Pharmacological targeting of SF3a1-MDM4 splicing vulnerability in ovarian cancer with rifaximin and antisense oligonucleotide

Ovarian cancer (OC) is the most deadly gynecological malignancy, mainly due to insufficient studies on its mechanisms and lack of effective therapies. Alternative splicing (AS) dysregulation has deepened understanding of cancer pathogenesis. As a constitutive molecular consisting spliceosome, the pathogenesis and therapeutic potential of SF3a1 in solid tumors are rarely studied. The expressions and prognostic values of SF3a1 were accessed using bioinformatics. The functions of SF3a1 were evaluated using gain- and loss-of-function strategies. Whole transcriptome sequencing and mass spectrometry analysis were conducted to capture signaling axis of SF3a1. Semi-qPCR, qRT–PCR, WB, IHC and rescue experiments were exploited to validate the sequencing results. Targeted antisense oligonucleotide (ASO) was designed and its treatment efficacy was verified. Virtual screening was used to identify small molecule inhibitor of SF3a1, whose therapeutic potential on OC was evaluated via in vitro and in vivo assays. This study found SF3a1 played an indispensable role in OC pathogenesis. SF3a1 knockdown impaired malignant behaviors and reprogrammed splicing landscape of OC cells. Skipped exon (SE) event of MDM4-exon6 (exon7 in mouse) increased, leading to formation of MDM4-short (MDM4-s) isoform, which was subsequently degraded. Total MDM4 level was therefore downregulated, leading to P53 pathway activation and OC inhibition. Additionally, ASO targeting MDM4 pre-mRNA sequence bound by SF3a1 mimicked the alternative regulation caused by SF3a1 knockdown, and showed significant inhibitory effect on OC proliferation. Rifaximin, identified as an inhibitor targeting SF3a1, effectively killed OC cells and enhanced cisplatin’s efficacy in combination therapy. Moreover, CDK6 was found to phosphorylate SF3a1 at S359, which decreased its protein half-life and influenced downstream MDM4 splicing. Our findings uncover the oncogenic impact of SF3a1 in OC and highlight the prospects to target it by rifaximin and downstream MDM4 AS by ASO, synergistically improving the therapeutic effectiveness of cisplatin in OC.