Longitudinal omics data and preclinical treatment identify proteasome inhibition as therapy for ibrutinib-resistant CLL

Chronic lymphocytic leukemia (CLL) is a malignant lymphoproliferative disorder characterized by the accumulation of small mature B cells in blood and secondary lymphoid tissues. Novel drugs, such as the Bruton tyrosine kinase (BTK) inhibitor ibrutinib, have greatly improved survival of CLL patients, nevertheless acquired drug resistance represents a major challenge the molecular mechanisms of which have not been fully elucidated yet. To overcome this limitation, we generated a mouse model of ibrutinib resistance by treating mice upon adoptive transfer of Eµ-TCL1 leukemia (TCL1-CLL) continuously with ibrutinib. After an initial response to the treatment, relapse under therapy occurs with an aggressive outgrowth of malignant cells, resembling observations in patients. To unravel relapse mechanism, we performed transcriptome and proteome analyses of sorted TCL1-CLL cells both during treatment and after relapse. Comparative analysis of these omics layers suggested alterations in the proteasome activity as a driver of ibrutinib resistance. Accordingly, we showed that preclinical treatment with the irreversible proteasome inhibitor (PI) carfilzomib administered upon ibrutinib resistance prolonged survival of mice, thus acting as salvage therapy. Longitudinal proteomic analysis of CLL patients with ibrutinib resistance identified deregulation in protein post-translational modifications. In addition, CLL cells from ibrutinib-resistant patients effectively responded to several PIs in co-culture assays. Altogether, our results from orthogonal omics approaches identified proteasome inhibition as potentially attractive salvage treatment option for CLL patients resistant or refractory to ibrutinib.

慢性淋巴细胞白血病（Chronic lymphocytic leukemia, CLL）是一种恶性淋巴增殖性疾病，以小成熟B细胞在血液及次级淋巴组织中蓄积为特征。新型药物如布鲁顿酪氨酸激酶（Bruton tyrosine kinase, BTK）抑制剂伊布替尼，极大改善了CLL患者的生存预后，但获得性耐药仍是当前面临的主要挑战，其分子机制尚未完全阐明。为突破这一局限，我们通过对过继转移Eµ-TCL1白血病（TCL1-CLL）的小鼠持续给予伊布替尼，构建了伊布替尼耐药的小鼠模型。小鼠在治疗初期出现应答后，会在治疗过程中复发，恶性细胞呈现侵袭性增殖，这与患者中的临床观测结果一致。为阐明复发机制，我们对分选获得的TCL1-CLL细胞在治疗期间及复发后分别开展了转录组与蛋白质组分析。对这些组学层面的比较分析提示，蛋白酶体活性改变是伊布替尼耐药的驱动因素。据此，我们证实，在伊布替尼耐药后使用不可逆蛋白酶体抑制剂（proteasome inhibitor, PI）卡非佐米进行临床前治疗，可延长小鼠的生存期，因此可作为挽救治疗手段。针对伊布替尼耐药的CLL患者开展的纵向蛋白质组分析发现，蛋白质翻译后修饰存在失调现象。此外，来自伊布替尼耐药患者的CLL细胞在共培养实验中对多种蛋白酶体抑制剂均产生了有效应答。综上，我们通过正交组学方法得到的研究结果表明，蛋白酶体抑制有望成为伊布替尼耐药或难治性CLL患者颇具吸引力的挽救治疗选择。