Dose

100%

50%

0%

IC50, EC50

Dose response curve

22 Days MEK Inhibitor 22 Days Vehicle Control

Growth of Tumor Xenografts in Mice after Drug Treatment

CK19

P-H3DAPI DAPI P-ERK

CK19

DAPI P-H3

CK19

DAPI P-ERK

CK19

L3.6pl

w/o MEK-inhibitor

L3.6pl

with MEK-inhibitor

Primary 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 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)

gain in the test DNA

balanced in the test DNA

loss in the test DNA

Test DNA isolated fromcancer cells(Cy3)

Reference DNAisolated fromcontrol(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

1 3 5 7 9 11 13 15 17 19 21X

Panc - 4.21

-1.5

-0.5

0.5

1.5

2.5

Lo

g2

Me

an

Ra

w R

ati

oExample 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 regressions

Acknowledgements:Martin McMahon (my boss)

McMahon Lab

Helen Diller Family Comprehensive Cancer Center UCSF