MEF2C is a critical regulator of human NK cell metabolism

Abstract Natural killer (NK) cells are critical for the first line of defense against viral infection and malignancy. While the transcriptional and epigenetic regulation of activated NK cells is well characterized in mice, these processes are not yet fully understood in human NK cells. We performed a targeted CRISPR/Cas9 ribonucleoprotein (RNP) transcription factor screen in mature primary human NK cells to identify putative transcription factors required for optimal effector function. The transcription factor myocyte enhancer factor 2C (MEF2C) emerged as a previously unidentified regulator of NK cell homeostasis, cytokine production, and cytotoxicity. MEF2C-deficient NK cells activated with IL-2 and IL-15 displayed impaired proliferation, degranulation, and production of granzyme B. CRISPR-mediated deletion of MEF2C resulted in disrupted glycolysis and oxidative phosphorylation using both SCENITH and Seahorse extracellular flux analysis. Liquid chromatography/mass spectrometry (LC/MS)-based metabolomics of MEF2C-deficient NK cells revealed reductions in the metabolites glyceraldehyde-3-phosphate and a-ketoglutarate/succinate, accompanied by increased accumulation of lipid metabolism products including phosphorylethanolamine and saturated long-chain fatty acids. In vivo, CRISPR/Cas9 RNP-mediated disruption of MEF2C expression in mouse NK cells resulted in decreased expansion during mouse cytomegalovirus infection. Together, these studies reveal MEF2C as a novel regulator of NK cell effector function through control of multiple critical cell-intrinsic metabolic pathways.