1
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Noble JA, Besançon S, Sidibé AT, Rozemuller EH, Rijkers M, Dadkhodaie F, de Bruin H, Kooij J, Martin HRN, Ogle GD, Mack SJ. Complete HLA genotyping of type 1 diabetes patients and controls from Mali reveals both expected and novel disease associations. HLA 2024; 103:e15319. [PMID: 38226399 PMCID: PMC10863981 DOI: 10.1111/tan.15319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/07/2023] [Accepted: 11/27/2023] [Indexed: 01/17/2024]
Abstract
HLA genotyping was performed on 99 type 1 diabetes (T1D) patients and 200 controls from Mali. Next-generation sequencing of the classical HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1, and -DPB1 loci revealed strong T1D association for all loci except HLA-C and -DPA1. Class II association is stronger than class I association, with most observed associations predisposing or protective as expected based on previous studies. For example, HLA-DRB1*03:01, HLA-DRB1*09:01, and HLA-DRB1*04:05 predispose for T1D, whereas HLA-DRB1*15:03 is protective. HLA-DPB1*04:02 (OR = 12.73, p = 2.92 × 10-05 ) and HLA-B*27:05 (OR = 21.36, p = 3.72 × 10-05 ) appear highly predisposing, although previous studies involving multiple populations have reported HLA-DPB1*04:02 as T1D-protective and HLA-B*27:05 as neutral. This result may reflect the linkage disequilibrium between alleles on the extended HLA-A*24:02~HLA-B*27:05~HLA-C*02:02~HLA-DRB1*04:05~HLA-DRB4*01:03~HLA-DQB1*02:02~HLA-DQA1*02:01~HLA-DPB1*04:02~HLA-DPA1*01:03 haplotype in this population rather than an effect of either allele itself. Individual amino acid (AA) analyses are consistent with most T1D association attributable to HLA class II rather than class I in this data set. AA-level analyses reveal previously undescribed differences of the HLA-C locus from the HLA-A and HLA-B loci, with more polymorphic positions, spanning a larger portion of the gene. This may reflect additional mechanisms for HLA-C to influence T1D risk, for example, through expression differences or through its role as the dominant ligand for killer cell immunoglobulin-like receptors (KIR). Comparison of these data to those from larger studies and on other populations may facilitate T1D prediction and help elucidate elusive mechanisms of how HLA contributes to T1D risk and autoimmunity.
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Affiliation(s)
- Janelle A Noble
- Children's Hospital Oakland Research Institute, Oakland, California, USA
- Department of Pediatrics, University of California, San Francisco, Oakland, California, USA
| | | | | | | | | | | | | | | | - Harper R N Martin
- Children's Hospital Oakland Research Institute, Oakland, California, USA
| | - Graham D Ogle
- Life for a Child Program, Diabetes Australia, Glebe, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Steven J Mack
- Department of Pediatrics, University of California, San Francisco, Oakland, California, USA
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2
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Philippon C, Tao S, Clement D, Haroun-Izquierdo A, Kichula KM, Netskar H, Brandt L, Oei VS, Kanaya M, Lanuza PM, Schaffer M, Goodridge JP, Horowitz A, Zhu F, Hammer Q, Sohlberg E, Majhi RK, Kveberg L, Önfelt B, Norman PJ, Malmberg KJ. Allelic variation of KIR and HLA tunes the cytolytic payload and determines functional hierarchy of NK cell repertoires. Blood Adv 2023; 7:4492-4504. [PMID: 37327114 PMCID: PMC10440473 DOI: 10.1182/bloodadvances.2023009827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/18/2023] [Accepted: 06/04/2023] [Indexed: 06/18/2023] Open
Abstract
The functionality of natural killer (NK) cells is tuned during education and is associated with remodeling of the lysosomal compartment. We hypothesized that genetic variation in killer cell immunoglobulin-like receptor (KIR) and HLA, which is known to influence the functional strength of NK cells, fine-tunes the payload of effector molecules stored in secretory lysosomes. To address this possibility, we performed a high-resolution analysis of KIR and HLA class I genes in 365 blood donors and linked genotypes to granzyme B loading and functional phenotypes. We found that granzyme B levels varied across individuals but were stable over time in each individual and genetically determined by allelic variation in HLA class I genes. A broad mapping of surface receptors and lysosomal effector molecules revealed that DNAM-1 and granzyme B levels served as robust metric of the functional state in NK cells. Variation in granzyme B levels at rest was tightly linked to the lytic hit and downstream killing of major histocompatibility complex-deficient target cells. Together, these data provide insights into how variation in genetically hardwired receptor pairs tunes the releasable granzyme B pool in NK cells, resulting in predictable hierarchies in global NK cell function.
