Phosphoproteomics reveals a crucial role of FLT3 in BCR::ABL1 independent resistant chronic myeloid leukemia

BCR::ABL1 drives chronic myeloid leukemia (CML) pathology and treatment, as revealed by the success of tyrosine kinase inhibitor (TKI) therapy. However, additional poorly characterized molecular mechanisms, acting independently of BCR::ABL1, play crucial roles in CML, contributing to leukemic stem cells (LSCs) persistence, drug resistance and disease progression. Here, by combining high sensitive mass spectrometry (MS)-based phosphoproteomics with the SignalingProfiler pipeline, we obtained two signaling maps reporting the BCR::ABL1 dependent and independent pro-survival signalling mechanisms, respectively. Crucial oncogenic pathways were deregulated in resistant cells. To unbiasedly discover therapeutic vulnerabilities, we implemented the Druggability Score, a computational algorithm ranking proteins according to their inferred ability to kill resistant cells when suppressed. By this strategy, we identified a novel and unexpected role for FLT3 in BCR::ABL1 independent resistance. Remarkably, pharmacological suppression of FLT3 triggers death of both resistant cell lines and patients-derived LSCs. Finally, we propose midostaurin treatment as a therapeutic option to improve the clinical outcome of non responder patients and eradicate LSCs.

BCR::ABL1介导慢性髓系白血病（chronic myeloid leukemia, CML）的病理进程与治疗应答，这一点已通过酪氨酸激酶抑制剂（tyrosine kinase inhibitor, TKI）疗法的临床成功得到验证。然而，尚有大量未被充分阐明的分子机制不依赖BCR::ABL1发挥作用，它们在CML进程中扮演关键角色，与白血病干细胞（leukemic stem cells, LSCs）的存活、耐药性产生及疾病进展密切相关。本研究将基于高灵敏度质谱法（mass spectrometry, MS）的磷酸化蛋白质组学与SignalingProfiler分析管线相结合，成功构建了两张信号通路图谱，分别对应依赖BCR::ABL1与不依赖BCR::ABL1的促存活信号机制。耐药细胞中存在关键致癌通路的失调异常。为无偏地识别治疗脆弱性，我们开发了成药性评分（Druggability Score）这一计算算法，该算法可根据蛋白被抑制后杀伤耐药细胞的预测能力对其进行排序。通过该策略，我们发现了FMS样酪氨酸激酶3（FLT3）在不依赖BCR::ABL1的耐药中此前未被认知的全新功能。值得注意的是，对FLT3进行药理学抑制可诱导耐药细胞系及患者来源的LSCs死亡。最终，我们提出将米哚妥林（midostaurin）疗法作为治疗选择，以改善无应答患者的临床结局并根除LSCs。