Investigating translation inhibition for the treatment of transcription inhibitor resistant Group 3 medulloblastoma

Group 3 medulloblastoma (MBL) patients experience dismal outcomes: nearly half of patients relapse after standard therapy, at which point no curative therapies exist. Thus, new treatment options are desperately needed. Group 3 MBL is driven by amplification and overexpression of the oncoprotein MYC. Targeting the transcription of MYC has shown promise in pre-clinical trials. However, transcription inhibition is only partially lethal in multiple Group 3 MBL models, where MBL cells develop resistance. To elucidate the drivers of resistance, we utilized D458 MBL cells engineered to be sensitive or resistant to the transcription inhibitor JQ1. We performed an unbiased genome-wide CRISPR/Cas9 screen to identify genes that are essential specifically in the resistant state. To understand the regulatory disconnect between gene expression and protein abundance, we integrated transcriptomic and proteomic profiling, comparing RNA levels to protein levels for key survival factors. Furthermore, we conducted pharmacological interaction studies in vitro, co-administering the FDA-approved translation inhibitor omacetaxine with BET inhibitors to evaluate potential synergistic effects on cell viability and to validate translation as a therapeutic target. Our CRISPR/Cas9 screen identified RNA translation machinery as a top preferential dependency in resistant MBL cells. Analysis of key oncogenes revealed a striking discordance between transcript and protein abundance; while transcription inhibition effectively reduced mRNA levels, the protein levels of survival factors such as MYC, MCL1, and PODXL were maintained or elevated in resistant cells. This suggests that resistant clones rely on enhanced translation efficiency or post-translational stability to preserve MYC function despite transcriptional blockade. Crucially, the combination of omacetaxine and BET inhibition demonstrated synergistic cell killing in Group 3 MBL models, effectively overcoming the resistance mechanism. These findings establish that resistance to transcription inhibition in Group 3 MBL is driven by a compensatory reliance on RNA translation and protein stabilization. By demonstrating that this resistance can be reversed through combined transcriptional and translational inhibition, our work highlights omacetaxine as a promising therapeutic agent for relapsed disease. Ongoing work will further dissect the specific post-translational modifications contributing to MYC persistence and validate these combination strategies in orthotopic xenograft models, with the ultimate goal of informing novel clinical trials for children with high-risk MBL.