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Affiliation(s)
- Camille Philippon
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Sudan Tao
- Department of Biomedical Informatics, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Dennis Clement
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Alvaro Haroun-Izquierdo
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Katherine M. Kichula
- Department of Biomedical Informatics, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO
| | - Herman Netskar
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Ludwig Brandt
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Vincent Sheng Oei
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Minoru Kanaya
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Pilar Maria Lanuza
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marie Schaffer
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Amir Horowitz
- Department of Oncological Sciences, The Marc and Jennifer Lipshultz Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Faming Zhu
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Quirin Hammer
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ebba Sohlberg
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rakesh Kumar Majhi
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
| | - Lise Kveberg
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Björn Önfelt
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Paul J. Norman
- Department of Biomedical Informatics, and Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO
| | - Karl-Johan Malmberg
- Precision Immunotherapy Alliance (PRIMA), Institute for Clinical medicine, The University of Oslo, Oslo, Norway
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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3
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Yigitbilek F, Ozdogan E, Abrol N, Park W, Hansen M, Dasari S, Stegall M, Taner T. Liver mesenchymal stem cells are superior inhibitors of NK cell functions through differences in their secretome compared to other mesenchymal stem cells. Front Immunol 2022; 13:952262. [PMID: 36211345 PMCID: PMC9534521 DOI: 10.3389/fimmu.2022.952262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
Liver-resident mesenchymal stem cells (L-MSCs) are superior inhibitors of alloreactive T cell responses compared to their counterparts from bone marrow (BM-MSCs) or adipose tissue (A-MSCs), suggesting a role in liver’s overall tolerogenic microenvironment. Whether L-MSCs also impact NK cell functions differently than other MSCs is not known. We generated and characterized L-MSCs, A-MSCs and BM-MSCs from human tissues. The mass spectrometry analysis demonstrated that L-MSC secretome is uniquely different than that of A-MSC/BM-MSC, with enriched protein sets involved in IFNγ responses and signaling. When co-cultured with primary human NK cells, L-MSCs but not other MSCs, decreased surface expression of activating receptors NKp44 and NKG2D. L-MSCs also decreased IFNγ secretion by IL-2-stimulated NK cells more effectively than other MSCs. Cytolytic function of NK cells were reduced significantly when co-cultured with L-MSCs, whereas A-MSCs or BM-MSCs did not have a major impact. Mechanistic studies showed that the L-MSC-mediated reduction in NK cell cytotoxicity is not through changes in secretion of the cytotoxic proteins Perforin, Granzyme A or B, but through increased production of HLA-C1 found in L-MSC secretome that inhibits NK cells by stimulating their inhibitory receptor KIRDL2/3. L-MSCs are more potent inhibitors of NK cell functions than A-MSC or BM-MSC. Combined with their T cell inhibitory features, these results suggest L-MSCs contribute to the tolerogenic liver microenvironment and liver-induced systemic tolerance often observed after liver transplantation.
