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

获得性耐药性（DR）在很大程度上限制了靶向癌症治疗的有效性，特别是对于 侵袭性疾病，如套细胞淋巴瘤（MCL），一种预后不良的B细胞淋巴瘤。最近， FDA批准的药物Venetoclax（ABT-199）是一种新型，强效和选择性的小分子BCL-2抑制剂， 临床上被认为是造血系统肿瘤的有效治疗方法，包括MCL。使用ABT-199 产生了戏剧性的反应;然而，对这种药物的耐药性的出现是致命的 MCL的进展。一旦MCL患者在ABT-199治疗期间或之后复发， 疾病进展迅速，死亡率加快。因此，迫切需要确定 ABT-199耐药性（AR），并确定目标，以提出具有切实疗效的新型治疗方案 潜力我们通过从MCL产生AR细胞系来模拟对ABT-199的耐药性，并表征 这些细胞中对ABT-199处理的适应性分子重编程。淋巴瘤小亚群 通过进入可逆药物，始终检测到逃避强选择性ABT-199压力的细胞 耐受“持久”状态（DTP），并因此导致DTP扩增群体（DTEP）， 获得真正的耐药性。假设MCL涉及多种机制， AR，我们应用网络范围内的，稳健的和无偏的方法来确定主要改变的MCL信号传导 AR进化过程中的路径。比我们预期的更加复杂和动态，我们观察到， 这些DTEP细胞赋予与BH 3家族蛋白相关的增加的存活力和克隆形成生长 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 没有药物，支持这些细胞在表观遗传学上被重新编程为耐药细胞的观点。 states.与这些结果一致，我们最初的药物筛选显示了对表观遗传的敏感性。 机械抑制剂（例如，与亲代细胞相比，ABT-199 DTEP细胞中的BRD 4、CDK 7）。一致 有了这个，我们的免疫沉淀测序（ChIP-Seq）和RNA-Seq检测显示动态超 DTEP MCL细胞中的增强子（SE）重塑，这种染色质改变与CDK 7介导的 在ABT-199抗性MCL细胞中的转录。我们认为转录和表观遗传适应性 对于在ABT-199治疗存在下持续存在的细胞的存活，需要这种应答。客观 这项建议的目的是战略性地靶向转录机制，并提供临床前验证， 靶向CDK 7/BRD 4，与BCL-2联合作为MCL的有效和持久治疗。与 表观遗传靶点和患者来源的异种移植（PDX）模型的小分子工具， 道实验室，各自的专业知识和独特的访问大量资源的主要MCL样品， 这项研究使我们能够深入了解MCL耐药生物学，并揭示一种新的机制- 治疗MCL患者。

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.