Transcriptional and Epigenetic Adaptation as Novel Therapeutic Vulnerabilities for Mantle Cell Lymphoma

获得性耐药(DR)在很大程度上限制了靶向癌症治疗的有效性，特别是对 侵袭性疾病，如套细胞淋巴瘤(MCL)，一种预后较差的B细胞淋巴瘤。最近， FDA批准的药物万乃克拉克斯(ABT-199)，一种新型的，有效的，选择性的小分子bcl2抑制剂， 临床上被认为是治疗包括MCL在内的血液系统肿瘤的有效方法。ABT-199的使用 产生了戏剧性的反应；然而，对这种药物的抗药性的出现导致了致命的 MCL的进展。一旦MCL患者从ABT-199治疗中复发，无论是在治疗中还是在治疗后，都有 疾病进展迅速，死亡率加快。因此，迫切需要界定 ABT-199耐药性(AR)和识别靶点，提出新的治疗方案，具有切实的疗效 潜力。我们通过从MCL中产生AR细胞株来模拟对ABT-199的耐药性，并表征了 这些细胞对ABT-199处理的适应性分子重编程。淋巴瘤的小亚群 一直检测到的细胞通过进入可逆药物来逃避强大的选择性ABT-199压力 容忍持久状态(DTP)，从而导致DTP扩展种群(DTEP)并最终 获得真正的抗药性。假设MCL涉及多种机制 AR，我们应用了全网、稳健和公正的方法来确定主要改变的MCL信令 AR进化过程中的途径。比我们预期的更复杂和更动态，我们观察到 这些DTEP细胞具有与BH3家族蛋白相关的活性和克隆生长能力 重新编程。有趣的是，DTEP细胞在长期传代后可以恢复到药物敏感状态 如果没有药物，支持这些细胞从表观遗传上重新编程为耐药的观点 各州。与这些结果一致，我们最初的药物筛查揭示了对表观遗传学的精致敏感性。 与亲本细胞相比，ABT-199 DTEP细胞中的机械抑制剂(如BRD4、CDK7)。排队 有了这一点，我们的免疫沉淀测序(ChIP-Seq)和RNA-Seq分析显示动态超 增强子(SE)在DTEP MCL细胞中的重塑，这种染色质改变与CDK7介导的 ABT-199耐药MCL细胞中的转录。我们认为转录和表观遗传的适应性 对于在ABT-199治疗中持续存在的细胞的生存来说，反应是必需的。目标是 这项建议的目的是战略性地瞄准转录机制，并通过以下方式提供临床前验证 靶向CDK7/BRD4，联合bcl2治疗MCL是一种有效和持久的治疗方法。与 用于表观遗传靶点的小分子工具和患者来源的异种移植(PDX)模型可用于气和 TAO实验室，各自的专业知识和独特的获取大量初级MCL样品的资源， 研究使我们能够对MCL耐药生物学获得有价值的见解，并揭示一种新的机制-- MCL患者的驱动式治疗。

Acquired drug resistance (DR) largely limits the effectiveness of targeted cancer therapies, especially for aggressive diseases, such as mantle cell lymphoma (MCL), a B-cell lymphoma with poor prognosis. Recently, FDA approved drug Venetoclax (ABT-199), a novel, potent and selective small-molecule BCL-2 inhibitor was clinically vetted as an effective therapy for hematopoietic tumors, including MCL. The use of ABT-199 produced a dramatic response; however, the emergence of resistance to this drug was ensued by fatal progression of the MCL. Once MCL patients relapse from ABT-199 treatment, either during or after, there is rapid disease progression and accelerated mortality. Thus, there is an urgent need to define mechanisms of ABT-199 resistance (AR) and identify targets to bring forward novel treatment options with tangible curative potential. We modeled drug resistance to ABT-199 by generating AR cell lines from MCL, and characterized the adaptive molecular reprogramming to ABT-199 treatment in these cells. Small subpopulations of lymphoma cells were consistently detected that evade strong selective ABT-199 pressure by entering a reversible drug tolerant 'persister' state (DTP), and consequently leading to a DTP expansion population (DTEP) and eventual acquisition of bona fide drug resistance. Given the premise that a myriad of mechanisms are involved in MCL AR, we applied network-wide, robust and unbiased approaches to determine the major altered MCL signaling pathways during AR evolution. More complex and more dynamic than we had anticipated, we observed that these DTEP cells conferred increased viability and clonogenic growth, associated with BH3 family protein reprogramming. Intriguingly, DTEP cells can revert back to drug sensitive states after long-term passaging without the drug, supporting the notion that these cells are epigenetically reprogrammed to drug resistant states. Consistent with these results, our initial drug screen revealed the exquisite sensitivity to epigenetic machinery inhibitors (e.g., BRD4, CDK7) in ABT-199 DTEP cells when compared with parental cells. In line with this, our immunoprecipitation-sequencing (ChIP-Seq) and RNA-Seq assays revealed dynamic super enhancer (SE) remodeling in DTEP MCL cells, and this chromatin alteration is associated with CDK7-mediated transcription in ABT-199 resistant MCL cells. We propose that transcriptional and epigenetic adaptive responses are required for the survival of cells that persist in the presence of ABT-199 therapy. The objective of this proposal is to strategically target transcriptional machinery and provide pre-clinical validation by targeting CDK7/BRD4, in combination with BCL-2 as an efficient and durable treatment for MCL. With the small molecule tools for epigenetic targets and patient-derived xenograft (PDX) model available in the Qi and Tao laboratories, respective expertise and the unique access to a large resource of primary MCL samples, the study allows us to gain valuable insights into MCL drug resistance biology and uncover a novel mechanism- driven therapy for MCL patients.