Lung cancer is the leading cause of cancer related mortality in both men and women. Chromosome 9p deletions and alterations occur early and often in lung cancer. The p16/CDKN2 locus, located on 9p, is suspected to be the major tumor suppressor gene inactivated in this tumor type. The prognosis for lung cancer patients is very poor, as reflected by an overall, 5-year survival rate of only 14%. The poor prognosis is largely due to a historical lack of effective early detection measures. We have previously identified a region of homozygous deletion on the short arm of chromosome 9p at the microsatellite marker D9S126. This region is distinct from the p16/CDKN2 tumor suppressor gene (TSG) locus and lies approximately 2 cM proximal. We proposed that the region harbors a TSG that may be important in lung tumorigenesis. To this end we have employed several techniques to identify genes within this chromosomal region. Currently, we have isolated several expressed sequence tags (ESTs) and genes mapping in or around D9S126. Additionally, we have used immunohistochemistry to analyze the expression of p16 in adenocarcinomas and squamous cell carcinomas of the lung and subsets of these tumors were analyzed for loss of heterozygosity (LOH) with microsatellite markers spanning the short arm of chromosome 9. The immunohistochemistry revealed a significant difference in the percent of tumors positive for p16 with the adenocarcinomas having a higher percentage of positive staining than the squamous cell carcinomas. Loss of heterozygosity analysis demonstrated that the pattern of loss was similar between p16 positive and negative squamous cell carcinomas. However, there were moderately significant differences in the LOH analysis between p16 positive adenocarcinomas and squamous cell carcinomas at some of the markers. Taken together, these data suggest that chromosome 9p may contain other tumor suppressor genes important in lung tumorigenesis and that the different patterns of LOH between squamous cell carcinomas and adenocarcinomas of the lung may indicate their locations. The Cot gene was originally identified by transfection of a human thyroid cancer DNA into SHOK cells. The gene was found to be oncogenic when altered at the 3' end, constitutively activating the protein. Sequencing analysis revealed that wild-type Cot is a MAP kinase kinase kinase expressed in a variety of cells including spleen, thymus, liver, and lung. Cot possesses the unique characteristic of activating multiple cascades, including both proliferative and apoptotic signal transduction pathways such as the MEK-1 and SEK-1 pathways, respectively. In NIH3T3 transfection assays utilizing lung tumor DNA, our lab identified a 3' alteration of Cot similar to the previous reports. We therefore proposed that oncogenic activation of Cot might play a role in lung tumor formation and development. The complete open reading frame of Cot was examined by polymerase chain reaction, single strand conformational polymorphism (PCR-SSCP) analysis in 40 lung tumor cell lines to identify mutations within the sequence. One mutation/polymorphism was identified in a cell line but did not result in an amino acid change. No other point mutations were found which might activate the gene. Using 3' RACE and DNA sequencing to analyze lung tumor cell lines that might harbor truncations or alterations at the 3' end of Cot did not identify any cell lines with activations of the gene through this mechanism. However, expression analysis by RT-PCR from lung tumor cell lines did demonstrate down-regulation of the Cot gene in small cell lung cancer cell lines and non-small cell lung cancer cell lines. In fact, two small cell lung tumor cell lines do not appear to express any Cot gene transcripts. Therefore, we are currently conducting Southern and Western blot analysis with these cell lines to identify genomic rearrangements or protein alterations. These experiments should help to understand the regulation of Cot and its role in cellular apoptosis, proliferation, and tumorigenic potential.