Abstract 2878: Development of the pre-cancer genome atlas (PCGA) for squamous cell lung carcinoma
Authors: Beane Jennifer E. , Campbell Joshua , Moy Christopher , Perdomo Catalina , Schaffer Michael , Mazzilli Sarah , Geshalter Yaron , Kantrowitz Jacob , Zhang Liye , Jenkins David , Pine Mary Beth , Dhillon Samjot , Liu Gang , Liu Hanqiao , Zhang Sherry , Vick Jessica , Monti Stefano , Johnson Evan , Platero Suso , Lenburg Marc , Reid Mary , Spira Avrum 
Published: August 2015

Abstract
Squamous cell cancer (SCC) of the lung is a leading cause of cancer mortality in the US, 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 events involved in the progression of PMLs to lung SCC are not clearly understood and not all PMLs go on to form carcinoma. By molecularly characterizing PMLs and non-lesion areas in the airway of individuals with PMLs we hypothesize that we will be able to identify early events in the process of lung carcinogenesis that lead to SCC. We used next-generation sequencing to profile bronchial brushings and 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 = 26), we sampled the PML(s) and the mainstem bronchus repeatedly over time (394 +/- 170 days) with serial bronchoscopies (5 +/- 3 biopsies/subject) as the PML progressed towards or regressed away from frank malignancy. mRNA-Seq (n = 192) and miRNA-Seq (n = 183) were performed on the endobronchial biopsies and brushings and exome-Seq was performed on blood DNA from these subjects. RNA-seq data was aligned to the hg19 and gene/transcript levels were summarized using RSEM/Ensembl 74 or Bedtools/ mirBase 18. Single nucleotide variants were quantified using a modified PRADA pipeline and GATK. We identified gene and miRNA expression changes as well as pathways that are associated with biopsy histological grade as well as progressive/stable disease. H&E stains of PMLs clustering with lesions of dissimilar grades were examined to show that molecular classification provides complementary information to pathological grading. Genes altered in the normal airway in the presence of a PML were significantly concordantly enriched with genes identified in the biopsies demonstrating a strong relationship between the PMLs and the field of injury. In addition, cancer-associated missense and loss-of-function mutations were detected in PMLs. One individual had cancer-associated mutations at the initial time point in a single moderate dysplastic PML. Upon resampling ∼40 months later, the PML had progressed to an in situ carcinoma while gaining additional mutations. Furthermore, an adjacent PML at this second time point, also in situ carcinoma, had a significantly overlapping set of mutations with the original lesion suggesting that clonal expansion and invasion occurred between temporal samplings. The multiomic characterization of PMLs reveals gene and miRNA expression changes and somatic mutations that are associated with the lesion severity and progressive disease. These studies provide insights into the early molecular events in the process of lung carcinogenesis and may be predictors of lung cancer risk and lesion progression as well as novel candidates for targeted or preventive therapy.
Citation Format: Jennifer E. Beane, Joshua Campbell, Christopher Moy, Catalina Perdomo, Michael Schaffer, Sarah Mazzilli, Yaron Geshalter, Jacob Kantrowitz, Liye Zhang, David Jenkins, Mary Beth Pine, Samjot Dhillon, Gang Liu, Hanqiao Liu, Sherry Zhang, Jessica Vick, Stefano Monti, Evan Johnson, Suso Platero, Marc Lenburg, Mary Reid, Avrum Spira. Development of the pre-cancer genome atlas (PCGA) for squamous cell lung carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2878. doi:10.1158/1538-7445.AM2015-2878