Abstract
Natural killer (NK) cells are fast-acting and versatile lymphocytes that are critical effectors of innate immunity, adaptive immunity, and placental development. Controlling NK cell function are the interactions between killer-cell immunoglobulin-like receptors (KIRs) and their HLA-A, HLA-B and HLA-C ligands. Due to the extensive polymorphism of both KIR and HLA class I, these interactions are highly diversified and specific combinations correlate with protection or susceptibility to a range of infectious, autoimmune, and reproductive disorders. Evolutionary, genetic, and functional studies are consistent with the interactions between KIR and HLA-C being the dominant control mechanism of human NK cells. In addition to their recognition of the C1 and C2 epitopes, increasing evidence points to KIR having a previously unrecognized selectivity for the peptide presented by HLA-C. This selectivity appears to be a conserved feature of activating KIR and may partly explain the slow progress made in identifying their HLA class I ligands. The peptide selectivity of KIR allows NK cells to respond, not only to changes in the surface expression of HLA-C, but also to the more subtle changes in the HLA-C peptidome, such as occur during viral infection and malignant transformation. Here, we review recent advances in understanding of human-specific KIR evolution and how the inhibitory and activating HLA-C receptors allow NK cells to respond to healthy cells, diseased cells, and the semi-allogeneic cells of the fetus.
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References
Abi-Rached L, Parham P (2005) Natural selection drives recurrent formation of activating killer cell immunoglobulin-like receptor and Ly49 from inhibitory homologues. J Exp Med 201(8):1319–1332
Abi-Rached L et al (2010) Human-specific evolution and adaptation led to major qualitative differences in the variable receptors of human and chimpanzee natural killer cells. PLoS Genet 6(11):e1001192
Adams EJ, Parham P (2001) Species-specific evolution of MHC class I genes in the higher primates. Immunol Rev 183:41–64
Alter G et al (2011) HIV-1 adaptation to NK-cell-mediated immune pressure. Nature 476(7358):96–100
Aranda-Romo S et al (2012) Killer-cell immunoglobulin-like receptors (KIR) in severe A (H1N1) 2009 influenza infections. Immunogenetics 64(9):653–662
Arase H et al (2002) Direct recognition of cytomegalovirus by activating and inhibitory NK cell receptors. Science 296(5571):1323–1326
Ayo CM et al (2015) Killer cell immunoglobulin-like receptors and their HLA ligands are related with the immunopathology of Chagas disease. PLoS Negl Trop Dis 9(5):e0003753
Ayo CM et al (2016) Ocular toxoplasmosis: susceptibility in respect to the genes encoding the KIR receptors and their HLA class I ligands. Sci Report 6:36632
Bari R et al (2009) Significant functional heterogeneity among KIR2DL1 alleles and a pivotal role of arginine 245. Blood 114(25):5182–5190
Beltrame LM et al (2013) Influence of KIR genes and their HLA ligands in susceptibility to dengue in a population from southern Brazil. Tissue Antigens 82(6):397–404
Besson C et al (2007) Association of killer cell immunoglobulin-like receptor genes with Hodgkin’s lymphoma in a familial study. PLoS One 2(5):e406
Bettencourt A et al (2014) The role of KIR2DS1 in multiple sclerosis—KIR in Portuguese MS patients. J Neuroimmunol 269(1–2):52–55
Bimber BN, Evans DT (2015) The killer-cell immunoglobulin-like receptors of macaques. Immunol Rev 267(1):246–258
Bimber BN et al (2008) Complete characterization of killer Ig-like receptor (KIR) haplotypes in Mauritian cynomolgus macaques: novel insights into nonhuman primate KIR gene content and organization. J Immunol 181(9):6301–6308
Blokhuis JH et al (2010) The mosaic of KIR haplotypes in rhesus macaques. Immunogenetics 62(5):295–306
Blokhuis JH et al (2017) KIR2DS5 allotypes that recognize the C2 epitope of HLA-C are common among Africans and absent from Europeans. Immunity, Inflammation and Disease, In Press.
