In summary, based on our multi-scale analysis, (i) the synergistic anti-tumor immunity of macrophages and lymphocytes favors cabozantinib and nivolumab, (ii) immune function regulators (i.e., GranB and PD-L1) were upregulated throughout the immune compartment in non-responders, (iii) Arg1/CCR6-expressing macrophages (hazard macrophages) is also a prominent feature in non-responders, (iv) close proximity to Arg1hi hazard macrophages and distance away from CD4+ T cells associate with poorer effector function of CD8+ T cells. Here, CD8A is linked to neoplasm.