Imatinib-Induced Changes in Protein Expression and ATP-Binding Affinities of Kinases in Chronic Myelocytic Leukemia Cells

Kinases
are crucial components in numerous cell signaling pathways.
Aberrant expression and activation of protein kinases are known to
be accompanied by many types of cancer, and more than 30 small-molecule
kinase inhibitors have been approved by the Food and Drug Administration
(FDA) for cancer chemotherapy. Biological and clinical applications
of small-molecule kinase inhibitors require comprehensive characterizations
about how these inhibitors modulate the protein expression and activities
of kinases at the entire proteome scale. In this study, we developed
a parallel-reaction monitoring (PRM)-based targeted proteomic method
to monitor the alterations in protein expression of kinases in K-562
chronic myelocytic leukemia (CML) cells elicited by treatment with
imatinib, an ABL kinase inhibitor approved by the FDA for CML treatment.
By employing isotope-coded ATP affinity probes together with liquid
chromatography-multiple-reaction monitoring (LC-MRM) analysis, we
also examined the modulation of the ATP-binding affinities of kinases
induced by imatinib treatment. The results revealed profound increases
in protein expression levels of a large number of kinases in K-562
cells upon treatment with imatinib, which is accompanied by substantial
decreases in ATP-binding capacities of many kinases. Apart from ABL
kinases, we identified a number of other kinases whose ATP-binding
affinities are markedly diminished upon imatinib treatment, including
CHK1, a checkpoint kinase involved in DNA damage response signaling.
Together, our targeted quantitative proteomic methods enabled, for
the first time, dual assessments of small-molecule kinase inhibitor-induced
changes in protein expression and ATP-binding affinities of kinases
in live cells.