Expression analysis of canonical and adaptive human NK cell subsets

The mechanisms underlying human natural killer (NK) cell phenotypic and functional heterogeneity are unknown. Here, we have described the emergence of diverse subsets of human NK cells selectively lacking expression of signaling proteins following cytomegalovirus (CMV) infection. The absence of B and myeloid cell-related signaling protein expression in these NK cell subsets correlated with promoter DNA hypermethylation. Genome-wide DNA methylation patterns were strikingly similar between CMV-associated adaptive NK cells and cytotoxic effector T cells, but differed from those of canonical NK cells. Functional interrogation demonstrated altered cytokine responsiveness in adaptive NK cells that was linked to reduced expression of the transcription factor PLZF. Furthermore, subsets of adaptive NK cells demonstrated significantly reduced functional responses to activated autologous T cells. The present results uncover a spectrum of epigenetically unique adaptive NK cell subsets that diversify in response to viral infection and have distinct functional capabilities compared to canonical NK cell subsets. Donor PBMC were screened for individuals where FcεRγ- and PLZF- NK cell subsets correlated with NKG2C surface expression. For the donors used in the expression analysis, 89.3±9.5% (mean±SD) or 3.6±2.6% expressed FcεRγ and 89.0±9.8% or 1.7±1.3% expressed PLZF of the canonical CD3-CD56dimCD57+NKG2A-NKG2C- or adaptive CD3-CD56dimCD57+NKG2A-NKG2C+ populations, respectively. Based on CD57, NKG2A and NKG2C expression, CD3-CD56dim NK cell subsets were sorted from 4 donors.