Tumor-independent host gene expression changes induced by tyrosine kinase inhibitors
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE112466 | GEO | 2018/03/29
REPOSITORIES: GEO
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Project description:Tumor-independent host gene expression changes induced by tyrosine kinase inhibitors
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Project description:Tyrosine kinase inhibitors (TKIs) are anti-cancer therapeutics used in long-term treatment. However, many of them cause cardiotoxicity with limited cure. We aim to define molecular mechanisms of cardiotoxicity that can be targeted for oncocardiology treatment. Eight TKIs with different levels of cardiotoxicity were selected and transcriptome responses of human cardiomyocytes to them at varying doses and times were profiled using a high throughput RNAseq technique. Transcriptome changes are classified into 7 clusters with mainly single-drug clusters. Drug-specific effects on the transcriptome dominate over dose-, time- or toxicity-dependent effects. Two clusters with three TKIs (afatinib, ponatinib and sorafenib) have the top enriched pathway as the endoplasmic reticulum stress. These TKIs cause an increase in reactive oxygen species, lipid peroxidation, or calcium, and induce biased endoplasmic reticulum stress on the PERK and the IRE1α pathway. Inhibiting either PERK or IRE1α blocks expression of cardiomyocyte injury and pro-inflammatory markers. Our data contain rich information about stress responses of human cardiomyocytes to specific TKIs, representing potential molecular mechanisms of cardiotoxicity. ER stress-induced inflammation is a promising therapeutic target to mitigate ponatinib- and sorafenib-induced cardiotoxicity
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Project description:Using a three-pronged MS-based proteomic approach, we assessed the mode-of-action of four clinically-relevant tyrosine kinase inhibitors in an epithelial cancer cell line. Here we defined the: (I) semi-quantitative tyrosine kinome; (II) drug interactome; and (III) drug-induced effects on the tyrosine signalome. We first examined the entire proteome and kinome profile expressed in the A431 cell line, and determined the relative abundance of all possible protein targets of the tyrosine kinase inhibitors. We therefore utilized a ‘shot-gun’ approach that involved a multidimensional separation-based proteomic strategy. To ensure maximal protein identification, we reduced sample complexity by strong cation exchange (SCX) chromatography, and analyzed all fractions by LC-MS/MS. To determine the direct targets of the four selected TKIs, we subjected the proteins extracted from the A431 cancer cell line to drug-coupled affinity matrices. By comparing the pull-down results from a lysate with a second identical lysate to which 20 uM of the inhibitor had been added to block binding to the beads, we were able to identify selective binding interactors using LC-MS/MS. This differential affinity pull-downs approach allowed us to also quantitatively evaluate the binding affinity of the tyrosine kinases to each of the drugs. To evaluate the global tyrosine phosphorylation dynamics that occurs in A431 cells upon treatment with each of the four inhibitors, phosphotyrosine peptides were enriched and identified by quantitative mass spectrometry. For this purpose, we treated the cells with each inhibitor for 2 h at appropriate concentrations adopted from reported studies. Cells were lysed, and the proteins digested with the proteases Lys-C and trypsin. To allow quantitation of the phosphorylated peptides originating from the three different peptide pools (control/imatinib/dasatinib or control/bosutinib/nilotinib), we used stable isotope dimethyl labeling. Subsequently, tyrosine-phosphorylated peptides were enriched by immunoprecipitation and analyzed by LC-MS/MS.
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