Dynamic data of drug response in cell line models of HER2-low breast cancer
The establishment of mathematical models depends on the availability of quantitative and time-resolved data covering all relevant reactions within the signaling network. This workpackage will contribute to unraveling key regulatory mechanisms controlling response towards novel EGFR/ERBB inhibitors. To this end, we will unravel information processing through signaling networks employing time-resolved perturbation experiments by targeted proteomics. Monolayer cultures of breast cancer cell lines will be challenged with e.g. BTC, AREG, and Heregulin-1ß (HRG) and signal modulation after inhibition with RG7116, pertuzumab, and RG7160 will be determined. Responses will be monitored at the receptor phosphorylation level as well as at the level of downstream signaling using reverse phase protein arrays (RPPA) as targeted proteomics approach. In addition, genome-wide transcriptional responses will be determined at selected time points to comprehensively assess response towards different stimuli. To evaluate cellular decision-making also at a functional and phenotypic level, corresponding assays (migration, apoptosis, cell cycle, metabolism) will be carried out in WP2. Quantitative data obtained by RPPA will be used to establish detailed mechanistic models describing the response of signaling pathways towards targeted inhibition by integrating also effects observed on the level of gene regulation.
Based on models developed for single drugs (WP3), combinatory drug treatments to fully inhibit the EGFR/ERBB module will be predicted and experimentally tested using the approach described above. This strategy will also be employed to study drug impact in an ERBB3-positive TNBCa cell line, RG7116R ER+ cell lines, TrasR BT474 as well as in TamR MCF-7 cell lines provided by WP2. Candidate biomarkers mediating response or resistance identified by mathematical modeling will be analyzed in patient samples (WP4).