Cell cycle reprogramming for therapeutic targeting of BTK in lymphoma

描述(申请人提供)：CDK4和CDK6在人类癌症中高表达，它们在细胞周期蛋白D存在的情况下驱动细胞周期进入和通过G1进展。以CDK4/6为靶点的第一种选择性抑制剂PD 0332991(Palbociclib)最近在人类癌症中取得了前所未有的临床疗效，特别是在乳腺癌中，当与来曲唑联合使用时，无进展生存率增加了两倍以上。套细胞淋巴瘤(MCL)是一种不可治愈的非霍奇金淋巴瘤，CDK4的过度表达和细胞周期蛋白D1的异常表达促进了细胞的无节制增殖，这是疾病进展的基础。在复发性MCL的第一阶段单药临床试验中，我们发现PD 0332991在一些MCL患者中产生了持久的临床疗效和肿瘤消退；但区分敏感性和耐药的机制尚不清楚。为了解决这个问题，我们现在已经证明：1)PD 0332991对CDK4/6的抑制导致底物(Rb)依赖的早期G1期停滞；2)延长早期G1期停滞(PG1)使Rb+癌细胞对不同临床相关药物的杀伤敏感；3)PG1重新编程源于将基因的表达限制在仅为早期G1的基因表达。我们进一步表明，PD 0332991最初在所有骨髓瘤患者的肿瘤细胞中诱导了pG1期，而不考虑他们随后与硼替佐米(PD-BTZ)联合使用时的临床反应。纵向RNA和外显子组测序显示，糖酵解和氧化还原动态平衡的选择性基因在pG1中受到调控，而PD-BTZ的耐药性与pG1中仅有1%(9/868)的基因被反向激活有关。在此基础上，我们认为pG1中糖酵解和氧化还原动态平衡的扰动与pG1中配对试剂特异性基因的调节协同作用，以重新编程MCL细胞进行细胞毒杀伤。为了进一步靶向CDK4，我们将通过将PD 0332991与伊布鲁替尼(一种不可逆布鲁顿酪氨酸激酶(BTK)抑制剂)结合来检验这一新假说。在对复发的MCL患者进行的I/II期单药临床试验中，ibrutinib取得了显着的总体临床有效率68%。然而，复发在一年多一点的时间内很常见，并经常伴随着肿瘤细胞的侵袭性增殖。我们将研究代谢扰动在抑制BTK的pG1重编程中的作用和机制(目标1)；确定PI3K抑制的pG1重编程是否可以覆盖伊布鲁替尼耐药(目标2)；并通过纵向功能基因组学(目标3)发现最能区分CDK4和BTK治疗靶向的敏感性和耐药性的关键中枢基因(目标3)。PD 0332991和伊布鲁替尼均已获得美国食品和药物管理局的突破性治疗称号。这项研究的成功完成有望揭示癌症代谢的细胞周期控制，并显著推进CDK4/CDK6和BTK在MCL和其他组织中的基于机制的靶向。

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.