Combined casein kinase II and MAPK signalling inhibition as a therapeutic strategy for metastatic colorectal cancer

Background Metastatic colorectal cancer (mCRC) remains a significant clinical challenge due to the emergence of drug resistance, highlighting the need for new therapeutic strategies. Aberrant regulation of the proteome drives cancer progression, and dissecting these alterations offers opportunities for targeted intervention. We aimed to identify candidate kinase dependencies in mCRC and to test a rational combination strategy in patient-derived models. Methods We performed proteomic and phosphoproteomic profiling of 10 mCRC tissues, their matched patient-derived organoids (PDOs) and normal colon mucosa, integrated with whole-exome sequencing. Kinase activities were inferred by kinase-substrate enrichment analysis. Silmitasertib-mediated casein kinase II (CKII) inhibition, alone and combined with the MEK inhibitor trametinib, was evaluated by ex vivo drug screening, western blot, flow cytometry and drug-interaction analysis across the PDO cohort and in normal colon PDOs. Results PDOs recapitulated the molecular features of matched tumours. Both tissues and PDOs showed consistently elevated CKII activity. Silmitasertib exerted heterogeneous antitumour activity, and resistance was associated with MAPK and Akt-mTOR signalling activity. Combining silmitasertib with trametinib produced an additive reduction of both resistance-associated pathways with little effect on the viability of normal colon PDOs. The combination also significantly reduced CKII activity, the abundance of active β-catenin and the colorectal cancer stem cell pool. Conclusions Phosphoproteomic profiling identified CKII as a therapeutic vulnerability in mCRC and provided a rationale for combining silmitasertib with MEK inhibition, offering a candidate combination strategy for mCRC.