primary data set included the transcriptomes of 182 lung adenoCa (Chitale et al, Oncogene 2009;28:2773). Two independent lung adenoCa transcriptome validation sets included 58 (Bild et al, Nature 2006;439:353) and 327 (Shedden et al, Nat Med 2008;14:822) subjects. Squamous cell carcinoma transcriptomes (n=53) were from Bild et al (Nature 2006). Survival analyses were performed using the Kaplan-Meier method (univariate) and Cox proportional hazard model (multivariate). Differential expression of selected genes between tumor subtypes was validated by immunohistochemistry.
Results: Gene expression analysis identified a subset of lung adenoCa that expressed high levels of airway BC signature genes (“BC-high adenoCa”). Compared to “BC-low adenoCa” (lung adenoCa expressing low levels of the airway BC signature genes), this subset of lung adenoCa exhibited more aggressive features with poorer tumor grade (p&lt;0.001), more advanced pathological tumor stage (p&lt;0.05), larger tumor size (p&lt;0.05), higher frequency of vascular invasion (p&lt;0.004), lymph node metastasis (p&lt;0.04) and a 43 month shorter median survival (log rank p&lt;0.001). Multivariate analysis, in which age, gender, smoking status, pathological stage, adenoCa with lepidic pattern (formerly BAC), and adjuvant therapy were included, demonstrated that high expression of the airway BC signature was an independent prognostic factor associated with shorter survival in lung adenoCa (hazard ratio; 1.59, 95% confidence interval; 1.14–2.22, p&lt;0.008). The strikingly shorter survival of BC-high vs BC-low adenoCa was verified in the 2 independent validation data sets. At the molecular level, BC-high adenoCa displayed higher frequency of KRAS mutations (p&lt;0.04), lower frequency of EGFR mutations (p&lt;0.03) and a distinct differentiation pattern characterized by a suppression of genes related to ciliated and Clara cells, accompanied by a broad activation of genes related to the epithelial-mesenchymal transition program (SNAIL, SLUG, TWIST1, CDH2). Compared to the lung SqCa characterized by overexpression of classical BC genes related to squamous differentiation (TP63, keratin KRT5, KRT6B), BC-high adenoCa exhibited up-regulation of novel BC genes including KRT7, members of the EGFR pathway (amphiregulin, ERBB receptor feedback inhibitor 1), and tissue factor pathway inhibitor 2. In total, 24% of the airway BC signature genes were expressed differentially between these 2 subtypes of lung cancer.
Conclusion: Activation of a unique airway BC program contributes to a distinct, more aggressive, BC-high subtype of human lung adenoCa, a novel subtype of lung adenoCa, which may originate from airway BC.