Application of a novel branched-DNA assay to quantify killer immunoglobulin-like receptor (KIR) mRNA expression identifies tissue compartmentalization in naïve and SIV-infected rhesus macaques

Abstract

Natural killer and cytotoxic CD8+ T cells are essential effectors of innate systemic antiviral and antitumor immune responses. Their effector functions and target cell recognition are partly regulated by a polymorphic family of activating and inhibitory killer-cell immunoglobulin-like receptors (KIRs) that interact with major histocompatibility complex (MHC) class I molecules. In Rhesus macaques (Macaca mulatta) (RM), a well-established model for studying simian immunodeficiency virus (SIV) infection and cellular immunobiology, the KIR gene family is highly diverse but remains poorly characterized across tissue compartments. In this study, we used a branched DNA, amplification-free assay with high specificity and reproducibility to simultaneously measure mRNA expression of six KIR genes (Mamu-KIR1D, Mamu-KIR3DH5, Mamu-KIR3DL2, Mamu-KIR3DL4, Mamu-KIR3DH, and Mamu-KIR3DL0) in mononuclear cells from peripheral blood, lymph nodes, and spleen of both naïve and chronically lentivirus-infected RM. Our findings reveal tissue-specific expression patterns of KIR genes that are differentially affected by chronic lentivirus infection, emphasizing the importance of compartmentalized KIR regulation in viral pathogenesis. This proof-of-concept study presents a reliable and scalable framework for the detailed characterization of the KIR gene repertoire in non-human primate models, providing a valuable alternative to traditional qPCR for profiling gene expression in complex tissues.