From the Lab to the Clinic: Gene-Expression Profiles That Are Associated with Mek-Inhibitor Sensitivity In Vitro Are Coordinately Co-Expressed in Breast Cancer Biopsy Samples from the I-SPY Trial (CALGB 150007/150012, ACRIN 6657).
Authors: Wolf D. , Das D. , Lenburg M. , Paquette J. , Spellman P. , Gray J. , Gray J. , Pusztai L. , Symmans F. , Hatzis C. , Esserman L. , van 't Veer L. , I-SPY Investigators . 
Published: December 2010

Abstract
There is increasing appreciation that response to breast cancer therapy is dependent on the specific characteristics of each tumor, as has also been observed in the first analyses of 221 patients treated by standard neo-adjuvant chemotherapy in the I-SPY 1 TRIAL (CALGB 150007/150012, ACRIN 6657). I-SPY 1 has collected full-genome gene expression data on pre-treatment biopsies as well as outcome data for initial tumor response (pathological assessment) and 3-year outcome data. In addition, we have established an in vitro high-throughput system using 50 breast cancer cell lines that can be used to identify gene-expression patterns predictive of drug sensitivity using 'Adaptive Splines'. Though several groups are using cell lines to develop drug response predictors, there is understandable skepticism as to whether the cancer cell lines have retained sufficient similarity to in vivo tumors to make such an endeavor successful.Methods: We used the in vitro cell lines to identify molecular markers of sensitivity to the MEK inhibitor CI1040. We next used the molecular data collected in I-SPY 1, in particular Affymetrix U133A data from 121 patients, to see whether subgroups could be identified among the ISPY patients that vary according to the expression of genes in this signature. In addition, we used the network visualization tool, EGAN, to identify biological networks among the significant predictors of CI-1040 sensitivity or resistance.Results: Analysis of in vitro data using adaptive splines identified 406 genes predictive of response to CI1040, of which 135 and 271 were expressed more highly in CI1040-resistant or -sensitive cell lines respectively. EGAN analyses of these predictors revealed multiple subnetworks and pathways as important. Some of these expression patterns could be corroborated in additional datasets. When we clustered the gene expression data from biopsies using the best linear-classifier based gene predictors of CI1040 sensitivity, the genes and patients each divided into two classes. Notably, most of the genes expressed more highly in the CI-1040-resistant cell lines formed one cluster, while most of the genes expressed more highly in the sensitive cell lines formed another cluster (p&lt;&lt;0.001; Fisher Exact Test), a strong indicator that these genes are similarly co-expressed in both cell lines and tumor samples. Preliminary results indicate that roughly a third of patients show a pattern of gene-expression that is similar to the CI1040-sensitive cell lines.Conclusion: The expression of genes identified to associate with CI1040 sensitivity in vitro show a similar pattern of co-expression in I-SPY patient samples. These data suggest that this CI1040-sensitivity predictor should be tested for its ability to predict the therapeutic response among patients receiving CI1040 (or other drugs in this class). The I-SPY 2 trial will include phase II targeted drugs for which predictor gene sets will be derived from our in vitro system and prospectively tested in patients receiving that treatment.
Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2042.