Perturbed function of natural killer cells by inflammatory cytokines in chronic myeloid leukemia

Abstract Natural killer (NK) cells’ mature phenotype and counts positively correlate with prolonged treatment-free survival in chronic myeloid leukemia (CML), while dysfunctional NK cells are predictive of relapse in leukemic patients. However, the molecular drivers of NK cell alterations during leukemia remain unclear. Given an established role of inflammatory cytokines in CML progression, we define the leukemic environmental cues impacting NK maturation and function in a BCR-ABL chimeric mouse model of CML where NK cells do not carry the CML oncogene. Reflecting clinical observations, NK cell frequencies and numbers are severely decreased in leukemic mice. Moreover, terminally mature NK subsets are the most affected, implying preferential loss of cells with potent anti-leukemic activity. In addition, this phenotype suggests a shift toward the immature cytokine-producing state of NK development, which could favor the survival of leukemia-initiating cells. We map the transcriptional landscape of NK cells using single-cell RNA-sequencing from multiple tissues. NK cells exposed to CML microenvironment possess a lowered expression of surface activating receptors such as Nkp46 while upregulating inhibitory molecules Tim-3 and TIGIT. BCR-ABL reversion for six weeks partially restored these defects, consistent with findings in patients before and after TKI initiation. Finally, we found that leukemia-associated soluble factors dampen target-specific degranulation of NK cells by applying serum samples from healthy or leukemic mice. These data indicate that the altered cytokine milieu contributes to NK cell dysfunction and represents an optimal target for NK-boosting CML immunotherapies of leukemia.