KIR gene complexity in primates: A genetic arsenal equipped to arm and control a killer

Natural killer (NK) cells represent a major component of the immune system, and are involved in the protection against pathogens, the surveillance of tumor cells, and the regulation of other players in the immune response. The education, activation and functioning of NK cells is tightly modulated by two major sets of inhibitory and activating receptors. A conserved set of NK cell receptors include members of the CD94:NKG2 family that recognize MHC-E molecules. The other set comprise the killer cell immunoglobulin-like receptors (KIR), which represent a diverse group of structurally similar transmembrane molecules. Members of the KIR family co-evolved with their diversified MHC-A, -B and -C ligands that are in a continuous arms race with pathogens. The KIR receptors are encoded within the Leukocyte Receptor Complex (LRC) on chromosome 19q13.4 and segregate independent from their MHC ligands. The KIR genes are arranged in a polygenic cluster conform a head-to-tail tandem organization, which is characterized by extensive diversification generated by point mutations and chromosomal recombination. As such, the KIR gene content is highly unique at an individual level and displays differential gene distribution at a population level. The highly variable KIR gene content, in combination with their polymorphic MHC class I ligands, is associated with differential susceptibility and protection in health and disease. In this thesis, we aimed to improve the KIR gene characterization in humans and macaques. The latter species is commonly used as model in preclinical studies to develop medicine and therapies. Their KIR gene system and NK cell biology display similarities to humans, with species-specific variation mainly reflected in the KIR receptor structure and haplotype organization. Initial transcriptome characterization studies using conventional sequencing techniques suggested a highly plastic KIR gene system in macaques that might exceed the complexity observed in humans. However, a comprehensive overview of the macaque KIR gene system is lacking. The application of single-molecule real-time (SMRT) sequencing platforms, which are commercialized by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), enables studies on the complexity of the KIR gene cluster at higher levels of resolution, with enhanced throughput and read length. These novel sequencing techniques provided comprehensive insights on KIR allele variation, chromosomal recombination events, fusion gene entities, alternative splicing profiles and KIR haplotype organizations, which together indicate a rapidly evolving KIR gene system in primates.