GSE109743
Bronchial premalignant lesions have distinct molecular subtypes associated with future histologic progression
Exposure to cigarette smoke creates a field of injury throughout the entire respiratory tract inducing genomic alterations that lead to an “at-risk” airway where and lung cancers develop.  Lung squamous cell carcinoma (SCC) arises in the epithelial layer of the bronchial airways and is often preceded by the development of premalignant lesions(PMLs). The presence of high-grade persistent or progressive PMLs is a marker of increased lung cancer risk both at the lesion site elsewhere in the lung.  Effective tools to identify and treat premalignant lesions at highest risk of progression to invasive carcinoma are lacking.  We profiled via RNA-Seq airway brushing and biopsies (divided into two cohorts: discovery and validation) obtained from high-risk smokers undergoing lung cancer screening via serial auto-fluorescence bronchoscopy procedures. We identified four distinct molecular subtypes (Proliferative, Inflammatory, Secretory, and Normal) in the bronchial biopsies that correspond to a spectrum of biological and morphological alterations.   The Proliferative subtype was enriched with dysplastic PMLs from current smokers that exhibit up-regulation of KRT5 and KI67 as well as metabolic and cell cycle pathways, and down-regulation of cilium-associated processes and FOXJ1 expression.  Molecular subtype classification in the validation cohort biopsies replicated these significant clinical and biological associations.  Airway brushes from normal fluorescing areas of the large airway classified as the Proliferative subtype specifically predicts the presence of biopsies of this same subtype.  Within the Proliferative subtype, genes associated with interferon signaling and antigen processing and presentation were observed to be down-regulated among dysplastic biopsies that persistent or progress in the future.  Innate and adaptive immune cells were computationally predicted to be depleted in these biopsies and this was confirmed via immunofluorescence staining of adjacent biopsies.  These findings provide a proof of concept that molecular biomarkers of endobronchial biopsies can enhance histopathological grading and that immunoprevention strategies are an important future direction in intercepting the progression of PMLs to lung cancer. Overall design: Endobronchial biopsies and brushings were obtained from high-risk subjects undergoing lung cancer screening at approximately 1-year intervals by white light and auto-fluorescence bronchoscopy and computed tomography at the Roswell Park Cancer Institute in Buffalo, NY.  Subjects were selected that had biopsies collected in repeat locations via serial bronchoscopies. mRNA sequencing was performed on a discovery cohort (DC) of samples comprising of endobronchial biopsies and brushes collected between 2010 and 2012 (n=30 subjects, n=197 biopsies, and n=91 brushings).  mRNA sequencing was subsequently performed on a validation cohort (VC) of samples comprising of endobronchial biopsies and brushes collected between 2010 and 2015 (n=20 subjects, n=111 biopsies, and n=49 brushings). The submitter declares that the raw data will be made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap) due to patient privacy concerns.