Cancer stem cell-related gene expression as a potential biomarker of response for first-in-class imipridone ONC201 in solid tumors

Cancer stem cells (CSCs) correlate with recurrence, metastasis and poor survival in clinical studies. Encouraging results from clinical trials of CSC inhibitors have further validated CSCs as therapeutic targets. ONC201 is a first-in-class small molecule imipridone in Phase I/II clinical trials for advanced cancer. We have previously shown that ONC201 targets self-renewing, chemotherapy-resistant colorectal CSCs via Akt/ERK inhibition and DR5/TRAIL induction. In this study, we demonstrate that the anti-CSC effects of ONC201 involve early changes in stem cell-related gene expression prior to tumor cell death induction. A targeted network analysis of gene expression profiles in colorectal cancer cells revealed that ONC201 downregulates stem cell pathways such as Wnt signaling and modulates genes (ID1, ID2, ID3 and ALDH7A1) known to regulate self-renewal in colorectal, prostate cancer and glioblastoma. ONC201-mediated changes in CSC-related gene expression were validated at the RNA and protein level for each tumor type. Accordingly, we observed inhibition of self-renewal and CSC markers in prostate cancer cell lines and patient-derived glioblastoma cells upon ONC201 treatment. Interestingly, ONC201-mediated CSC depletion does not occur in colorectal cancer cells with acquired resistance to ONC201. Finally, we observed that basal expression of CSC-related genes (ID1, CD44, HES7 and TCF3) significantly correlate with ONC201 efficacy in >1000 cancer cell lines and combining the expression of multiple genes leads to a stronger overall prediction. These proof-of-concept studies provide a rationale for testing CSC expression at the RNA and protein level as a predictive and pharmacodynamic biomarker of ONC201 response in ongoing clinical studies.

癌症干细胞（cancer stem cells, CSCs）在临床研究中与肿瘤复发、转移及不良预后显著相关。CSC抑制剂的临床试验已获得令人振奋的阳性结果，进一步验证了CSCs可作为肿瘤治疗靶点。ONC201是一款针对晚期癌症开展I/II期临床试验的首创类（first-in-class）小分子imipridone化合物。我们此前的研究表明，ONC201可通过抑制Akt/ERK通路并诱导DR5/TRAIL表达，靶向具备自我更新能力且对化疗耐药的结直肠癌CSCs。
本研究证实，ONC201的抗CSC作用涉及肿瘤细胞死亡诱导前的干细胞相关基因表达早期改变。对结直肠癌细胞的基因表达谱开展靶向网络分析后发现，ONC201可下调包括Wnt信号通路（Wnt signaling）在内的干细胞相关通路，并调控已知可调节结直肠癌、前列腺癌及胶质母细胞瘤中细胞自我更新能力的基因（ID1、ID2、ID3及ALDH7A1）。研究针对各肿瘤类型，在RNA及蛋白水平验证了ONC201介导的CSC相关基因表达改变。据此，我们观察到，经ONC201处理后，前列腺癌细胞系及患者来源的胶质母细胞瘤细胞的自我更新能力及CSC标志物均受到抑制。
有趣的是，在获得性ONC201耐药的结直肠癌细胞中，并未出现ONC201介导的CSC耗竭现象。
最后，我们在超过1000株癌细胞系中发现，CSC相关基因（ID1、CD44、HES7及TCF3）的基础表达水平与ONC201的疗效显著相关，且联合多个基因的表达可获得更强的整体预测效能。本项概念验证研究为在当前正在进行的临床试验中，将CSC的RNA及蛋白表达水平作为ONC201疗效的预测性及药效学生物标志物开展检测提供了理论依据。