Abstract A05: Bronchial premalignant lesions have distinct molecular subtypes associated with future histologic progression
Authors: Beane Jennifer E. , Mazzilli Sarah , Tassinari Ania , Campbell Joshua , Moy Christopher , Schaffer Michael , Perdomo Catalina , Jenkins David , Pine Mary Beth , Liu Gang , Zhang Sherry , Lin Hangqio , Vick Jessica , Johnson Evan , Platero Suso , Stevenson Christopher , Lenburg Marc , Reid Mary , Dhillon Samjot , Spira Avrum 
Published: February 2019

Abstract
Squamous cell carcinoma (SCC) of the lung is a leading cause of cancer mortality in the U.S. due to late-stage diagnosis and lack of effective treatments. Lung SCC arises in the epithelial layer of the bronchial airways and is often preceded by the development of premalignant lesions (PMLs). The molecular alterations involved in the progression of PMLs to lung SCC are not clearly understood as not all PMLs progress to carcinoma. We hypothesize that molecular characterization of PMLs and nonlesion areas will allow us to identify alterations associated with histology and lesion progression.
We used mRNA sequencing to profile biopsies obtained from high-risk smokers undergoing lung cancer screening by auto-fluorescence bronchoscopy and CT at the Roswell Park Cancer Institute in Buffalo, NY. For each subject (n=49), a brushing of the airway field (normal fluorescing area) and endobronchial biopsies were collected over time in repeat locations with serial bronchoscopies. The discovery cohort, included 29 subjects, 197 biopsies, and 91 brushes, while the validation cohort included 20 subjects, 111 biopsies and 49 brushes. The mRNA-Seq data were aligned to hg19 using STAR, and gene/transcript levels were summarized using RSEM. Immune, stromal, and epithelial cell content were inferred using xCell. Biopsy molecular subtypes were discovered using consensus clustering in the discovery cohort and used to train a nearest centroid subtype predictor to assign subtypes in the validation cohort and the brushes.
We identified four distinct molecular subtypes in the discovery cohort bronchial biopsies using genes (n=3936) co-expressed across the the discovery cohort brushes and biopsies and two additional RNA-seq lung SCC-related datasets. One of the four molecular subtypes is enriched (p&lt;0.001) for samples with dysplasia histology, high basal cell content, and the classic SCC tumor subtype. These associations are replicated in the validation cohort. There is also significant concordance between the molecular subtypes defined in the biopsies and their corresponding brush from the normal-appearing airway. Genes associated with IFN-gamma signaling and T cell-mediated immunity were observed to be downregulated among lesions that remained stable or progressed to more severe histology within the high-grade subtype. Staining adjacent biopsies to those profiled revealed that decreased expression of genes related to T cell-mediated immunity is associated with decreased numbers of CD4+ and CD8+T cells within the lesions and the surrounding tissue.
We have identified four molecular subclasses of premalignant lung SCC lesions that may associate with prognosis. Molecular classification of PMLs may lead to biomarkers of future disease progression that could be used to stratify patients into prevention trials and to monitor efficacy of the treatment. Additionally, the results suggest that personalized lung cancer chemoprevention that targets specific cancer-related pathways or the immune system may have potential therapeutic benefits.
Citation Format: Jennifer E. Beane, Sarah Mazzilli, Ania Tassinari, Joshua Campbell, Christopher Moy, Michael Schaffer, Catalina Perdomo, David Jenkins, Mary Beth Pine, Gang Liu, Sherry Zhang, Hangqio Lin, Jessica Vick, Evan Johnson, Suso Platero, Christopher Stevenson, Marc Lenburg, Mary Reid, Samjot Dhillon, Avrum Spira. Bronchial premalignant lesions have distinct molecular subtypes associated with future histologic progression [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr A05.