Circadian regulator REV-ERBa is a master regulator of tumor lineage plasticity and an effective therapeutic target [RNA-Seq]

Epigenetic and transcriptional dysregulation plays a fundamental role in tumor lineage plasticity (LP). However, the underlying mechanisms, especially for the initial events of LP development, are still poorly understood. Here, we report that in progression of prostate cancer from adenocarcinoma to treatment-induced neuroendocrine prostate cancer (t-NEPC), anti-AR signaling inhibitors (ARSIs) reprogram the function of a circadian regulator/nuclear receptor REV-ERBa by switching its target gene programs from kinase signaling and metabolic programs to programs of LP, which includes neurogenesis, stem cell and epithelia to mesenchymal transition (EMT) as well as over fifteen LP drivers including POU3F2/BRN2, ASCL1, FOXA2, ONECUT2 and MYCN. Unexpectedly, REV-ERBa facilitates the chromatin occupancy of BRN2, ASCL1 and FOXA1 in their activation of LP programs, thus functioning as a master regulator of ARSI-induced LP driver network. Mechanistically, REV-ERBa induces chromatin accessibility and H3K27ac modification at promoters of LP genes through its recruitment of BRD4 and p300. Overexpression of REV-ERBa alone is sufficient to induce LP and neuroendocrine phenotype and confers cell resistance to ARSI in adenocarcinoma cells. Loss of REV-ERBa potently inhibits NEPC cell growth and abolishes the expression of LP drivers and gene programs. Pharmacological inhibition of REV-ERBa exhibits high potency in blocking the growth of NEPC tumors including patient-derived xenografts. Our findings reveal that therapy-induced LP development entails a coordinated induction of a network of LP drivers and that REV-ERBa is a novel master regulator of the network and a promising therapeutic target for treatment of advanced prostate cancer such as NEPC. Overall design: RNA-seq profiling of circadian regulator REV-ERBa inhibition or overexpression in prostate cancer cells and PDX tumors.

表观遗传与转录失调在肿瘤谱系可塑性（tumor lineage plasticity, LP）中发挥核心调控作用。然而其潜在机制，尤其是LP发生的初始事件，目前仍未得到充分阐明。本研究聚焦于前列腺腺癌向治疗诱导型神经内分泌前列腺癌（treatment-induced neuroendocrine prostate cancer, t-NEPC）的进展过程，发现抗雄激素信号通路抑制剂（anti-AR signaling inhibitors, ARSIs）可通过重编程节律调节因子/核受体REV-ERBa的靶基因程序，将其调控方向从激酶信号通路与代谢程序切换至LP相关程序。该程序涵盖神经发生、干细胞特性及上皮间质转化（epithelial-mesenchymal transition, EMT），同时包含POU3F2/BRN2、ASCL1、FOXA2、ONECUT2与MYCN在内的15种以上LP驱动因子。

出乎意料的是，REV-ERBa可促进BRN2、ASCL1及FOXA1的染色质结合以激活LP相关程序，因此作为ARSIs诱导的LP驱动因子网络的核心调控因子发挥功能。机制层面，REV-ERBa通过招募BRD4与p300，诱导LP基因启动子区域的染色质开放性与H3K27乙酰化修饰。仅过表达REV-ERBa即可诱导前列腺腺癌细胞发生LP并获得神经内分泌表型，同时使细胞对ARSIs产生耐药性。敲除REV-ERBa可显著抑制t-NEPC细胞增殖，并消除LP驱动因子及相关基因程序的表达。对REV-ERBa进行药物抑制可有效阻断t-NEPC肿瘤（包括患者来源异种移植模型patient-derived xenografts, PDX）的生长。

本研究结果揭示，治疗诱导的LP发生需要LP驱动因子网络的协同激活，REV-ERBa是该网络的新型核心调控因子，同时也是治疗晚期前列腺癌（如t-NEPC）的潜在治疗靶点。实验整体设计：对前列腺癌细胞及PDX肿瘤中的REV-ERBa进行抑制或过表达处理后开展RNA测序（RNA-seq）转录组分析。