IPD—the Immuno Polymorphism Database

Robinson, James T.; Halliwell, Jason A.; McWilliam, Hamish; López, Rodrigo; Marsh, Steven G.E.

doi:10.1093/nar/gks1140

Cited by 240 publications

(135 citation statements)

References 47 publications

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“…2b). None of these changes has been identified in the 27 KIR2DL4 allotypes described to date (Goodridge et al 2007; Hou et al 2011; Robinson et al 2013). The glutamine residue at position 109 introduces a third alternative amino acid at a known polymorphic site (Fig.…”

Section: Resultsmentioning

confidence: 93%

“…When required, PCR products were cloned using Topo-pcr2.1 vector (Invitrogen, Carlsbad, CA) and sequenced using M13 and internal primers. Four newly-discovered KIR alleles were validated as recommended by the curators of the Immuno Polymorphism Database (IPD) (Robinson et al 2013). For each individual in which a ‘new allele’ was detected, five or more clones for the allele were sequenced.…”

Section: Methodsmentioning

confidence: 99%

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KIR diversity in Māori and Polynesians: populations in which HLA-B is not a significant KIR ligand

et al. 2014

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HLA class I molecules and killer cell immunoglobulin-like receptors (KIR) form a diverse system of ligands and receptors that individualize human immune systems in ways that improve the survival of individuals and populations. Human settlement of Oceania by island-hopping East and Southeast Asian migrants started ~3,500 years ago. Subsequently, New Zealand was reached ~750 years ago by ancestral Māori. To examine how this history impacted KIR and HLA diversity, and their functional interaction, we defined at high resolution the allelic and haplotype diversity of the 13 expressed KIR genes in 49 Māori and 34 Polynesians. Eighty KIR variants, including four ‘new’ alleles, were defined; as were 35 centromeric and 22 telomeric KIR region haplotypes, which combine to give >50 full-length KIR haplotypes. Two new and divergent variant KIR form part of a telomeric KIR haplotype, which appears derived from Papua New Guinea and was probably obtained by the Asian migrants en route to Polynesia. Māori and Polynesian KIR are very similar, but differ significantly from African, European, Japanese and Amerindian KIR. Māori and Polynesians have high KIR haplotype diversity with corresponding allotype diversity being maintained throughout the KIR locus. Within the population each individual has a unique combination of HLA class I and KIR. Characterizing Māori and Polynesians is a paucity of HLA-B allotypes recognized by KIR. Compensating for this deficiency are high frequencies (>50%) of HLA-A allotypes recognized by KIR. These HLA-A allotypes are ones that modern humans likely acquired from archaic humans at a much earlier time.

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Section: Resultsmentioning

confidence: 93%

Section: Methodsmentioning

confidence: 99%

KIR diversity in Māori and Polynesians: populations in which HLA-B is not a significant KIR ligand

et al. 2014

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“…The cross-reactivity of the anti-human KIR2D mAb NKVFS1 with D233 allotypes of Mamu-KIR3DL01, which comprise 20 of the 27 defined Mamu-KIR3DL01 allotypes (45), effectively doubles the number of KIR-defined NK cell subsets that can be studied in the rhesus macaque. Although several mAbs to rhesus macaque KIRs were recently described, only one was specific for a single KIR (52).…”

Section: Discussionmentioning

confidence: 99%

“…The final sequence assemblies were then blasted against a database of all KIRs published in Genbank to determine the identity of the KIR alleles for each animal. Allele designations were assigned by the Immuno Polymorphism Database (45). …”

Section: Methodsmentioning

confidence: 99%

KIR3DL01 Recognition of Bw4 Ligands in the Rhesus Macaque: Maintenance of Bw4 Specificity since the Divergence of Apes and Old World Monkeys

Schafer

Colantonio

Neidermyer

et al. 2014

The Journal of Immunology

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The identification of MHC class I ligands for rhesus macaque KIRs is fundamental to our basic understanding of KIR and MHC class I co-evolution and to the study of NK cell responses in this non-human primate model for AIDS and other viral diseases. Here we show that Mamu-KIR3DL01, which is expressed by approximately 90% of rhesus macaques, recognizes MHC class I molecules with a Bw4 motif. Primary NK cells expressing Mamu-KIR3DL01 were identified by staining with a mAb herein shown to bind Mamu-KIR3DL01 allotypes with an aspartic acid at position 233. The cytolytic activity of Mamu-KIR3DL01+ NK cells was suppressed by cell lines expressing the Bw4 molecules Mamu-B*007:01, -B*041:01, -B*058:02, and -B*065:01. The Bw4 motif was necessary for Mamu-KIR3DL01 recognition, since substitutions in this region abrogated Mamu-KIR3DL01+ NK cell inhibition. However, the presence of a Bw4 motif was not sufficient for recognition, since another Bw4 molecule, Mamu-B*017:01, failed to suppress the cytolytic activity of these NK cells. Replacement of three residues in Mamu-B*017:01, predicted to be KIR-contacts based on the 3-dimensional structure of the human KIR3DL1-HLA-Bw4 complex, with the corresponding residues at these positions for the other Mamu-Bw4 ligands restored Mamu-KIR3DL01+ NK cell inhibition. These results define the ligand specificity of one of the most polymorphic and commonly expressed KIRs in the rhesus macaque, and reveal similarities in Bw4 recognition by Mamu-KIR3DL01 and human KIR3DL1, despite the absence of an orthologous relationship between these two KIRs or conservation of surface residues predicted to interact with MHC class I ligands.

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“…4). 132 However, the exploration of functional allotypic variation in activating KIR is in its infancy, and several studies point to its potential importance. Examples include the observation that KIR2DS1 allotypes recognize C2‐bearing HLA‐C with a range of avidities40 and that KIR3DS1*014, but not KIR3DS1*013, recognizes the HLA‐Bw4 epitope 65.…”

Section: Kir Ligand Bindingmentioning

confidence: 99%

Deciphering the killer‐cell immunoglobulin‐like receptor system at super‐resolution for natural killer and T‐cell biology

et al. 2016

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SummaryKiller‐cell immunoglobulin‐like receptors (KIRs) are components of two fundamental biological systems essential for human health and survival. First, they contribute to host immune responses, both innate and adaptive, through their expression by natural killer cells and T cells. Second, KIR play a key role in regulating placentation, and hence reproductive success. Analogous to the diversity of their human leucocyte antigen class I ligands, KIR are extremely polymorphic. In this review, we describe recent developments, fuelled by methodological advances, that are helping to decipher the KIR system in terms of haplotypes, polymorphisms, expression patterns and their ligand interactions. These developments are delivering deeper insight into the relevance of KIR in immune system function, evolution and disease.

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IPD—the Immuno Polymorphism Database

Cited by 240 publications

References 47 publications

KIR diversity in Māori and Polynesians: populations in which HLA-B is not a significant KIR ligand

KIR diversity in Māori and Polynesians: populations in which HLA-B is not a significant KIR ligand

KIR3DL01 Recognition of Bw4 Ligands in the Rhesus Macaque: Maintenance of Bw4 Specificity since the Divergence of Apes and Old World Monkeys

Deciphering the killer‐cell immunoglobulin‐like receptor system at super‐resolution for natural killer and T‐cell biology

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