Epithelial Ovarian Cancer (EOC) is characterised by frequent platinum (PT) resistant recurrences. Dysregulated transcriptional and alternative splicing (AS), also involving transcriptional Cyclin Dependent Kinases (CDKs), emerged as mechanisms of PT-adaptation. CDK12 maintains genome stability by regulating the elongation and splicing of DNA damage repair (DDR) genes, yet its splicing co-regulators remain undefined. We therefore investigated CDK12/13 as central drivers of RNA-processing programs underlying PT resistance and as actionable therapeutic targets in EOC.

CDK12/13 mutational status was assessed in 196 primary EOC samples using NGS and ddPCR, integrated with public database analysis. Pharmacological CDK12/13 inhibition (CDK12i), alone or combined with PT or PARP inhibitors, was evaluated in PT-sensitive and -resistant EOC cells and patient-derived primary models. Several CDK12i-resistant EOC cell lines were generated to explore adaptive mechanisms. High-coverage RNA sequencing (99 samples) was performed to evaluate transcriptional and AS remodelling induced by PT or CDK12i. Finally, we assessed CDK12i in vivo efficacy in both syngeneic and PDX models.

CDK12 is the most frequently mutated transcriptional CDK in EOC, followed by CDK13. CDK12i exerts potent antiproliferative activity across PT-sensitive and -resistant models, with the orally available inhibitor CT7439, recently FDA-cleared for clinical trials, showing higher potency. CDK12i restored PT and PARP inhibitor sensitivity, prevented PT-resistant clone emergence, and reduced tumour growth and metastasis in vivo. Acquired CDK12i resistance conferred enhanced PT sensitivity. Transcriptomic profiling revealed that CDK12i deeply reshapes RNA-processing, modulating Ribosome and Splicing KEGG gene sets. PT and CDK12i modulated distinct AS subsets within DDR pathways. Remarkably, the magnitude of Fanconi Anemia (FA)–associated AS alterations correlated with intrinsic sensitivity to PT or CDK12i, with minimal perturbation in PT-resistant models under PT. Conversely, CDK12i-resistant cells exhibited PT-induced enrichment of AS events in FA and Base Excision Repair genes, linking pathway-specific splicing rewiring to different drug response. Mechanistically, CDK12 interacts with the splicing regulator SFPQ/p54nrb, driving its distribution in transcriptional condensates. Consistently, p54nrb is required for CDK12-SFPQ interaction and CDK12i-induced splicing reprogramming and cytotoxicity in both PT-sensitive and -resistant cells.

We propose that the therapeutic potential of CDK12i extends beyond DDR regulation to a key role in RNA processing and AS, affecting EOC survival and potentially offering a novel strategy to PT-resistant patients, for whom very few therapeutic options are currently available.

Ashwani Bahl is Chief Scientific Officer of Carrick Therapeutics.