Besides analyses of specific alternative splicing (AS) variants, little is known about AS regulatory pathways and programs involved in anticancer drug resistance. Doxorubicin is widely used in breast cancer chemotherapy. Here, we identified 1723 AS events and 41 splicing factors regulated in a breast cancer cell model of acquired resistance to doxorubicin. An RNAi screen on splicing factors identified the little studied ZRANB2 and SYF2, whose depletion partially reversed doxorubicin resistance. By RNAi and RNA-seq in resistant cells, we found that the AS programs controlled by ZRANB2 and SYF2 were enriched in resistance-associated AS events, and converged on the ECT2 splice variant including exon 5 (ECT2-Ex5+). Both ZRANB2 and SYF2 were found associated with ECT2 pre-messenger RNA, and ECT2-Ex5+ isoform depletion reduced doxorubicin resistance. Following doxorubicin treatment, resistant cells accumulated in S phase, which partially depended on ZRANB2, SYF2 and the ECT2-Ex5+ isoform. Finally, doxorubicin combination with an oligonucleotide inhibiting ECT2-Ex5 inclusion reduced doxorubicin-resistant tumor growth in mouse xenografts, and high ECT2-Ex5 inclusion levels were associated with bad prognosis in breast cancer treated with chemotherapy. Altogether, our data identify AS programs controlled by ZRANB2 and SYF2 and converging on ECT2, that participate to breast cancer cell resistance to doxorubicin.

中文翻译：

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ZRANB2 和 SYF2 介导的剪接程序在 ECT2 上汇聚，参与乳腺癌细胞对阿霉素的耐药性。

除了对特定选择性剪接 (AS) 变体的分析外，人们对抗癌药物耐药性中涉及的 AS 调控途径和程序知之甚少。阿霉素广泛用于乳腺癌化疗。在这里，我们鉴定了在多柔比星获得性耐药的乳腺癌细胞模型中受调节的 1723 个 AS 事件和 41 个剪接因子。对剪接因子的 RNAi 筛选发现了很少被研究的 ZRANB2 和 SYF2，它们的缺失部分逆转了阿霉素耐药性。通过在耐药细胞中进行RNAi和RNA-seq，我们发现由ZRANB2和SYF2控制的AS程序富含与耐药相关的AS事件，并且集中在包括外显子5（ECT2-Ex5+）在内的ECT2剪接变体上。ZRANB2 和 SYF2 均被发现与 ECT2 前信使 RNA 相关，并且 ECT2-Ex5+ 同工型耗尽可降低阿霉素耐药性。阿霉素治疗后，耐药细胞在S期积累，这部分依赖于ZRANB2、SYF2和ECT2-Ex5+亚型。最后，阿霉素与抑制 ECT2-Ex5 包含的寡核苷酸组合可减少小鼠异种移植物中阿霉素耐药肿瘤的生长，并且高 ECT2-Ex5 包含水平与化疗治疗的乳腺癌的不良预后相关。总而言之，我们的数据确定了由 ZRANB2 和 SYF2 控制并汇聚于 ECT2 的 AS 程序，这些程序参与乳腺癌细胞对阿霉素的耐药性。