Malaria-driven expansion of adaptive-like functional CD56-negative NK cells correlates with clinical immunity to malaria

Natural Killer (NK) cells likely play an important role in immunity to malaria, but whether repeated malaria modifies the NK cell response remains unclear. Here, we comprehensively profiled the NK cell response in a cohort of 264 Ugandan children. Repeated malaria exposure was associated with expansion of an atypical, CD56neg population of NK cells that differed transcriptionally, epigenetically, and phenotypically from CD56dim NK cells, including decreased expression of PLZF and the Fc receptor g chain, increased histone methylation, and increased protein expression of LAG-3, KIR and LILRB1. CD56neg NK cells were highly functional, displaying greater antibody dependent cellular cytotoxicity than CD56dim NK cells, and higher frequencies of these cells were associated with protection against symptomatic malaria and high parasite densities. Importantly, following marked reductions in malaria transmission, frequencies of these cells rapidly declined, suggesting that continuous exposure to malaria is required to maintain this modified, adaptive-like NK cell subset. Approximately 1,000,000 cells from 10 patient samples were stained with Human TruStain FcX Fc Blocking Reagent (BioLegend, 422302) for 10 min at room temperature. The cells were stained for 30 min at 4 °C. Cells were then washed twice with PBS supplemented with 2% FCS and 2 mM EDTA (Sigma) before resuspending in PBS and counting. Approximately 10,000 cells per sample were loaded onto the 10x Chromium controller. ATAC-Seq was performed on 2 samples from the same Ugandan child: one in 2013 when malaria transmission was high, and one in 2015 when transmission had decreased due to insecticide spraying.