Cooperative and antagonistic interactions between sub-clones favour the co-existence of multiple resistance mechanisms in melanoma

Resistance to targeted therapies develops in the majority of patients, with numerous different mechanisms having been documented. This is frequently linked to intra-tumour heterogeneity and cancer cells transitioning into different states. In this study, we demonstrate cooperativity between co-occurring resistant states in a single tumour. Using BRAF mutant melanoma as a paradigm, we generate three different resistant states within a single model and demonstrate that they have varying differentiation states, capacities to migrate, and have very few common additional therapeutic vulnerabilities. Through a combination of experiments, including using Cre-mediated recombination to generate heterogeneity in existing tumours, and in silico modelling, we show that intra-tumour heterogeneity is the most favoured state for therapy resistant tumours. This is under-pinned by signalling between different melanoma states, with YAP1 active cells providing supporting signals for other cells but inhibiting their own proliferation. Optimal disease control requires targeting both the YAP1 active cell state and the inter-cellular communication networks. We identify the histone demethylase inhibitor GSK-J4 as being particularly effective in targeting both features of resistant tumours, and demonstrate its ability to control melanoma with multiple concurrent resistance mechanisms.