High-dimensional mass cytometry analysis of NK cell alterations in AML identifies a subgroup with adverse clinical outcome

Natural killer (NK) cells are major antileukemic immune effectors. Leukemic blasts have a negative impact on NK cell function and promote the emergence of phenotypically and functionally impaired NK cells. In the current work, we highlight an accumulation of CD56⁻CD16⁺ unconventional NK cells in acute myeloid leukemia (AML), an aberrant subset initially described as being elevated in patients chronically infected with HIV-1. Deep phenotyping of NK cells was performed using peripheral blood from patients with newly diagnosed AML (n = 48, HEMATOBIO cohort, {"type":"clinical-trial","attrs":{"text":"NCT02320656","term_id":"NCT02320656"}}NCT02320656) and healthy subjects (n = 18) by mass cytometry. We showed evidence of a moderate to drastic accumulation of CD56⁻CD16⁺ unconventional NK cells in 27% of patients. These NK cells displayed decreased expression of NKG2A as well as the triggering receptors NKp30 and NKp46, in line with previous observations in HIV-infected patients. High-dimensional characterization of these NK cells highlighted a decreased expression of three additional major triggering receptors required for NK cell activation, NKG2D, DNAM-1, and CD96. A high proportion of CD56⁻CD16⁺ NK cells at diagnosis was associated with an adverse clinical outcome and decreased overall survival (HR = 0.13; P = 0.0002) and event-free survival (HR = 0.33; P = 0.018) and retained statistical significance in multivariate analysis. Pseudotime analysis of the NK cell compartment highlighted a disruption of the maturation process, with a bifurcation from conventional NK cells toward CD56⁻CD16⁺ NK cells. Overall, our data suggest that the accumulation of CD56⁻CD16⁺ NK cells may be the consequence of immune escape from innate immunity during AML progression.

Natural killer (NK) cells are critical cytotoxic effectors involved in leukemic blast recognition, tumor cell clearance, and maintenance of long-term remission (1). NK cells directly kill target cells without prior sensitization, enabling lysis of cells stressed by viral infections or tumor transformation. NK cells are divided into different functional subsets according to CD56 and CD16 expression (2–4). CD56^bright NK cells are the most immature NK cells found in peripheral blood. This subset is less cytotoxic than mature NK cells and secretes high amounts of chemokines and cytokines such as IFNγ and TNFα. These cytokines have a major effect on the infected or tumor target cells and play a critical role in orchestration of the adaptive immune response through dendritic cell activation. CD56^dimCD16⁺ NK cells, which account for the majority of circulating human NK cells, are the most cytotoxic NK cells. NK cell activation is finely tuned by integration of signals from inhibitory and triggering receptors, in particular, those of NKp30, NKp46 and NKp44, DNAM-1, and NKG2D (5). Upon target recognition, CD56^dimCD16⁺ NK cells release perforin and granzyme granules and mediate antibody-dependent cellular cytotoxicity through CD16 (FcɣRIII) to clear transformed cells.NK cells are a major component of the antileukemic immune response, and NK cell alterations have been associated with adverse clinical outcomes in acute myeloid leukemia (AML) (6–9). Therefore, it is crucial to better characterize AML-induced NK cell alterations in order to optimize NK cell–targeted therapies. During AML progression, NK cell functions are deeply altered, with decreased expression of NK cell–triggering receptors and reduced cytotoxic functions as well as impaired NK cell maturation (6, 9–13). Cancer-induced NK cell impairment occurs through various mechanisms of immune escape, including shedding and release of ligands for NK cell–triggering receptors; release of immunosuppressive soluble factors such as TGFβ, adenosine, PGE2, or L-kynurenine; and interference with NK cell development, among others (14).Interestingly, these mechanisms of immune evasion are also seen to some extent in chronic viral infections, notably HIV (2). In patients with HIV, NK cell functional anergy is mediated by the release of inflammatory cytokines and TGFβ, the presence of MHC^low target cells, and the shedding of ligands for NK cell–triggering receptors (2). As a consequence, some phenotypical alterations described in cancer patients are also induced by chronic HIV infections, with decreased expression of major triggering receptors such as NKp30, NKp46, and NKp44 (15, 16); decreased expression of CD16 (17); and increased expression of inhibitory receptors such as T cell immunoreceptor with Ig and ITIM domains (TIGIT) (18) all observed. In addition, patients with HIV display an accumulation of CD56⁻CD16⁺ unconventional NK cells, a highly dysfunctional NK cell subset (19, 20). Mechanisms leading to the loss of CD56 are still poorly described, and the origin of this subset of CD56⁻ NK cells is still unknown. To date, two hypotheses have been considered: CD56⁻ NK cells could be terminally differentiated cells arising from a mixed population of mature NK cells with altered characteristics or could expand from a pool of immature precursor NK cells (21). Expansion of CD56⁻CD16⁺ NK cells is mainly observed in viral noncontrollers (19, 20). Indeed, CD56 is an important adhesion molecule involved in NK cell development, motility, and pathogen recognition (22–27). CD56 is also required for the formation of the immunological synapse between NK cells and target cells, lytic functions, and cytokine production (26, 28). As a consequence, CD56⁻CD16⁺ NK cells display lower degranulation capacities and decreased expression of triggering receptors, perforin, and granzyme B, dramatically reducing their cytotoxic potential, notably against tumor target cells (2, 19, 20, 29, 30). In line with this loss of the cytotoxic functions against tumor cells, patients with concomitant Burkitt lymphoma and Epstein-Barr virus infection display a dramatic increase of CD56⁻CD16⁺ NK cells (30), which could represent an important hallmark of escape to NK cell immunosurveillance in virus-driven hematological malignancies.To our knowledge, this population has not been characterized in the context of nonvirally induced hematological malignancies. In the present work, we investigated the presence of this population of unconventional NK cells in patients with AML, its phenotypical characteristics, and the consequences of its accumulation on disease control. Finally, we explored NK cell developmental trajectories leading to the emergence of this phenotype.