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Affiliation(s)
| | - Elif Ozdogan
- Department of Surgery, Mayo Clinic, Rochester, MN, United States
| | - Nitin Abrol
- Department of Surgery, Mayo Clinic, Rochester, MN, United States
| | - Walter D. Park
- Department of Surgery, Mayo Clinic, Rochester, MN, United States
| | | | - Surendra Dasari
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Mark D. Stegall
- Department of Surgery, Mayo Clinic, Rochester, MN, United States
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | - Timucin Taner
- Department of Surgery, Mayo Clinic, Rochester, MN, United States
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
- *Correspondence: Timucin Taner,
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4
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Vollmers S, Lobermeyer A, Niehrs A, Fittje P, Indenbirken D, Nakel J, Virdi S, Brias S, Trenkner T, Sauer G, Peine S, Behrens GM, Lehmann C, Meurer A, Pauli R, Postel N, Roider J, Scholten S, Spinner CD, Stephan C, Wolf E, Wyen C, Richert L, Norman PJ, Sauter J, Schmidt AH, Hoelzemer A, Altfeld M, Körner C. Host KIR/HLA-C Genotypes Determine HIV-Mediated Changes of the NK Cell Repertoire and Are Associated With Vpu Sequence Variations Impacting Downmodulation of HLA-C. Front Immunol 2022; 13:922252. [PMID: 35911762 PMCID: PMC9334850 DOI: 10.3389/fimmu.2022.922252] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/13/2022] [Indexed: 12/29/2022] Open
Abstract
NK cells play a pivotal role in viral immunity, utilizing a large array of activating and inhibitory receptors to identify and eliminate virus-infected cells. Killer-cell immunoglobulin-like receptors (KIRs) represent a highly polymorphic receptor family, regulating NK cell activity and determining the ability to recognize target cells. Human leukocyte antigen (HLA) class I molecules serve as the primary ligand for KIRs. Herein, HLA-C stands out as being the dominant ligand for the majority of KIRs. Accumulating evidence indicated that interactions between HLA-C and its inhibitory KIR2DL receptors (KIR2DL1/L2/L3) can drive HIV-1-mediated immune evasion and thus may contribute to the intrinsic control of HIV-1 infection. Of particular interest in this context is the recent observation that HIV-1 is able to adapt to host HLA-C genotypes through Vpu-mediated downmodulation of HLA-C. However, our understanding of the complex interplay between KIR/HLA immunogenetics, NK cell-mediated immune pressure and HIV-1 immune escape is still limited. Therefore, we investigated the impact of specific KIR/HLA-C combinations on the NK cell receptor repertoire and HIV-1 Vpu protein sequence variations of 122 viremic, untreated HIV-1+ individuals. Compared to 60 HIV-1- controls, HIV-1 infection was associated with significant changes within the NK cell receptor repertoire, including reduced percentages of NK cells expressing NKG2A, CD8, and KIR2DS4. In contrast, the NKG2C+ and KIR3DL2+ NK cell sub-populations from HIV-1+ individuals was enlarged compared to HIV-1- controls. Stratification along KIR/HLA-C genotypes revealed a genotype-dependent expansion of KIR2DL1+ NK cells that was ultimately associated with increased binding affinities between KIR2DL1 and HLA-C allotypes. Lastly, our data hinted to a preferential selection of Vpu sequence variants that were associated with HLA-C downmodulation in individuals with high KIR2DL/HLA-C binding affinities. Altogether, our study provides evidence that HIV-1-associated changes in the KIR repertoire of NK cells are to some extent predetermined by host KIR2DL/HLA-C genotypes. Furthermore, analysis of Vpu sequence polymorphisms indicates that differential KIR2DL/HLA-C binding affinities may serve as an additional mechanism how host genetics impact immune evasion by HIV-1.
