SF3B1 mutations are recurrent in chronic lymphocytic leukemia (CLL), particularly enriched in clinically aggressive stereotyped subset #2. To investigate their impact, we conducted RNA-sequencing of 18 SF3B1^MUT and 17 SF3B1^WT subset #2 cases and identified 80 significant alternative splicing events (ASEs). Notable ASEs concerned exon inclusion in the non-canonical BAF (ncBAF) chromatin remodeling complex subunit, BRD9, and splice variants in eight additional ncBAF complex interactors. Long-read RNA-sequencing confirmed the presence of splice variants, and extended analysis of 139 CLL cases corroborated their association with SF3B1 mutations. Overexpression of SF3B1^K700E induced exon inclusion in BRD9, resulting in a novel splice isoform with an alternative C-terminus. Protein interactome analysis of the BRD9 splice isoform revealed augmented ncBAF complex interaction, while exhibiting decreased binding of auxiliary proteins, including SPEN, BRCA2, and CHD9. Additionally, integrative multi-omics analysis identified a ncBAF complex-bound gene quartet on chromosome 1 with higher expression levels and more accessible chromatin in SF3B1^MUT CLL. Finally, Cancer Dependency Map analysis and BRD9 inhibition displayed BRD9 dependency and sensitivity in cell lines and primary CLL cells. In conclusion, spliceosome dysregulation caused by SF3B1 mutations leads to multiple ASEs and an altered ncBAF complex interactome, highlighting a novel pathobiological mechanism in SF3B1^MUT CLL.

SF3B1 突变在慢性淋巴细胞白血病 （CLL） 中反复出现，尤其在临床侵袭性刻板印象的亚群 #2 中丰富。为了研究它们的影响，我们对 18 例 SF3B1^MUT 和 17 例 SF3B1^WT 子集 #2 病例进行了 RNA 测序，并确定了 80 例重要的选择性剪接事件 （ASE）。值得注意的 ASE 涉及非经典 BAF （ncBAF） 染色质重塑复合物亚基中的外显子、BRD9 和另外 8 个 ncBAF 复合物相互作用物中的剪接变体。长读长 RNA 测序证实了剪接变体的存在，对 139 例 CLL 病例的扩展分析证实了它们与 SF3B1 突变的关联。SF3B1^K700E 的过表达诱导 BRD9 中的外显子包涵，导致具有替代 C 端的新型剪接亚型。BRD9 剪接亚型的蛋白质相互作用组分析显示 ncBAF 复合物相互作用增强，同时表现出辅助蛋白（包括 SPEN、BRCA2 和 CHD9）的结合降低。此外，综合多组学分析在 1 号染色体上鉴定了一个 ncBAF 复合体结合基因四重奏，在 SF3B1^MUT CLL 中具有更高的表达水平和更容易接近的染色质。最后，癌症依赖图分析和 BRD9 抑制显示细胞系和原代 CLL 细胞中的 BRD9 依赖性和敏感性。总之，SF3B1 突变引起的剪接体失调导致多个 ASE 和 ncBAF 复合物相互作用组改变，突出了 SF3B1^MUT CLL 中的一种新的病理生物学机制。