Cross-species gene expression analysis of human, canine and murine natural killer cells suggests convergence of activated dog and human transcriptomic profiles

Abstract

Abstract Key species differences exist between human and murine natural killer (NK) cells. Although outbred dogs are a link for translational NK studies, better characterization of dog NK cells is needed. We used RNAseq to profile resting and activated NK cells from mice, dogs and humans. Cells were isolated based on putative NK cell populations from healthy humans (CD56+CD3−), beagles (CD5dim) and C57BL/6J mice (NK1.1+CD3−) and sequenced from steady-state or following exposure to irradiated human feeder cells (K562 clone 9) with 100 IU/mL rhIL-2 × 14 days (human and dog) or 1000 IU/mL rhIL-2 × 7 days. Purity of expanded human and dog NK cells was ~ 90%, while for mouse it was ~ 70%. We performed differential gene expression (DGE) across species and conditions using ~7000 1:1 orthologous genes. DGE revealed distinct transcriptional profiles for each species (FDR <0.05). Hierarchical clustering demonstrated mouse NK cells as an outgroup compared to dog and human. PCA showed within-species spatial clustering of resting NK cells. After activation, variance between dog and human NK cells decreased, variance between human and mouse NK cells increased (PC1 40%, PC2 28%). Species differed in expression of key genes after activation, including PRF1, GZMA, SPP1, IL2RB, CTSD and FCER1G, which showed greater increases in abundance counts in mice than dogs and humans. In this first transcriptomic sequencing of dog NK cells, we show distinct gene profiles of resting cells across the most commonly used mouse, dog, and human NK populations, with convergence of dog and human NK cells upon stimulation under these standard conditions. By defining the cross-species comparative transcriptional profiles of putative NK cells, these data fill a gap in translational NK studies.