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Affiliation(s)
| | | | | | - Pia Fittje
- Leibniz Institute of Virology, Hamburg, Germany
| | | | | | | | - Sebastien Brias
- Leibniz Institute of Virology, Hamburg, Germany
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Gabriel Sauer
- Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Sven Peine
- Institute for Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Georg M.N. Behrens
- Department for Rheumatology and Clinical Immunology, Hannover Medical School, Hannover, Germany
| | - Clara Lehmann
- Department I for Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Anja Meurer
- Center for Internal Medicine and Infectiology, Munich, Germany
| | - Ramona Pauli
- Medizinisches Versorgungszentrum (MVZ) am Isartor, Munich, Germany
| | - Nils Postel
- Prinzmed, Practice for Infectious Diseases, Munich, Germany
| | - Julia Roider
- Department of Internal Medicine IV, Department of Infectious Diseases, Ludwig-Maximilians University Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | | | - Christoph D. Spinner
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Technical University of Munich, School of Medicine, University Hospital rechts der Isar, Department of Internal Medicine II, Munich, Germany
| | - Christoph Stephan
- Infectious Diseases Unit, Goethe-University Hospital Frankfurt, Frankfurt, Germany
| | | | - Christoph Wyen
- Department I for Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, Cologne, Germany
- Praxis am Ebertplatz, Cologne, Germany
| | - Laura Richert
- University of Bordeaux, Inserm U1219 Bordeaux Population Health, Inria Sistm, Bordeaux, France
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO, United States
| | | | | | - Angelique Hoelzemer
- Leibniz Institute of Virology, Hamburg, Germany
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Marcus Altfeld
- Leibniz Institute of Virology, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Christian Körner
- Leibniz Institute of Virology, Hamburg, Germany
- *Correspondence: Christian Körner,
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5
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Pollock NR, Harrison GF, Norman PJ. Immunogenomics of Killer Cell Immunoglobulin-Like Receptor (KIR) and HLA Class I: Coevolution and Consequences for Human Health. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2022; 10:1763-1775. [PMID: 35561968 PMCID: PMC10038757 DOI: 10.1016/j.jaip.2022.04.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/12/2022]
Abstract
Interactions of killer cell immunoglobin-like receptors (KIR) with human leukocyte antigens (HLA) class I regulate effector functions of key cytotoxic cells of innate and adaptive immunity. The extreme diversity of this interaction is genetically determined, having evolved in the ever-changing environment of pathogen exposure. Diversity of KIR and HLA genes is further facilitated by their independent segregation on separate chromosomes. That fetal implantation relies on many of the same types of immune cells as infection control places certain constraints on the evolution of KIR interactions with HLA. Consequently, specific inherited combinations of receptors and ligands may predispose to specific immune-mediated diseases, including autoimmunity. Combinatorial diversity of KIR and HLA class I can also differentiate success rates of immunotherapy directed to these diseases. Progress toward both etiopathology and predicting response to therapy is being achieved through detailed characterization of the extent and consequences of the combinatorial diversity of KIR and HLA. Achieving these goals is more tractable with the development of integrated analyses of molecular evolution, function, and pathology that will establish guidelines for understanding and managing risks. Here, we present what is known about the coevolution of KIR with HLA class I and the impact of their complexity on immune function and homeostasis.
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Affiliation(s)
- Nicholas R Pollock
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo
| | - Genelle F Harrison
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo.
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6
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Meazza R, Falco M, Canevali P, Loiacono F, Colomar-Carando N, Muntasell A, Rea A, Mingari MC, Locatelli F, Moretta L, Lopez-Botet M, Pende D. Characterization of KIR + NK cell subsets with a monoclonal antibody selectively recognizing KIR2DL1 and blocking the specific interaction with HLA-C. HLA 2022; 100:119-132. [PMID: 35439359 PMCID: PMC9543057 DOI: 10.1111/tan.14640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/07/2022] [Accepted: 04/17/2022] [Indexed: 11/28/2022]
Abstract
The phenotypic identification of different NK cell subsets allows more in‐depth characterization of KIR repertoire and function, which are of potential interest in KIR and disease association studies. KIR genes are highly polymorphic, but a great homology exists among the various sequences and few monoclonal antibodies (mAbs) specifically recognize a single KIR. This is the case of HP‐DM1 which was demonstrated by analysis of cell transfectants and epitope mapping to be exclusively KIR2DL1‐specific, covering all allotypes identified to date, except for KIR2DL1*022 and *020, and also to react with KIR2DS1*013. Here, we compared in immunofluorescence analyses the staining of HP‐DM1 with other available mAbs to precisely identify KIR2DL1+ NK cells in potential donors for αβT/B‐depleted haplo‐HSCT, with known KIR genotype. HP‐DM1 mAb was used in combination with EB6 or 11PB6 (anti‐KIR2DL1/S1 and anti‐KIR2DL3*005), 143211 (anti‐KIR2DL1/S5), and HP‐MA4 (anti‐KIR2DL1/S1/S3/S5) mAbs, allowing the accurate identification of different KIR+ NK cell subsets. These phenotypic evaluations appeared useful to dissect the expression pattern of various KIR2D in NK cells from KIR2DL3*005+ individuals, particularly if KIR2DS1 is present. HP‐DM1 mAb remarkably refined NK cell phenotyping of donors carrying KIR2DS5, either in the centromeric or telomeric region. Functional assays with KIR2DL1+/S1+/S5+ NK cells confirmed that only HP‐DM1 exclusively reacts with KIR2DL1. Finally, we demonstrated that HP‐DM1 mAb blocked KIR2DL1 recognition of C2+ HLA‐C. Altogether, the data support that HP‐DM1 is a unique reagent valuable for characterizing KIR+ NK cell subsets.
