Synergistic Drug Combinations with a CDK4/6 Inhibitor in T-Cell Acute Lymphoblastic Leukemia

While significant progress has been made in the treatment of T-cell acute lymphoblastic leukemia (T-ALL), approximately 10-20% of newly diagnosed patients will experience either induction failure or relapse. Additionally, fewer than 50% of T-ALL patients who experience a relapse are long-term survivors. New targeted therapies are needed for the treatment of this disease.

Multiple lines of evidence point to Cyclin D3/CDK4/6 as a potential therapeutic target in T-ALL. Cyclin D3 (CCND3), a direct target of activated NOTCH1, is upregulated in T-ALL, and CCND3 null animals are refractory to NOTCH1 driven T-ALL. CCND3 binds and activates CDK4/6, and the CCND3-CDK complex phosphorylates the tumor suppressor RB leading to cell cycle progression. Previous studies have demonstrated that CDK4/6 small-molecule inhibition is an effective therapeutic strategy for the treatment of NOTCH1-driven T-ALL mouse models.

Using the publicly available Genomics of Drug Sensitivity in Cancer data set, we identified NOTCH1 mutations as a biomarker of response and RB mutations as a biomarker of resistance to the CDK4/6 inhibitor palbociclib. We validated that RB null status predicts resistance to the Novartis CDK4/6 inhibitor LEE011 in a panel of T-ALL cell lines. Interestingly, we identified both NOTCH1 mutant, as well as NOTCH1 wildtype, T-ALL cell lines that were sensitive to LEE011 treatment. Mining of publicly available data revealed that CDK6 is consistently marked by a super-enhancer in T-ALL cell lines, both NOTCH1 mutant and wildtype, suggesting another potential reason for sensitivity to CDK4/6 inhibition in this lineage. Treatment with LEE011 also led to a dose-dependent cell cycle arrest and cell death in T-ALL cells, including MOLT4 (NOTCH1 mutant) and MOLT16 (NOTCH1 wildtype).

Combinations of drugs with CDK4/6 inhibitors will likely be critical for the successful translation of this drug class because they generally do not induce cell death. Combinations with cytotoxic chemotherapy are predicted to be antagonistic, however, as most of these drugs rely on rapidly proliferating cells, and CDK4/6 inhibition induces cell cycle arrest. To discover effective, and immediately translatable combination therapies with LEE011 in T-ALL, we performed combination studies of LEE011 with agents standardly used for T-ALL treatment, including corticosteroids, methotrexate, mercaptopurine, asparaginase, vincristine and doxorubicin. Combinations of LEE011 with methotrexate, mercaptopurine, vincristine or asparaginase were antagonistic in T-ALL cell lines while the combination with doxorubicin was additive.  Combination treatment of LEE011 with corticosteroids had a synergistic effect on cell viability in MOLT4 and MOLT16 cell lines as measured by excess over Bliss additive and isobologram analyses. This combination also decreased phospho RB signaling, increased cell cycle arrest and induced cell death to a greater degree than either drug alone. LEE011 treatment increased CCND3 protein levels, an effect mitigated by glucocorticoid treatment, one possible mechanism contributing to the observed synergy. Additionally, the combination of LEE011 with everolimus, an mTOR inhibitor, was synergistic in these cell lines.

We next extended testing to in vivo models of T-ALL. In a MOLT16 orthotopic mouse model, the combination of LEE011 and everolimus significantly prolonged mouse survival compared to treatment with each individual drug alone. The combination of LEE011 with dexamethasone did not extend survival over treatment with LEE011 alone and dexamethasone was inactive in vivo. Both LEE011 and everolimus had on-target activity in the treated mice as measured by inhibition of peripheral blood phospho-RB and phospho-4EBP1. We then tested the combination of LEE011 with dexamethasone in a second mouse model, a MOLT4 orthotopic model. Here, the combination of LEE011 with dexamethasone was more effective in prolonging survival compared to each treatment alone, supporting a heterogeneous response to the combination of LEE011 with dexamethasone in vivo.

We conclude that LEE011 is active in T-ALL, and that combination therapy with corticosteroids and/or mTOR inhibitors warrants further investigation in the clinical setting.