Prediction and validation of a human immunodeficiency with CRISPR

Inborn errors of immunity (IEI) result in increased morbidity and mortality from infections. However, discovering new IEIs is limited by the clinical identification of rare patient cohorts. To predict immunodeficiency-associated genes in a patient-independent approach, we performed a targeted CRISPR-Cas9 knockout screen in healthy human donor-derived PBMCs and identified myocyte enhancer factor 2C (MEF2C) as essential for primary human natural killer (NK) cell functionality ex vivo. MEF2C haploinsufficient (MCHS) patients and mice displayed impaired NK cell development, ex vivo function, and increased susceptibility to viral infection. MEF2C was required for cytokine-induced changes in NK cell metabolism and SREBP-mediated lipid homeostasis, and oleic acid supplementation restored MCHS patient NK cell cytotoxic function. Thus, we demonstrate a CRISPR-based methodology in primary human immune cells to accelerate the identification of new IEIs, and apply this approach to predict and validate a new NK cell immunodeficiency associated with metabolic and functional defects.