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Affiliation(s)
| | | | | | | | - Natalia Colomar-Carando
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Aura Muntasell
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Anna Rea
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Maria Cristina Mingari
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Franco Locatelli
- Department of Hematology/Oncology and Cell and Gene Therapy, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy.,Department of Gynecology/Obstetrics and Pediatrics, Sapienza University, Rome, Italy
| | - Lorenzo Moretta
- Department of Immunology, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Miguel Lopez-Botet
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniela Pende
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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7
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Falco M, Meazza R, Alicata C, Canevali P, Muntasell A, Bottino C, Moretta L, Pende D, Lopez-Botet M. Epitope characterization of a monoclonal antibody that selectively recognizes KIR2DL1 allotypes. HLA 2022; 100:107-118. [PMID: 35411634 PMCID: PMC9544867 DOI: 10.1111/tan.14630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022]
Abstract
Killer immunoglobulin‐like receptor (KIR) genes code for a family of inhibitory and activating receptors, finely tuning NK cell function. Numerous studies reported the relevance of KIR allelic polymorphism on KIR expression, ligand affinity, and strength in signal transduction. Although KIR variability, including gene copy number and allelic polymorphism, in combination with HLA class I polymorphism, impacts both KIR expression and NK cell education, only a precise phenotypic analysis can define the size of the different KIRpos NK cell subsets. In this context, reagents recognizing a limited number of KIRs is essential. In this study, we have characterized the specificity of an anti‐KIR mAb termed HP‐DM1. Testing its binding to HEK‐293T cells transfected with plasmids coding for different KIRs, we demonstrated that HP‐DM1 mAb exclusively reacts with KIR2DL1. Using site‐directed mutagenesis, we identified the four amino acids relevant for HP‐DM1 recognition: M44, S67, R68, and T70. HP‐DM1 mAb binds to a conformational epitope including M44, the residue crucial for HLA‐C K80 recognition by KIR2DL1. Based on the HP‐DM1 epitope characterization, we could extend its reactivity to all KIR2DL1 allotypes identified except for KIR2DL1*022 and, most likely, KIR2DL1*020, predicting that it does not recognize any other KIR with the only exception of KIR2DS1*013. Moreover, by identifying the residues relevant for HP‐DM1 binding, continuously updating of its reactivity will be facilitated.
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Affiliation(s)
| | | | | | | | - Aura Muntasell
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Cristina Bottino
- IRCCS Istituto Giannina Gaslini, Genoa, Italy.,DIMES, University of Genoa, Genoa, Italy
| | | | - Daniela Pende
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Miguel Lopez-Botet
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
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8
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Vollmers S, Lobermeyer A, Körner C. The New Kid on the Block: HLA-C, a Key Regulator of Natural Killer Cells in Viral Immunity. Cells 2021; 10:cells10113108. [PMID: 34831331 PMCID: PMC8620871 DOI: 10.3390/cells10113108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 11/01/2022] Open
Abstract
The human leukocyte antigen system (HLA) is a cluster of highly polymorphic genes essential for the proper function of the immune system, and it has been associated with a wide range of diseases. HLA class I molecules present intracellular host- and pathogen-derived peptides to effector cells of the immune system, inducing immune tolerance in healthy conditions or triggering effective immune responses in pathological situations. HLA-C is the most recently evolved HLA class I molecule, only present in humans and great apes. Differentiating from its older siblings, HLA-A and HLA-B, HLA-C exhibits distinctive features in its expression and interaction partners. HLA-C serves as a natural ligand for multiple members of the killer-cell immunoglobulin-like receptor (KIR) family, which are predominately expressed by natural killer (NK) cells. NK cells are crucial for the early control of viral infections and accumulating evidence indicates that interactions between HLA-C and its respective KIR receptors determine the outcome and progression of viral infections. In this review, we focus on the unique role of HLA-C in regulating NK cell functions and its consequences in the setting of viral infections.
