Transcriptional Insights into KIR-educated NK cells — ASN Events

Transcriptional Insights into KIR-educated NK cells (#115)

Sofia I Celli 1 , Ana Codo 1 , Cameron Manes 2 , Christopher Collora 1 , Katherine M Kichula 1 , Noah Cline 1 , Tonya Brunetti 2 , Laurent Gapin 2 , Karl-Johan Malmberg 3 4 , Paul J Norman 1 2 , Liyen Loh 2
  1. Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
  2. Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
  3. The Precision Immunotherapy Alliance, Institute for Clinical Medicine, The University of Oslo, Oslo, Norway
  4. The Center for Infectious Medicine, Department of Medicine, Karolinska Institutet , Solna, Sweden

Natural killer (NK) cells are an innate lymphocyte population that contribute important effector responses during viral infections and tumor surveillance. Critical to NK cell function is the interaction between expressed inhibitory receptors and their cognate ligands, which allows for potent NK cell cytotoxic responses against altered self through a process known as NK cell education. Inhibitory killer cell immunoglobulin-like receptors (KIR) KIR3DL1, KIR2DL1, and KIR2DL3 recognize HLA class I molecules as ligands, and contribute potently to NK cell education. Using our biorepository of high-resolution KIR and HLA genotyped donor PBMCs, we stimulated ex vivo NK cells with the HLA class I deficient cell line 721.221 to demonstrate increased degranulation from genotype-predicted KIR3DL1, KIR2DL1, or KIR2DL3-educated NK cells. We demonstrate increased cytokine and degranulation responses from NK cells educated by two inhibitory KIR, but not three. Although the NK cell education response phenotype and requirements for inhibitory receptor-ligand pairs are well-established, whether transcriptional heterogeneity exists in these education states remains unknown. Based on their HLA-C genotype, we identified 3 donors having uneducated KIR2DL1 and educated KIR2DL3 NK cells. From each donor, we sorted mature NK cells expressing KIR2DL1 or KIR2DL3 for single cell RNA sequencing. Our analysis reveals that the KIR2DL3-educated compartment, relative to KIR2DL1-uneducated, contains a significantly expanded cluster with features of adapted NK cells, based on scoring with an adapted NK cell gene signature and expression of genes including KLRC2, CD2, and IL32. This is consistent across all 3 donors. Overall, this work suggests that either the differentiation of adapted NK cells is restricted to educated NK cells, or that the process of NK cell education renders cells more adapted-like. Ongoing work will investigate this difference.