SF3B3-mediated alternative splicing of ATP2B4 via exon 21 skipping contributes to the progression of bladder cancer

While alternative splicing is increasingly recognized in cancer, its specific regulators and functional consequences in bladder cancer remain largely uncharted. This study aims to investigate the role of abnormal alternative splicing of ATP2B4 in the progression of bladder cancer. Exon sequencing data from The Cancer Genome Atlas were analyzed using bioinformatics algorithms, revealing significant exon skipping events in bladder cancer. Then, confirm the dysregulated expression of specific transcripts in bladder cancer tissues. Additionally, ATP2B4 was overexpressed or knocked down in tumor cells for in vitro functional experiments. Experimental results show that ATP2B4 produces two transcripts: the full-length transcript (ATP2B4-V1) and the spliced transcript (ATP2B4-V2), where the spliced transcript skips exon 21. ATP2B4-v2 is highly expressed in bladder cancer tissues, while ATP2B4-v1 is mainly expressed in non-cancerous tissues and normal bladder epithelium. Moreover, a higher PSI (Percent Spliced In) value for exon 21, indicative of greater ATP2B4-V1 expression, was correlated with improved survival in bladder cancer patients. In vitro functional assays demonstrated that the ATP2B4 splicing variant (ATP2B4-V2) enhanced the proliferation, migration, and invasion of bladder cancer cells, whereas the full-length transcript (ATP2B4-V1) exerted an opposing effect. We also identified a group of splicing factors, among which the splicing factor SF3B3 (Splicing Factor 3b Subunit 3) was found to promote the skipping of exon 21 of ATP2B4, and explored their role in regulating ATP2B4 precursor mRNA. The results showed that SF3B3 could promote the skipping of exon 21 of ATP2B4, resulting in an increased proportion of bladder cancer cells and enhanced carcinogenicity. SF3B3 promotes the skipping of ATP2B4 exon 21, leading to the preferential expression of an oncogenic isoform (ATP2B4-V2) which promotes the malignant phenotype of bladder cancer cells, suggesting that targeting alternative splicing regulation may represent a promising therapeutic strategy.