Abstract 2844: RNA interference kinome-wide screen reveals a role for PDK1 in acquired resistance to CDK4/6 inhibition ER-positive breast cancer (2015)

Abstract Background: Small molecule inhibitors that target the CDK4/6/cyclinD1 pathway are in clinical development. Clinical trials combining the CDK4/6 inhibitor pallbociclib and the aromatase inhibitor letrozole have demonstrated significantly improved clinical outcomes in patients with ER-positive breast cancer. This combination is likely to be approved for the treatment of patients with this breast cancer subtype. However, as for other targeted therapies, development of resistance to CDK4/6 inhibitors in a significant fraction of patients is anticipated. Therefore, there is a need to develop potent therapeutic strategies to circumvent drug resistance. Methods: We performed a high-throughput RNAi kinome screen targeting 720 kinases to identify potentially targetable molecules whose inhibition in combination with the CDK4/6 inhibitor LEE011 induced synthetic lethality in MCF7 ER+ breast cancer cells. Results: The sensitivity index (SI) score, which measures the influence of siRNA-induced gene knockdown on drug sensitivity, was calculated for each siRNA in MCF7 cells treated with LEE011 (IC50, 144 nM). A cutoff of SI &gt;0.15 (2 standard deviations above the mean) was used for hit selection. Individual knockdown of 15 (2.1%) kinases sensitized MCF7 cells to the CDK4/6 inhibitor (p&lt;0.05). 3-phosphoinositide dependent protein kinase 1 (PDK1) was identified as the top hit (SI = 0.32) whose downregulation sensitized MCF7 cells to LEE011. This was confirmed with independent siRNAs in ER+ MCF7, T47D, HCC1428 and HCC1500 breast cancer cell lines. Pharmacological inhibition of PDK1 with the ATP-competitive, small molecule inhibitor GSK2334470 synergistically inhibited proliferation of MCF7 and T47D cells (combination index 0.19-0.89). LEE011-resistant MCF7 and T47D cells were generated by chronic treatment with doses of LEE011 up to 1 μM. These cells displayed increased PDK1 protein expression compared to parental cells. Inhibition of PDK1 with siRNA or GSK2334470 resensitized the LEE011-resistant cells to the CDK4/6 inhibitor. LEE011-resistant MCF7 cells expressed high levels of phosphorylated S6 ribosomal protein (pS6), an effector of the PDK1 substrate p70S6K. Genetic (with siRNA) and pharmacological inhibition of PDK1 (with GSK2334470) abrogated pS6 levels whereas inhibition of AKT with the small molecule inhibitor AZD5363 did not affect pS6 levels, suggesting that PDK1 mediates resistance to CDK4/6 inhibition via p70S6K/pS6 signaling in an AKT-independent manner. Conclusions: These studies suggest that PDK1 inhibition can overcome resistance to the CDK4/6 inhibitor LEE011 and offer a rationale for further translational and clinical investigation of combinations of CDK4/6 and PDK1 inhibitors in ER+ breast cancer. Citation Format: Valerie M. Jansen, Neil E. Bhola, Joshua A. Bauer, Carlos L. Arteaga. RNA interference kinome-wide screen reveals a role for PDK1 in acquired resistance to CDK4/6 inhibition ER-positive breast cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2844. doi:10.1158/1538-7445.AM2015-2844