Figure (A) Scatterplots of basal gene and protein expression levels for EGFR (left, strongly correlated) and KDR (right, not correlated) in cancer cell lines. (B) Boxplot of Pearson correlations between trametinib IC₅₀ values and basal expression levels of 214 proteins. High expression of phosphorylated MEK is strongly related to trametinib response.

Identifying drug-response biomarkers is essential for selecting which patients are most likely to respond to novel anti-cancer drugs. As an extension of the established Oncolines bioinformatics analyses services, we have launched ProteomicsProfiler™. Similar to the existing bioinformatics services, such as gene mutation and gene expression analysis, ProteomicsProfiler™ is based on Oncolines® cancer cell line profiling data. In the new analysis, drug response is related to the basal expression levels of more than 7,000 proteins. Correlations between drug response and expression levels of phosphorylated proteins are also analyzed. In a new case study we illustrate the added value of novel biomarker discovery at the protein level using ProteomicsProfiler™.

While DNA mutations and alterations in gene expression are commonly used to explain cellular and clinical responses to anti-cancer drugs, they may not fully explain observed responses for all anti-cancer drugs. Additionally, gene expression levels may not directly translate to protein expression levels (Figure A). ProteomicsProfiler™ addresses these gaps by facilitating the identification of cell line drug response determinants that might otherwise remain unnoticed. An example is illustrated in Figure B, which shows that the MEK inhibitor trametinib is especially effective in cell lines characterized by elevated expression of phosphorylated MEK.

Visit our more detailed information about the new ProteomicsProfiler™ service or check out the full case study on the MEK inhibitor trametinib