The identification of individuals at high risk for lung cancer is critical for individualized clinical management and is important for the identification of suitable subjects for chemoprevention trials. Using chromosome in situ hybridization (CISH) technology, we previously demonstrated the presence of chromosomal instability and multifocal clonal/subclonal outgrowths in the bronchial epithelium of current and former smokers. We also verified the presence of these clonal/subclonal outgrowths in normal-appearing bronchial epithelium in lung cancer resections using fluorescence inter-simple sequence repeat PCR (FISSR-PCR) analysis, a DNA fingerprinting methodology. To evaluate and compare FISSR-PCR and CISH technologies for accessing genetic instability and clonal/subclonal outgrowth, we subjected frozen bronchial biopsies obtained prior to entry onto a chemoprevention trial to FISSR-PCR analysis from sixteen (16) current smokers without lung cancer. The group of biopsies from these same individuals have previously been analyzed by CISH and exhibited a wide range of chromosomal changes. Multiple regions (i.e., 1-4 areas each) of bronchial epithelium and stroma were microdissected, and purified genomic DNA was analyzed by FISSR-PCR using three sets of primers ((CA)8RG, (CA)8RY, and (AGC)4Y), providing a maximum of 350 informative DNA bands of varying lengths. Overall, we detected from 0 to 55 total band changes per microdissected epithelial region (median = 1.6 per 100 DNA bands). Different regions within the same bronchial biopsies showed both common and distinct DNA band changes, suggesting subclonal variations even within a single biopsy. We also detected from 0-20 total band changes per microdissected stromal region (median = 1.0 per 100 DNA bands), suggesting the presence of clonal outgrowths even in the stroma. Interestingly, bronchial biopsies with high clonal frequencies showed increased clonal change in the associated stroma (p =0.04, two-tailed chi square). Importantly, bronchial biopsies from individuals showing high clonal changes by FISSR-PCR also showed evidence of high clonal change by CISH (R2 = 0.3). These results confirm the existence of clonal/subclonal outgrowths in both the bronchial epithelium and stroma of smokers. With future improvements in microdissection, automated genomic DNA extraction, and DNA sequencing, FISSR-PCR has potential to be a sensitive method with high dynamic range to detect clonal/subclonal outgrowths in lung tissue. Such a methodology may be of use in identifying individuals at high risk for developing lung cancer. Supported in part by DAMD17-02-1-0706, NIH/NCI CA-91844, and EDRN NCI CA-86390.

[Proc Amer Assoc Cancer Res, Volume 47, 2006]