Cell cycle reprogramming for therapeutic targeting of BTK in lymphoma

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DESCRIPTION (provided by applicant): CDK4 and CDK6, which drive cell cycle entry and progression through G1 in the presence of cyclin D, are overexpressed at a high frequency in human cancers. Targeting CDK4/6 with the first selective inhibitor, PD 0332991 (palbociclib), has recently achieved unprecedented clinical efficacy in human cancers, especially in breast cancer, where it more than tripled the progression free survival when combined with letrozole. In mantle cell lymphoma (MCL), an incurable non-Hodgkin lymphoma, CDK4 overexpression and aberrant cyclin D1 expression drive unrestrained proliferation that underlies disease progression. In the first Phase I single-agent clinical trial in recurrent MCL, we showed that PD 0332991 resulted in a durable clinical response with tumor regression in some MCL patients; but the mechanism that differentiates sensitivity and resistance is unknown. To address this question, we have now shown that 1) Inhibition of CDK4/6 by PD 0332991 leads to substrate (Rb)-dependent early G1 arrest; 2) prolonged early G1 arrest (pG1) sensitizes Rb+ cancer cells for killing by diverse clinically-relevant agents; 3) pG1 reprogramming stems from restricting the expression of genes to those scheduled for early G1 only. We further showed that PD 0332991 induced pG1 in tumor cells of all MCL patients initially, regardless of their subsequent clinical response when used in combination with bortezomib (PD-Btz). Longitudinal RNA and exome sequencing revealed that selective genes in glycolysis and redox homeostasis were regulated in pG1 and that resistance to PD-Btz was associated with converse activation of only 1% (9 /868) of the genes that were repressed in pG1 in MCL cells of responding-patients. On this basis, we propose that perturbation of glycolysis and redox homeostasis in pG1 cooperates with regulation of partner agent-specific genes in pG1 to reprogram MCL cells for cytotoxic killing. To advance targeting CDK4, we will test this novel hypothesis by combining PD 0332991 with ibrutinib, an irreversible Bruton's tyrosine kinase (BTK) inhibitor. Ibrutinib has achieved a remarkable overall clinical response rate of 68% in a Phase I/II single-agent clinical trial in recurrent MCL patients. However, relapse is common in slightly over a year, and is often accompanied by aggressive proliferation of tumor cells. We will investigate the role and mechanism of metabolic perturbation in pG1 reprogramming for BTK inhibition (Aim 1); determine if pG1 reprogramming for PI3K inhibition can override ibrutinib resistance (Aim 2); and discover key hub genes that best discriminate sensitivity and resistance to therapeutic targeting of CDK4 and BTK by longitudinal functional genomics (Aim 3). PD 0332991 and ibrutinib have both attained the Breakthrough Therapy Designation by the FDA. Successful completion of this study is anticipated to shed light on cell cycle control of cancer metabolism and significantly advance mechanism-based targeting of CDK4/CDK6 and BTK in MCL and beyond.