Haplotype-based analysis of KIR-gene profiles in a south european population-distribution of standard and variant Haplotypes, and identification of novel recombinant structures

Inhibitory Killer-cell Immunoglobulin-like Receptors (KIR) specific for HLA class I molecules enable human natural killer cells to monitor altered antigen presentation in pathogen-infected and tumor cells. KIR genes display extensive copy-number variation and allelic polymorphism. They organize in a series of variable arrangements, designated KIR haplotypes, which derive from duplications of ancestral genes and sequence diversification through point mutation and unequal crossing-over events. Genomic studies have established the organization of multiple KIR haplotypes-many of them are fixed in most human populations, whereas variants of those have less certain distributions. Whilst KIR-gene diversity of many populations and ethnicities has been explored superficially (frequencies of individual genes and presence/absence profiles), less abundant are in-depth analyses of how such diversity emerges from KIR-haplotype structures. We characterize here the genetic diversity of KIR in a sample of 414 Spanish individuals. Using a parsimonious approach, we manage to explain all 38 observed KIR-gene profiles by homo- or heterozygous combinations of six fixed centromeric and telomeric motifs; of six variant gene arrangements characterized previously by us and others; and of two novel haplotypes never detected before in Caucasoids. Associated to the latter haplotypes, we also identified the novel transcribed KIR2DL5B * 0020202 allele, and a chimeric KIR2DS2/KIR2DL3 gene (designated KIR2DL3 * 033) that challenges current criteria for classification and nomenclature of KIR genes and haplotypes.This work was supported by grants SAF2016-80363-C2-1/2-R (Spanish Ministry of Economy and Competitiveness (MINECO)-FEDER, EU), and PCIN-2015-191-C02-02 (FP7-MINECO Infect-ERA program) to CV and ML-B. MM was supported by Fundación Asociación Española Contra el Cáncer (AECC) grant GCB15152947MELE. EC was supported, successively, by grants SAF2010–22153-C03, Fundació La Marató de TV3 121531, and PCIN-2015-191-C02-02. AM was supported by Instituto de Salud Carlos III (ISCIII)/FEDER grant PI19/00328