Bonagura VR et al (2010) Activating killer cell immunoglobulin-like receptors 3DS1 and 2DS1 protect against developing the severe form of recurrent respiratory papillomatosis. Hum Immunol 71(2):212–219
Borhis G et al (2013) A peptide antagonist disrupts NK cell inhibitory synapse formation. J Immunol 190(6):2924–2930
Boyington JC, Sun PD (2002) A structural perspective on MHC class I recognition by killer cell immunoglobulin-like receptors. Mol Immunol 38(14):1007–1021
Boyington JC et al (2000) Crystal structure of an NK cell immunoglobulin-like receptor in complex with its class I MHC ligand. Nature 405(6786):537–543
Braud VM et al (1998) HLA-E binds to natural killer cell receptors CD94/NKG2A, B and C. Nature 391(6669):795–799
Cassidy S et al (2015) Peptide selectivity discriminates NK cells from KIR2DL2- and KIR2DL3-positive individuals. Eur J Immunol 45(2):492–500
Chandran V et al (2014) Killer-cell immunoglobulin-like receptor gene polymorphisms and susceptibility to psoriatic arthritis. Rheumatology (Oxford) 53(2):233–239
Colonna M et al (1993) HLA-C is the inhibitory ligand that determines dominant resistance to lysis by NK1- and NK2-specific natural killer cells. Proc Natl Acad Sci U S A 90(24):12000–12004
Diaz-Pena R et al (2015) Activating killer immunoglobulin-like receptors genes are associated with increased susceptibility to ankylosing spondylitis. Clin Exp Immunol 180(2):201–206
Estefania E et al (2007) Influence of KIR gene diversity on the course of HSV-1 infection: resistance to the disease is associated with the absence of KIR2DL2 and KIR2DS2. Tissue Antigens 70(1):34–41
Fadda L et al (2010) Peptide antagonism as a mechanism for NK cell activation. Proc Natl Acad Sci U S A 107(22):10160–10165
Fan QR, Long EO, Wiley DC (2001) Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1-HLA-Cw4 complex. Nat Immunol 2(5):452–460
Fusco C et al (2010) KIRs and their HLA ligands in remitting-relapsing multiple sclerosis. J Neuroimmunol 229(1–2):232–237
Garcia KC, Adams EJ (2005) How the T cell receptor sees antigen—a structural view. Cell 122(3):333–336
Gendzekhadze K et al (2009) Co-evolution of KIR2DL3 with HLA-C in a human population retaining minimal essential diversity of KIR and HLA class I ligands. Proc Natl Acad Sci U S A 106(44):18692–18697
Gonzalez-Galarza FF et al (2011) Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. Nucleic Acids Res 39(Database issue):D913–D919
Goodridge JP et al (2013) HLA-F and MHC class I open conformers are ligands for NK cell Ig-like receptors. J Immunol 191(7):3553–3562
Graef T et al (2009) KIR2DS4 is a product of gene conversion with KIR3DL2 that introduced specificity for HLA-A*11 while diminishing avidity for HLA-C. J Exp Med 206(11):2557–2572
Guerini FR et al (2012) Activating KIR/HLA complexes in classic Kaposi’s Sarcoma. Infect Agent Cancer 7:9
Guethlein LA et al (2007) Evolution of killer cell Ig-like receptor (KIR) genes: definition of an orangutan KIR haplotype reveals expansion of lineage III KIR associated with the emergence of MHC-C. J Immunol 179(1):491–504
Guethlein LA et al (2015) Co-evolution of MHC class I and variable NK cell receptors in placental mammals. Immunol Rev 267(1):259–282
Hiby SE et al (2004) Combinations of maternal KIR and fetal HLA-C genes influence the risk of preeclampsia and reproductive success. J Exp Med 200(8):957–965
Hiby SE et al (2008) Association of maternal killer-cell immunoglobulin-like receptors and parental HLA-C genotypes with recurrent miscarriage. Hum Reprod 2008; 23 (4): 972-976. doi:10.1093/humrep/den011
Hiby SE et al (2010) Maternal activating KIRs protect against human reproductive failure mediated by fetal HLA-C2. J Clin Invest 120(11):4102–4110
Hiby SE et al (2014) Maternal KIR in combination with paternal HLA-C2 regulate human birth weight. J Immunol 192(11):5069–5073
Hilton HG et al (2012) Mutation at positively selected positions in the binding site for HLA-C shows that KIR2DL1 is a more refined but less adaptable NK cell receptor than KIR2DL3. J Immunol 189(3):1418–1430
