Although clonal neo-antigen burden is associated with improved response to immune therapy, the functional basis for this remains unclear.,Here we study this question in a novel controlled mouse melanoma model that enables us to explore the effects of intra-tumor heterogeneity (ITH) on tumor aggressiveness and immunity independent of tumor mutational burden.,Induction of UVB-derived mutations yields highly aggressive tumors with decreased anti-tumor activity.,However, single-cell-derived tumors with reduced ITH are swiftly rejected.,Their rejection is accompanied by increased T cell reactivity and a less suppressive microenvironment.,Using phylogenetic analyses and mixing experiments of single-cell clones, we dissect two characteristics of ITH: the number of clones forming the tumor and their clonal diversity.,Our analysis of melanoma patient tumor data recapitulates our results in terms of overall survival and response to immune checkpoint therapy.,These findings highlight the importance of clonal mutations in robust immune surveillance and the need to quantify patient ITH to determine the response to checkpoint blockade.,•Novel mouse system to uncouple tumor mutational load and tumor heterogeneity•Lower tumor heterogeneity leads to decreased tumor growth because of immune rejection•Both clone numbers and their genetic diversity mediate tumor growth and rejection•Tumor heterogeneity is linked to patient survival and checkpoint blockade response,Novel mouse system to uncouple tumor mutational load and tumor heterogeneity,Lower tumor heterogeneity leads to decreased tumor growth because of immune rejection,Both clone numbers and their genetic diversity mediate tumor growth and rejection,Tumor heterogeneity is linked to patient survival and checkpoint blockade response,Syngeneic mouse models of melanoma and human patient data are used to explore the effect of intra-tumor heterogeneity on immune response and demonstrate that heterogeneity predicts immunotherapy outcomes better than mutational burden.
Activating mutations in BRAF kinase are common in melanomas.,Clinical trials with PLX4032, the mutant-BRAF inhibitor, show promising preliminary results in patients selected for the presence of V600E mutation.,However, activating V600K mutation is the other most common mutation, yet patients with this variant are currently excluded from the PLX4032 trials.,Here we present evidence that a patient bearing the BRAF V600K mutation responded remarkably to PLX4032, suggesting that clinical trials should include all patients with activating BRAF V600E/K mutations.