Abstract
Resistance to chemotherapy can occur through a wide variety of mechanisms. Typically, resistance tyrosine kinase inhibitors (TKIs) is thought to arise from kinase mutations or signaling pathway reprogramming—however, “off-target” adaptations enabling survival in the presence of TKIs without resistant mutations are poorly understood. Previously, we established cell line resistance models for the three most commonly used TKIs in chronic myeloid leukemia treatment, and found that their resistance to cell death was not attributed entirely to failure of kinase inhibition. In the present study, we performed global, integrated proteomic and transcriptomic profiling of these cell lines to describe the mechanisms of resistance at the protein and gene expression level. We used whole transcriptome RNA sequencing and SWATH-based data-independent acquisition mass spectrometry (DIA-MS). This MS approach does not require isotopic labels and provides quantitative measurements of proteins in a comprehensive, unbiased fashion: a significantly greater proportion of proteins are reliably quantified with this method, in comparison to traditional MS methods. The proteomic and transcriptional data were correlated to generate an integrated understanding of the gene expression and protein alterations associated with TKI resistance. We identified mechanisms of resistance that were unique to each TKI. Additionally, we defined mechanisms of resistance that were common to all TKIs tested. Resistance to all of the TKIs was associated with the oxidative stress responses, hypoxia signatures, and apparent metabolic reprogramming of the cells. Metabolite profiling and glucose-dependence experiments showed that the resistant cells relied on glycolysis (particularly through the pentose phosphate pathway) more heavily than the sensitive cells, which supported the idea that metabolism alterations were associated with resistant cell survival. These experiments are the first to report a global, integrated proteomic and transcriptomic analysis of TKI resistance. These data suggest that targeting metabolic pathways along with TKI treatment may overcome pan-TKI resistance.
Key PointsAlterations to metabolism are a common feature of target-mutation-independent resistance in CML cells across multiple clinically relevant TKIs.
Carbonic anhydrase 1 (CA1) and α-synuclein (SNCA) are novel functional markers of metabolic reprogramming in TKI resistant CML cells.