Hilton HG et al (2015a) Polymorphic HLA-C receptors balance the functional characteristics of KIR haplotypes. J Immunol 195(7):3160–3170
Hilton HG et al (2015b) Loss and gain of natural killer cell receptor function in an African hunter-gatherer population. PLoS Genet 11(8):e1005439
Hilton HG et al (2017a) Resurrecting KIR2DP1: a key intermediate in the evolution of human inhibitory NK cell receptors that recognize HLA-C. J Immunol 198(5):1961–1973
Hilton HG et al. (2017b) The intergenic recombinant HLA-B*46:01 has a distinctive peptidome which includes KIR2DL3 ligands. Cell Reports 19(7):1394–1405
Holm SJ et al (2005) Distinct HLA-C/KIR genotype profile associates with guttate psoriasis. J Invest Dermatol 125(4):721–730
Holzemer A et al (2015) Selection of an HLA-C*03:04-restricted HIV-1 p24 gag sequence variant is associated with viral escape from KIR2DL3+ natural killer cells: data from an observational cohort in South Africa. PLoS Med 12(11):e1001900 discussion e00
Horowitz A et al. (2016) Class I HLA haplotypes form two schools that educate NK cells in different ways. Sci Immunol 1(3)
Hou L et al (2010a) African Americans exhibit a predominant allele in the midst of extensive KIR2DL1 allelic diversity. Tissue Antigens 76(1):31–34
Hou YF et al (2010b) Disparate distribution of activating and inhibitory killer cell immunoglobulin-like receptor genes in patients with systemic lupus erythematosus. Lupus 19(1):20–26
Hou Y et al (2015) Association of killer cell immunoglobulin-like receptor and human leucocyte antigen-Cw gene combinations with systemic lupus erythematosus. Clin Exp Immunol 180(2):250–254
Jarduli LR et al (2014) Influence of KIR genes and their HLA ligands in the pathogenesis of leprosy in a hyperendemic population of Rondonopolis, Southern Brazil. BMC Infect Dis 14:438
Jiao YL et al (2008) Polymorphisms of KIRs gene and HLA-C alleles in patients with ankylosing spondylitis: possible association with susceptibility to the disease. J Clin Immunol 28(4):343–349
Jobim M et al (2008) A study of the killer cell immunoglobulin-like receptor gene KIR2DS1 in a Caucasoid Brazilian population with psoriasis vulgaris. Tissue Antigens 72(4):392–396
Kennedy PR et al (2016) Activating KIR2DS4 is expressed by uterine NK cells and contributes to successful pregnancy. J Immunol 197(11):4292–4300
Khakoo SI et al (2004) HLA and NK cell inhibitory receptor genes in resolving hepatitis C virus infection. Science 305(5685):872–874
King A et al (2000) Surface expression of HLA-C antigen by human extravillous trophoblast. Placenta 21(4):376–387
Kruse PH, Rosner C, Walter L (2010) Characterization of rhesus macaque KIR genotypes and haplotypes. Immunogenetics 62(5):281–293
Li JT et al (2016) Killer cell immunoglobulin-like receptor genes and their Hla-C ligands in Hashimoto thyroiditis in a Chinese population. Endocr Pract 22(8):935–940
Littera R et al (2016) Exploring the role of killer cell immunoglobulin-like receptors and their HLA class I ligands in autoimmune hepatitis. PLoS One 11(1):e0146086
Liu J et al (2014) Activating killer cell immunoglobulin-like receptor 2DS2 binds to HLA-A*11. Proc Natl Acad Sci U S A 111(7):2662–2667
Lu C et al (2012) Association of killer cell immunoglobulin-like receptors with pulmonary tuberculosis in Chinese Han. Genet Mol Res 11(2):1370–1378
Luszczek W et al (2004) Gene for the activating natural killer cell receptor, KIR2DS1, is associated with susceptibility to psoriasis vulgaris. Hum Immunol 65(7):758–766
Malnati MS et al (1995) Peptide specificity in the recognition of MHC class I by natural killer cell clones. Science 267(5200):1016–1018
Malnati MS et al (2017) Activating killer immunoglobulin receptors and HLA-C: a successful combination providing HIV-1 control. Sci Report 7:42470
Martin MP et al (2002) Cutting edge: susceptibility to psoriatic arthritis: influence of activating killer Ig-like receptor genes in the absence of specific HLA-C alleles. J Immunol 169(6):2818–2822
