Finding Biomarkers Specific for Early Stages of Lung Cancer Using SAGE Data

1. Invasive CIS CIS Normal PERMUTATION TEST PERMUTATION TEST Top 2000 Ranked Top 2000 Ranked 79 Finding Biomarkers Specific for Early Stages of Lung Cancer Using SAGE Data Chan, Timothy1, MacAulay, Calum2, Lam, Wan2 , Lam, Stephen2 , Lonergan, Kim2 , Ng, Raymond2. University of British Columbia, Vancouver, Canada BC Cancer Agency, Vancouver, Canada Overview Criteria for CIS Biomarker Desmosomes • Fold change of CIS/Normal average expression must be > 10 • Fold change of CIS/Normal average expression must be > 5 • Fold change of CIS/Metaplasia average expression must be > 2 • Permutation score > 2.35 for both sets (p-value of 0.01) • The 5-year survival rate of an advanced lung cancer patient is only about 10%. • If the cancer is caught early at the CIS (carcinoma in situ) stage, the 5-year survival rate is 90%. • Currently, there are no studies have isolated biomarkers for this elusive CIS stage. Results • We propose using lung SAGE data to isolate genes specific for CIS stages of lung cancer that are not present in bronchial metaplasia tissue. • After applying the above criteria we obtained 18 tags. • 14 had unigene ids and 11 mapped to genes with names. Top 18 Filtered Tags Objective • To find a set of candidate genes that are highly expressed in the CIS stages and lowly expressed in normal tissues, metaplasia tissues, and invasive tissues. • To determine whether these genes are good candidate biomarkers from a biological stand point. • To discover whether the expression level of these genes associated genes lead to the understanding of the inner workings of the early stages of the disease. • Desmocollin 2 and desmoglein 3 are major components of cell adhesion molecules which play an important role in epithelial adhesion. • Other desmosome families of the armadillo proteins (PKPs) and plakins were also found to be higher expressed (refer to boxplots). • Squamous cell carcinoma cells overxpressing desmosomal cadherins have been shown to inhibit invasion. Methodology Other Genes Sample Genes • Othere genes involved include ones involved in EGFR trafficking, phosphatase genes, and a tyrosine kinase receptors. • All the genes were looked up on NCBI’s EST database to find where they are expressed. All these genes were found to be expressed in various tissues. • A calcium-dependent glycoprotein that is a member of the desmocollin subfmaily of the cadherin superfamily • Found primarily in epithelial cells where they constitute the adhesive proteins of the desmosome cell-cell junction anad are required for cell adhesion To conduct our experiment we used 1 metaplasia library, 15 smoked-damaged (normal) libraries, 6 invasive libraries, and 5 CIS libraries. 27 SAGE Conclusion Steps • From our results we were unable to find a clear biomarker found that was exclusive to its tissue type (that is only found or produced by lung). • Our study on the mRNA levels of the intercellular adhesion molecules suggest that when a squamous lung cell enters the early stages of lung cancer, adhesion genes are up regulated. • As it enters the invasive stages, we hypothesize that these cancer cells have obtained the ability to obtain its own nutrients and thus do not need to anchor onto bronchial epithelial tissues. • Interestingly, oral squamous cell carcinoma cells overexpressing desmosomal cadherins have been shown to inhibit invasion. • A calcium-binding transmembrane glycoprotien component of desmosomes in vertebrate and epithelial cells. • A member of the cadherin cell adhesion molecule. Associated Genes *NOTE: pink box is the best mapped tag* Future Directions PKP3 (PLAKOPHILIN 3) • Biological validation involving protein expression is required for our above hypothesis as SAGE only looks at the cell at the mRNA level. • Analysis of other pathways involving the other set of genes need to done. • It would be also interesting to look at the genes that are turned off or down-regulated in CIS stages but abundantly expressed in normal and invasive stages. JUP (Plakoglobin)