Our high-resolution map of immune responses in CML reveals active CD56dimCD16 + CCL4 + IFNG + TIGIT + NK cell phenotype and the inhibitory LGALS9 – TIM3 and PVR – TIGIT pathways controlling the NK and CML cell interactions, validated also with in vitro co-culture. Here, HAVCR2 is linked to chronic myelogenous leukemia, BCR-ABL1 positive.