Miyashita R et al (2006) Association of killer cell immunoglobulin-like receptor genotypes with microscopic polyangiitis. Arthritis Rheum 54(3):992–997
Moesta AK et al (2008) Synergistic polymorphism at two positions distal to the ligand-binding site makes KIR2DL2 a stronger receptor for HLA-C than KIR2DL3. J Immunol 180(6):3969–3979
Moesta AK et al (2010) Humans differ from other hominids in lacking an activating NK cell receptor that recognizes the C1 epitope of MHC class I. J Immunol 185(7):4233–4237
Moffett A, Colucci F (2015) Co-evolution of NK receptors and HLA ligands in humans is driven by reproduction. Immunol Rev 267(1):283–297
Moffett-King A (2002) Natural killer cells and pregnancy. Nat Rev Immunol 2(9):656–663
Momot T et al (2004) Association of killer cell immunoglobulin-like receptors with scleroderma. Arthritis Rheum 50(5):1561–1565
Nakimuli A et al (2015) A KIR B centromeric region present in Africans but not Europeans protects pregnant women from pre-eclampsia. Proc Natl Acad Sci U S A 112(3):845–850
Niepieklo-Miniewska W et al (2013) Protective effect of the KIR2DS1 gene in atopic dermatitis. Gene 527(2):594–600
Nikitina-Zake L et al (2004) Killer cell immunoglobulin-like receptor genes in Latvian patients with type 1 diabetes mellitus and healthy controls. Ann N Y Acad Sci 1037:161–169
Nourse JP et al (2012) The KIR2DS2/DL2 genotype is associated with adult persistent/chronic and relapsed immune thrombocytopenia independently of FCGR3a-158 polymorphisms. Blood Coagul Fibrinolysis 23(1):45–50
Nowak I et al (2015) KIR2DS5 in the presence of HLA-C C2 protects against endometriosis. Immunogenetics 67(4):203–209
Older Aguilar AM et al (2010) Coevolution of killer cell Ig-like receptors with HLA-C to become the major variable regulators of human NK cells. J Immunol 185(7):4238–4251
Older Aguilar AM et al (2011) Natural variation at position 45 in the D1 domain of lineage III killer cell immunoglobulin-like receptors (KIR) has major effects on the avidity and specificity for MHC class I. Immunogenetics 63(8):543–547
Oliveira LM et al (2017) Reduced frequency of two activating KIR genes in patients with sepsis. Hum Immunol 78(4):363–369
Parham P, Moffett A (2013) Variable NK cell receptors and their MHC class I ligands in immunity, reproduction and human evolution. Nat Rev Immunol 13(2):133–144
Parham P et al (2010) Primate-specific regulation of natural killer cells. J Med Primatol 39(4):194–212
Pellett F et al (2007) KIRs and autoimmune disease: studies in systemic lupus erythematosus and scleroderma. Tissue Antigens 69(Suppl 1):106–108
Pende D et al (2009) Anti-leukemia activity of alloreactive NK cells in KIR ligand-mismatched haploidentical HSCT for pediatric patients: evaluation of the functional role of activating KIR and redefinition of inhibitory KIR specificity. Blood 113(13):3119–3129
Peruzzi M et al (1996) Peptide sequence requirements for the recognition of HLA-B*2705 by specific natural killer cells. J Immunol 157(8):3350–3356
Pydi SS et al (2013) Killer cell immunoglobulin like receptor gene association with tuberculosis. Hum Immunol 74(1):85–92
Pyo C-W, Guethlein LA, Vu Q, Wang R, Abi-Rached L, Norman PJ, Marsh SGE, Miller JS, Parham P, Geraghty DE, Matsunami H (2010) Different patterns of evolution in the centromeric and telomeric regions of group A and B haplotypes of the human killer cell ig-Like receptor locus. PLoS ONE 5(12):e15115
Rajagopalan S, Long EO (1997) The direct binding of a p58 killer cell inhibitory receptor to human histocompatibility leukocyte antigen (HLA)-Cw4 exhibits peptide selectivity. J Exp Med 185(8):1523–1528
Ramirez-De los Santos S et al (2012) Associations of killer cell immunoglobulin-like receptor genes with rheumatoid arthritis. Dis Markers 33(4):201–206
Salim PH et al (2010) Killer cell immunoglobulin-like receptor (KIR) genes in systemic sclerosis. Clin Exp Immunol 160(3):325–330
Saulquin X, Gastinel LN, Vivier E (2003) Crystal structure of the human natural killer cell activating receptor KIR2DS2 (CD158j). J Exp Med 197(7):933–938
