Natural killer cell–mediated cytotoxicity shapes the clonal evolution of B cell leukaemia

Abstract The term cancer immunoediting describes the dual role by which the immune system can suppress and promote tumour growth and is divided into three phases: elimination, equilibrium and escape. The role of NK cells has mainly been attributed to the elimination phase. Here we show that NK cells play a role in all three phases of cancer immunoediting. Extended co-culturing of DNA barcoded mouse BCR/ABLp185+ B-cell acute lymphoblastic leukaemia (B-ALL) cells with NK cells allowed for a quantitative measure of NK cell–mediated immunoediting. Although most tumour cell clones were efficiently eliminated by NK cells, a certain fraction of tumour cells harboured an intrinsic primary resistance. Furthermore, DNA barcoding revealed tumour cell clones with secondary resistance, which stochastically acquired resistance to NK cells. NK cell–mediated cytotoxicity put a selective pressure on B-ALL cells, which led to an outgrowth of primary and secondary resistant tumour cell clones, which were characterised by an IFN-γ signature. Besides well-known regulators of immune evasion, our analysis of NK cell–resistant tumour cells revealed the upregulation of genes, including Ly6a, which we found to promote leukaemic-cell resistance to NK cells. Translation of our findings to the human system showed that high expression of LY6E on tumour cells impaired their physical interaction with NK cells and led to worse prognosis in leukaemia patients. Our results demonstrate that tumour cells are actively edited by NK cells during the equilibrium phase and use different avenues to escape NK cell–mediated eradication.