Slide 1Slide 2Slide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Dose100%50%0%IC50, EC50Dose response curve22 Days MEK Inhibitor 22 Days Vehicle ControlGrowth of Tumor Xenografts in Mice after Drug TreatmentCK19P-H3DAPI DAPI P-ERKCK19DAPI P-H3CK19DAPI P-ERKCK19L3.6pl w/o MEK-inhibitorL3.6plwith MEK-inhibitorPrimary tumor sections:Drug Sensitivities:•IC50 values of CI-1040 for 22 pancreatic cancer cell lines were measured.•The cell lines rank from sensitive to resistant: low IC50  sensitive; high IC50  resistant•Why is that important to know?Patients show often various degrees of sensitivities to drugs.It would not be smart to treat a patient with a drug if he is not sensitive enough (side effects).It would be good to have a knowledge about drug sensivities of a patient in advance.How can we get such a knowledge? measuring biomarkers for drug sensitivities (gene expression profiling, comparative genomic hybridization, proteomics)Binding of a strand of DNA to a complementary strand of DNA or RNA:Adenine binds to ThymineGuanine binds to CytosineIn RNA Thymine is replaced by Uracil.The binding or annealing of complementary strands is highly sequence specific.Microarray technology:ExamplesGene expression profilingArray based comparative genomic hybridization (aCGH)gain in the test DNA balanced in the test DNAloss in the test DNATest DNA isolated fromcancer cells(Cy3)Reference DNAisolated fromcontrol(Cy5)Image (CCD camera)and data analysis using softwareArray CGH (aCGH): a microarray based technologyHuman chromosomes become fragmentizedDNA fragments become spotted on glass slide1 3 5 7 9 11 13 15 17 19 21XPanc - 4.21-1.5-0.50.51.52.5Log2 Mean Raw RatioExample of an aCGH profile: Array contains roughly 2500 printed DNA fragments covering the human genome at 1.4 Mbp resolution. Ratio > 0  Tumor DNA is overrepresented: gain in copy number (amplifications)Ratio < 0  Tumor DNA is underrepresented: loss in copy number (deletions)Combining drug sensitivities with array CGH:•We have measured copy number changes in 22 cell lines.•We also determined the drug sensitivities of those cell lines to CI-1040.Question: Can we find copy number changes that correlate with sensitivity or resistance to CI-1040?More precise: Can we find signatures of copy number changes that characterize sensitive or resistant cell lines?Answer: Student T-test; linear regressionsAcknowledgements:Martin McMahon (my boss)McMahon LabHelen Diller Family Comprehensive Cancer Center