Saunders PM et al (2015) A bird’s eye view of NK cell receptor interactions with their MHC class I ligands. Immunol Rev 267(1):148–166
Seymour LA et al (2014) The presence of KIR2DS5 confers protection against adult immune thrombocytopenia. Tissue Antigens 83(3):154–160
Sheereen A et al (2011) A study of KIR genes and HLA-C in Vogt-Koyanagi-Harada disease in Saudi Arabia. Mol Vis 17:3523–3528
Sim MJ et al (2017) Canonical and cross-reactive binding of NK cell inhibitory receptors to HLA-C allotypes is dictated by peptides bound to HLA-C. Front Immunol 8:193
Smith HR et al (2002) Recognition of a virus-encoded ligand by a natural killer cell activation receptor. Proc Natl Acad Sci U S A 99(13):8826–8831
Stewart CA et al (2005) Recognition of peptide-MHC class I complexes by activating killer immunoglobulin-like receptors. Proc Natl Acad Sci U S A 102(37):13224–13229
Storkus WJ et al (1992) Peptide-induced modulation of target cell sensitivity to natural killing. J Immunol 149(4):1185–1190
Suzuki Y et al (2004) Genetic polymorphisms of killer cell immunoglobulin-like receptors are associated with susceptibility to psoriasis vulgaris. J Invest Dermatol 122(5):1133–1136
Thiruchelvam-Kyle L et al. (2017) The activating human NK cell receptor KIR2DS2 recognizes a beta2-microglobulin-independent ligand on cancer cells. J Immunol
Uhrberg M et al (1997) Human diversity in killer cell inhibitory receptor genes. Immunity 7(6):753–763
Valiante NM et al (1997) Functionally and structurally distinct NK cell receptor repertoires in the peripheral blood of two human donors. Immunity 7(6):739–751
van der Ploeg K et al (2017) Modulation of human leukocyte antigen-C by human cytomegalovirus stimulates KIR2DS1 recognition by natural killer cells. Front Immunol 8:298
van der Slik AR et al (2003) KIR in type 1 diabetes: disparate distribution of activating and inhibitory natural killer cell receptors in patients versus HLA-matched control subjects. Diabetes 52(10):2639–2642
van Teijlingen NH et al (2014) Sequence variations in HIV-1 p24 Gag-derived epitopes can alter binding of KIR2DL2 to HLA-C*03:04 and modulate primary natural killer cell function. AIDS 28(10):1399–1408
VandenBussche CJ et al (2006) A single polymorphism disrupts the killer Ig-like receptor 2DL2/2DL3 D1 domain. J Immunol 177(8):5347–5357
Vilches C et al (2000) KIR2DL5, a novel killer-cell receptor with a D0-D2 configuration of Ig-like domains. J Immunol 164(11):5797–5804
Wauquier N et al (2010) Association of KIR2DS1 and KIR2DS3 with fatal outcome in Ebola virus infection. Immunogenetics 62(11–12):767–771
Williams F et al (2005) Activating killer cell immunoglobulin-like receptor gene KIR2DS1 is associated with psoriatic arthritis. Hum Immunol 66(7):836–841
Wilson MJ et al (2000) Plasticity in the organization and sequences of human KIR/ILT gene families. Proc Natl Acad Sci U S A 97(9):4778–4783
Winter CC et al (1998) Direct binding and functional transfer of NK cell inhibitory receptors reveal novel patterns of HLA-C allotype recognition. J Immunol 161(2):571–577
Xiong S et al (2013) Maternal uterine NK cell-activating receptor KIR2DS1 enhances placentation. J Clin Invest 123(10):4264–4272
Yen JH et al (2001) Major histocompatibility complex class I-recognizing receptors are disease risk genes in rheumatoid arthritis. J Exp Med 193(10):1159–1167
Zappacosta F et al (1997) Peptides isolated from HLA-Cw*0304 confer different degrees of protection from natural killer cell-mediated lysis. Proc Natl Acad Sci U S A 94(12):6313–6318
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This article is published in the Special Issue MHC Genes and Their Ligands in Health and Disease with Editor Prof. Ronald Bontrop.
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Hilton, H.G., Parham, P. Missing or altered self: human NK cell receptors that recognize HLA-C. Immunogenetics 69, 567–579 (2017). https://doi.org/10.1007/s00251-017-1001-y
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DOI: https://doi.org/10.1007/s00251-017-1001-y