Exposure to genotoxic carcinogens in tobacco smoke is a major cause of lung cancer. However, the effect this has on DNA copy number and genomic stability during lung carcinogenesis is unclear. Here we used bacterial artificial chromosome array-based comparative genomic hybridization to examine the effect of NNK, a potent human lung carcinogen present in tobacco smoke, on the major genomic changes occurring during mouse lung adenocarcinogenesis. Observed were significantly more gross chromosomal changes in NNK-induced tumors compared with the spontaneous tumors. An average of 5.6 chromosomes were affected by large-scale changes in DNA copy number per NNK-induced tumor compared with only 2.0 in spontaneous lung tumors (p = 0.017). Further analysis showed that gains on chromosomes 6 and 8, and losses on chromosomes 11 and 14 were more common in NNK-induced tumors (p <= 0.002). The changes on chromosomes 8, 11, and 14 were positively (p <= 0.001) associated with the degree of chromosome instability (CIN). This association was less significant for gains on chromosomes 6 and 12 (p = 0.035). In contrast, loss of distal chromosome 4 was very frequent (71%) in both NNK-induced and spontaneous tumors, and showed no association with CIN phenotype. Each of these chromosomes contains sites of orthology with those altered in human lung adenocarcinomas, suggesting similar roles in human lung cancer. We next investigated the mechanism of NNK-induced CIN and found that a genotoxic metabolite of this carcinogen causes numerous karyotypic changes in lung epithelial cells. With similar changes evident in NNK-induced tumors, this suggests that the persistence of such damage in exposed lung epithelia may initiate CIN during lung carcinogenesis. These results show for the first time that NNK potently induces gross chromosomal alterations in lung adenocarcinogenesis and modulates the evolutionary pathway of these tumors through the recruitment of genes with altered DNA copy number. (c) 2006 Elsevier Inc. All rights reserved.