Mutations in splicing factor 3B subunit 1 (SF3B1) frequently occur in patients with chronic lymphocytic leukemia (CLL) and myelodysplastic syndromes (MDSs). These mutations have different effects on the disease prognosis with beneficial effect in MDS and worse prognosis in CLL patients. A full-length transcriptome approach can expand our knowledge on SF3B1 mutation effects on RNA splicing and its contribution to patient survival and treatment options. We applied long-read transcriptome sequencing (LRTS) to 44 MDS and CLL patients, as well as two pairs of isogenic cell lines with and without SF3B1 mutations, and found >60% of novel isoforms. Splicing alterations were largely shared between cancer types and specifically affected the usage of introns and 3′ splice sites. Our data highlighted a constrained window at canonical 3′ splice sites in which dynamic splice-site switches occurred in SF3B1-mutated patients. Using transcriptome-wide RNA-binding maps and molecular dynamics simulations, we showed multimodal SF3B1 binding at 3′ splice sites and predicted reduced RNA binding at the second binding pocket of SF3B1^K700E. Our work presents the hitherto most-complete LRTS study of the SF3B1 mutation in CLL and MDS and provides a resource to study aberrant splicing in cancer. Moreover, we showed that different disease prognosises result most likely from the different cell types expanded during carcinogenesis rather than different mechanisms of action of the mutated SF3B1. These results have important implications for understanding the role of SF3B1 mutations in hematological malignancies and other related diseases.

中文翻译：

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CLL 和 MDS 患者的长读长转录组测序揭示了 SF3B1 突变的分子效应


剪接因子 3B 亚基 1 （SF3B1） 突变经常发生在慢性淋巴细胞白血病 （CLL） 和骨髓增生异常综合征 （MDS） 患者中。这些突变对疾病预后的影响不同，其中对 MDS 有益，而对 CLL 患者预后较差。全长转录组方法可以扩展我们对 SF3B1 突变对 RNA 剪接的影响及其对患者生存和治疗选择的贡献的知识。我们对 44 例 MDS 和 CLL 患者以及两对有和没有 SF3B1 突变的同基因细胞系应用长读长转录组测序 （LRTS），发现 >60% 的新型亚型。剪接改变在癌症类型之间主要共享，并特别影响内含子和 3' 剪接位点的使用。我们的数据强调了经典 3' 剪接位点的受限窗口，其中动态剪接位点切换发生在 SF3B1 突变患者中。使用转录组范围的 RNA 结合图和分子动力学模拟，我们显示了 SF3B1 在 3' 剪接位点的多模式结合，并预测了 SF3B1^K700E 第二个结合口袋处的 RNA 结合减少。我们的工作提出了迄今为止最完整的 CLL 和 MDS 中 SF3B1 突变的 LRTS 研究，并为研究癌症中的异常剪接提供了资源。此外，我们表明，不同的疾病预后很可能是由于致癌过程中扩增的不同细胞类型，而不是突变的 SF3B1 的不同作用机制。这些结果对于理解 SF3B1 突变在血液系统恶性肿瘤和其他相关疾病中的作用具有重要意义。