An archaic HLA class I receptor allele diversifies natural killer cell-driven immunity in First Nations peoples of Oceania.

Genetic variation in host immunity impacts the disproportionate burden of infectious diseases that can be experienced by First Nations peoples. Polymorphic human leukocyte antigen (HLA) class I and killer cell immunoglobulin-like receptors (KIRs) are key regulators of natural killer (NK) cells, which mediate early infection control. How this variation impacts their responses across populations is unclear. We show that HLA-A ^∗ 24:02 became the dominant ligand for inhibitory KIR3DL1 in First Nations peoples across Oceania, through positive natural selection. We identify KIR3DL1 ^∗ 114, widespread across and unique to Oceania, as an allele lineage derived from archaic humans. KIR3DL1 ^∗ 114 ⁺ NK cells from First Nations Australian donors are inhibited through binding HLA-A ^∗ 24:02. The KIR3DL1 ^∗ 114 lineage is defined by phenylalanine at residue 166. Structural and binding studies show phenylalanine 166 forms multiple unique contacts with HLA-peptide complexes, increasing both affinity and specificity. Accordingly, assessing immunogenetic variation and the functional implications for immunity are fundamental toward understanding population-based disease associations.
Competing Interests: Declaration of interests A.G.I. has shares in Galatea Bio, Inc. G.F.H. is currently an employee of Tempus AI. S.C.W. is currently an employee of Miltenyi Biotec Asia Pacific Pte Ltd. L.H. is affiliated with the Department of Internal Medicine II, University Hospital Tübingen, Tübingen, Germany. J.W. is affiliated with The Malignant Hematology, Transplantation, and Cellular Therapy Services, Alfred Health, Melbourne, VIC, Australia. S.Z. is affiliated with the Protein Production Facility (PPF) of the Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia. G.M.-M. is affiliated with the HLA Histocompatibility and Immunogenetics Laboratory, Vitalant, Phoenix, AZ, USA. J.P.V. is affiliated with St. Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia.
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