Gene regulatory programs of NK cells show that NCAM1 (CD56) and KIRs are controlled by genetically polymorphic distal regulatory elements [scATAC-seq]

Owing to their immunoprotective properties, natural killer (NK) cells are critical for the innate response to pathogens, as well as a new wave of cancer immunotherapy that harnesses natural cytotoxicity. We sought to understand the genetic and epigenetic drivers behind human specific NK cell receptors, so that we can better understand the underlying cellular function. Here, we present a transcriptomic, proteomic (CITE-seq), and chromatin (single nuclei ATAC-seq and Hi-C) analysis of human peripheral NK cell subsets, uncovering key regulatory programs governing NK cell differentiation. Through integrative multi-omics, we demonstrate that CD56bright versus CD56dim NK cell subsets have differential distal regulatory element (DRE) landscapes, with fewer accessible DREs in the CD56dim NK cells. We combine epigenetic, chromatin looping, and human genetic data to show mechanisms governing the NCAM1 (encoding CD56) and KIR loci. For example, we identify NCAM1 DREs that bind STAT in most NK cells, while identifying a genetic cohort that has motifs for binding repressive BLIMP1 at the DRE and resulting in less CD56 expression. Together, our findings reveal novel epigenetic and transcriptomic systems for regulation of NK cells cytotoxicity and diversity, deepening our understanding of their function and how transcription factor networks govern CD56bright versus CD56dim phenotypes. Natural killer (NK) cells were isolated from peripheral blood mononuclear cells (PBMCs) using the RosetteSep™ Human NK Cell Enrichment Cocktail (STEMCELL Technologies). ). Following the addition of the cocktail, density gradient centrifugation was performed using Ficoll-Paque to separate enriched NK cells from the remaining blood components. This was performed on three different blood samples. Nuclei were isolated from NK cells and 10x Genomics snATAC-seq protocol was performed