Although lung cancer is the leading cause of cancer death in the United States and is ranked second only to bladder cancer in proportion of cases due to past occupational exposures, the genetic changes associated with progression of the disease are not well understood. We used Spectral Karyotyping (SKY), mapping with fluorescently labeled genomic clones (FISH), comparative genomic hybridization (CGH) on a BAC array, 5 kB NimbleGen CGH array, expression array, real time polymerase chain reaction and Western blot to analyze 15 primary adenocarcinoma and 9 pairs of high and low invasive cell cultures to detect molecular changes. The medial portion of chromosome 4 was deleted in 66.0% + 12.0 of the cell lines. FISH mapping and CGH array further narrowed the region of genetic alteration. The minimal region of deletion occurred at 39.6 centimorgans (cM). Duplication of chromosome 4 at 10 to 35 cM occurred in 68.0% + 11.0 of the cell cultures. Expression array analysis demonstrated increased expression of a proposed oncogene, Kruppel-like factor 4, tyrosine kinase receptor EphA2, Cyclin E, and a group of ubiquintination factors. Analysis of genes within the deleted region of chromosome 4 demonstrated decreased expression of the cell cycle inhibitory factor p16 at 39 cM, the NR4A3 receptor involved in apoptosis at 42.7 cM, the differentiation factor Forkhead Box D3 at 45 cM and the apoptotic factor Cathepsin D at 50 cM. Western blot analysis showed that Cathepsin D protein was produced at very low levels and was not processed to the mature form. IGFII receptor, the processing protein for Cathepsin D, was also expressed at very low levels. The homologous linkage groups on human chromosomes 9p21, 1p36 and 9q are altered in human lung adenocarcinoma. Alteration in copy number and expression of the genes on chromosome 4 may play a functional role in lung cancer development and may aid in the identification of mouse and human lung cancer susceptibility genes.
98th AACR Annual Meeting-- Apr 14-18, 2007; Los Angeles, CA