Assessing lung cancer risk in bronchial dysplasia by identification of prognostic gene expression profiles
Authors: Coldren Christopher D. , Sugita Michio , Gao Dexiang , Miller York E. , Merrick Daniel T. , Franklin Wilbur A. , Keith Robert L. , Hirsch Fred R. , Geraci Mark W. , Nemenoff Raphael A. 
Published: May 2015

Abstract
Bronchial dysplasia (BD) is a premalignant lesion that develops frequently in smokers and is thought to be a direct precursor of squamous cell carcinoma of the lung. Identification of BD lesions that are associated with high risk for progression to cancer is important so that adequate follow-up and establishment of chemopreventive therapy can be provided. We have reviewed specimens from the Colorado SPORE in lung cancer tissue bank to determine if persistence of BD over time is related to the initial degree of histologic atypia and the development of lung cancer, and to select appropriate groups of BD to assess for the presence of potential prognostic markers by microarray gene expression analysis.
Histologic diagnoses (1=normal, 2=hyperplasia, 3=metaplasia, 4-6=mild, moderate and severe dysplasia, 7=CIS and 8=cancer) and clinical data from 186 subjects enrolled in SPORE bronchoscopy protocols that underwent at least two bronchoscopies were obtained from the SPORE database. 2,847 biopsies from 1,119 sites were assigned to baseline diagnostic groups according to the first non-normal biopsy obtained at a site. Atypia in follow-up biopsies was assessed per annum. Aditionally, RNA was extracted from bronchoscopic biopsies snap frozen in liquid nitrogen at collection. Cryostat sections were produced to establish histology and RNA was then extracted from the remaining tissue for gene expression analysis. Gene expression profiles for persistent and non-persistent BDs are being assessed on the Affymetrix Human Gene 1.0 ST array.
A direct correlation between the degree of atypia at baseline and degree of atypia at follow-up was found at all time intervals (.25-1, 1-2, 2-3, 3-4 and &gt;4 years follow-up biopsies) except for the 3-4 year timeframe. Biopsy sites from subjects with squamous cell lung cancer diagnosed prior to, during or after participation in bronchoscopy studies showed one full point higher histologic diagnosis on follow-up than sites with equivalent baseline diagnoses in subjects without known cancer. An interim assessment of data quality in 20 RNA specimens from baseline biopsies processed for gene expression analysis has been completed. Quality measurements show that distribution of signal intensity is similar across the cohort indicating comparability of specimens from the different study groups as defined by their histologic diagnoses on follow-up biopsy. Expression data from 40 specimens is targeted for the final dataset.
The degree of atypia in BD is higher at sites with higher levels of a baseline atypia and in subjects with a history of or subsequent development of squamous cell carcinoma of the lung. These features suggest that persistence of BD over time may be indicative of risk for the development of invasive lung cancer. Preliminary data from ongoing gene expression analyses of BD of differing outcomes indicates that consistent data quality can be produced across the specimen types to be studied. This suggests that the gene expression analysis will be adequate to detect differentially expressed genes with the potential to provide prognostic information in BD and reveal targets for the chemoprevention of lung cancer.