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Dose response curve Response 100% 50% 0% IC50, EC50 Dose Growth of Tumor Xenografts in Mice after Drug Treatment 22 Days MEK Inhibitor 22 Days Vehicle Control Primary tumor sections: DAPI P-H3 DAPI P-ERK L3.6pl w/o MEK-inhibitor CK19 CK19 L3.6pl DAPI P-H3 DAPI P-ERK with MEK-inhibitor CK19 CK19 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 Thymine Guanine binds to Cytosine In 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) Array CGH (aCGH): a microarray based technology Human chromosomes become fragmentized Reference DNA isolated from control (Cy5) Test DNA isolated from cancer cells (Cy3) gain in the test DNA loss in the test DNA balanced in the test DNA DNA fragments become spotted on glass slide Image (CCD camera) and data analysis using software Example of an aCGH profile: Array contains roughly 2500 printed DNA fragments covering the human genome at 1.4 Mbp resolution. Log2 Mean Raw Ratio 1 2.5 3 5 7 9 11 13 15 17 19 21X Panc - 4.21 1.5 0.5 -0.5 -1.5 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 regressions Acknowledgements: Martin McMahon (my boss) McMahon Lab Helen Diller Family Comprehensive Cancer Center UCSF