1. Dose Response 100% 50% 0% IC50, EC50 Dose response curve

2. 22 Days MEK Inhibitor22 Days Vehicle Control Growth of Tumor Xenografts in Mice after Drug Treatment

3. CK19 P-H3DAPI P-ERK CK19 DAPIP-H3 CK19 DAPIP-ERK CK19 L3.6pl w/o MEK-inhibitor L3.6pl with MEK-inhibitor Primary tumor sections:

4. 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)

5. 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.

6. Microarray technology: Examples  Gene expression profiling  Array based comparative genomic hybridization (aCGH)

7. gain in the test DNA balanced in the test DNA loss in the test DNA Test DNA isolated from cancer cells (Cy3) Reference DNA isolated from control (Cy5) Image (CCD camera) and data analysis using software Array CGH (aCGH): a microarray based technology Human chromosomes become fragmentized DNA fragments become spotted on glass slide

8. 1 3 5 7 9 11 13 15 17 19 21X Panc - 4.21 -1.5 -0.5 0.5 1.5 2.5 Log2 Mean Raw Ratio Example 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)

9. 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

10. Acknowledgements: Martin McMahon (my boss) McMahon Lab Helen Diller Family Comprehensive Cancer Center UCSF