Mechanisms of Natural Killer cell expansion and neoplastic transformation

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One of the paradigmatic feature of adaptive lymphocytes is to undergo clonal expansion upon antigen encounter. Natural Killer (NK) cells are innate lymphocytes lacking rearranged receptors that are rapidly activated in response to pathogen/danger signals or cytokines. Remarkably, infection with human cytomegalovirus (CMV) induces the expansion of a subset of peptide-specific adaptive NKG2C+ NK cells undergoing global transcriptional and epigenetic remodeling, similar to memory cells. In our preliminary data, we have performed scRNAseq, scATACseq, CITE-seq as well as analysis of mitochondrial DNA (mtDNA) mutations to track clonality within human NK cells from CMV+ and CMV- healthy donors ex vivo. This analysis revealed that, in contrast to the conventional NK cell pool, human memory NKG2C+ NK cells in CMV+ donors comprise of stable clonal expansions, displaying two major types of open chromatin domains: first, a shared signature featured by all adaptive NK cells across CMV+ donors (“public memory”); second, a diverse set of unique open chromatin regions associated with the drastic expansions of individual, stable NK cell clones (“private memory”). Based on this unexpected finding, we hypothesize that clonality and the epigenetic features associated to it might be advantageous for NK cell expansion but might put them at risk of neoplastic transformation. Interestingly, abnormal proliferations of NK cells, more recently classified as chronic lymphoproliferative disease of NK cells (CLPD-NK), comprise 15% of mature large granular lymphocytes (LGL) disorders, a spectrum of conditions ranging from lymphocytosis to overt leukemia. The pathophysiological mechanisms underlying CLPD-NK cell expansions, the degree of their clonality and epigenetic remodeling remain unclear. In this project, we will combine scRNAseq, scATACseq, CITE-seq and mtDNA mutation analysis to study NK cells from healthy CMV+ and CMV- individuals as well as from patients with diagnosed CLPD-NK with different clinical spectra in order to identify possible common epigenetic features and clonal relationships with conventional and memory NK cells from healthy donors and/or within patients. Altogether, this project will shed light on new aspects of NK cell biology, as well as into the pathophysiology of CLPD-NK disorders, and opens a perspective on the identification of new diagnostic and prognostic markers associated to disease.