Phosphoproteomic profiling of T cell acute lymphoblastic leukemia reveals targetable kinases and combination treatment strategies

Abstract

Protein kinase inhibitors are amongst the most successful cancer treatments, but targetable kinases activated by genomic abnormalities are rare in T cell acute lymphoblastic leukemia. Nevertheless, kinases can be activated in the absence of genetic defects. Thus, phosphoproteomics can provide information on pathway activation and signaling networks that offer opportunities for targeted therapy. Here, we describe a mass spectrometry-based global phosphoproteomic profiling of 11 T cell acute lymphoblastic leukemia cell lines to identify targetable kinases. We report a comprehensive dataset consisting of 21,000 phosphosites on 4,896 phosphoproteins, including 217 kinases. We identify active Src-family kinases signaling as well as active cyclin-dependent kinases. We validate putative targets for therapy ex vivo and identify potential combination treatments, such as the inhibition of the INSR/IGF-1R axis to increase the sensitivity to dasatinib treatment. Ex vivo validation of selected drug combinations using patient-derived xenografts provides a proof-of-concept for phosphoproteomics-guided design of personalized treatments.

Identification of a Novel Curcumin Derivative Influencing Notch Pathway and DNA Damage as a Potential Therapeutic Agent in T-ALL

“…Recently, it has been shown that treatments with dinaciclib, a CDK1, CDK2, CDK5, and CDK9 inhibitor, arrested cell cycle progression in the G2/M phase and induced programmed cell death in T-ALL cells [ 74 ]. In particular, the kinases CDK1 and CDK2 were found to be among the top relevant kinases in a panel of T-ALL samples, and their inhibition by milciclib counteracted survival in cell lines and patient-derived xenografts of T-ALL [ 75 ], thus suggesting the targeting of these CDKs for pharmacological intervention in T-cell hematological malignancies. Consistent with this, we found that KOPT-K1 cells were highly sensitive to pharmacological inactivation of CDK1 by its commercially available inhibitor Ro3306, as 48 h of exposure to this drug decreased cell survival in a dose-dependent manner with an IC 50 of 2.481 ± 0.332 μM ( Figure S20 ).…”

“…Finally, to explore the feasibility of CD2066 application for chemotherapy-free drug combinations, we evaluated its effects in association with the inhibition of CDK1, recently found hyperactivated in T-ALL and, therefore, indicated as an appealing pharmacological target [ 74 , 75 ]. Our preliminary data on its combination with the commercially available CDK1 inhibitor Ro3306 revealed the compounds’ synergic antiviability effects associated with enhanced cell death, cell-cycle block in S-G2-M phases, and strong downregulation of pro-survival signals, such as pAKT in the KOPT-K1 cell line.…”

Notch Partners in the Long Journey of T-ALL Pathogenesis

“…Other inhibitors that interfere with the maturation of NOTCH receptors, such as fucose analogs (6-alkynyl and 6-alkenyl fucose), which interfere with the O -fucosyltransferase 1 (POFUT1)-dependent transfer of O -fucose to epidermal growth factor (EGF) repeats of NOTCH receptors, have proved to successfully impair DLL1 and DLL4 interactions with NOTCH receptors [ 85 ]. On the other hand, recent phosphoproteomic and expression-based screenings have revealed novel targetable kinases potentially involved in the NOTCH1-launched oncogenesis program and in GSI resistance [ 86 , 87 , 88 , 89 , 90 , 91 ]. Some examples are Src-family kinases and active cyclin-dependent kinases [ 90 ] and protein kinase C (PKC) delta [ 89 ].…”

“…On the other hand, recent phosphoproteomic and expression-based screenings have revealed novel targetable kinases potentially involved in the NOTCH1-launched oncogenesis program and in GSI resistance [ 86 , 87 , 88 , 89 , 90 , 91 ]. Some examples are Src-family kinases and active cyclin-dependent kinases [ 90 ] and protein kinase C (PKC) delta [ 89 ].…”

Targeting Leukemia-Initiating Cells and Leukemic Niches: The Next Therapy Station for T-Cell Acute Lymphoblastic Leukemia?

“…Other pathways required for T-ALL also include the overactive kinase signals, such as tyrosine kinase signaling. Dasatinib is a potent tyrosine kinase inhibitor (TKI) that has shown satisfactory efficacy and acceptable safety in T-ALL, alone or in combination with chemotherapy [ 164 , 165 , 166 , 167 , 168 ]. However, TKIs are not very potent in eradicating the LSCs in chronic myeloid leukemia [ 169 , 170 ].…”