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9
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Guethlein LA, Beyzaie N, Nemat-Gorgani N, Wang T, Ramesh V, Marin WM, Hollenbach JA, Schetelig J, Spellman SR, Marsh SGE, Cooley S, Weisdorf DJ, Norman PJ, Miller JS, Parham P. Following Transplantation for Acute Myelogenous Leukemia, Donor KIR Cen B02 Better Protects against Relapse than KIR Cen B01. THE JOURNAL OF IMMUNOLOGY 2021; 206:3064-3072. [PMID: 34117109 DOI: 10.4049/jimmunol.2100119] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/10/2021] [Indexed: 12/11/2022]
Abstract
In the treatment of acute myelogenous leukemia with allogeneic hematopoietic cell transplantation, we previously demonstrated that there is a greater protection from relapse of leukemia when the hematopoietic cell transplantation donor has either the Cen B/B KIR genotype or a genotype having two or more KIR B gene segments. In those earlier analyses, KIR genotyping could only be assessed at the low resolution of gene presence or absence. To give the analysis greater depth, we developed high-resolution KIR sequence-based typing that defines all the KIR alleles and distinguishes the expressed alleles from those that are not expressed. We now describe and analyze high-resolution KIR genotypes for 890 donors of this human transplant cohort. Cen B01 and Cen B02 are the common CenB haplotypes, with Cen B02 having evolved from Cen B01 by deletion of the KIR2DL5, 2DS3/5, 2DP1, and 2DL1 genes. We observed a consistent trend for Cen B02 to provide stronger protection against relapse than Cen B01 This correlation indicates that protection depends on the donor having inhibitory KIR2DL2 and/or activating KIR2DS2, and is enhanced by the donor lacking inhibitory KIR2DL1, 2DL3, and 3DL1. High-resolution KIR typing has allowed us to compare the strength of the interactions between the recipient's HLA class I and the KIR expressed by the donor-derived NK cells and T cells, but no clinically significant interactions were observed. The trend observed between donor Cen B02 and reduced relapse of leukemia points to the value of studying ever larger transplant cohorts.
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Affiliation(s)
- Lisbeth A Guethlein
- Department of Structural Biology, Stanford University, Stanford, CA.,Department of Microbiology and Immunology, Stanford University, Stanford, CA
| | - Niassan Beyzaie
- Department of Structural Biology, Stanford University, Stanford, CA.,Department of Microbiology and Immunology, Stanford University, Stanford, CA
| | - Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University, Stanford, CA.,Department of Microbiology and Immunology, Stanford University, Stanford, CA
| | - Tao Wang
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI
| | | | - Wesley M Marin
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | - Jill A Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA
| | | | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Campus, London, United Kingdom.,University College London Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Sarah Cooley
- Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN; and
| | - Daniel J Weisdorf
- Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN; and
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Aurora, CO
| | - Jeffrey S Miller
- Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN; and
| | - Peter Parham
- Department of Structural Biology, Stanford University, Stanford, CA; .,Department of Microbiology and Immunology, Stanford University, Stanford, CA
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10
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Abstract
In all human cells, human leukocyte antigen (HLA) class I glycoproteins assemble with a peptide and take it to the cell surface for surveillance by lymphocytes. These include natural killer (NK) cells and γδ T cells of innate immunity and αβ T cells of adaptive immunity. In healthy cells, the presented peptides derive from human proteins, to which lymphocytes are tolerant. In pathogen-infected cells, HLA class I expression is perturbed. Reduced HLA class I expression is detected by KIR and CD94:NKG2A receptors of NK cells. Almost any change in peptide presentation can be detected by αβ CD8+ T cells. In responding to extracellular pathogens, HLA class II glycoproteins, expressed by specialized antigen-presenting cells, present peptides to αβ CD4+ T cells. In comparison to the families of major histocompatibility complex (MHC) class I, MHC class II and αβ T cell receptors, the antigenic specificity of the γδ T cell receptors is incompletely understood.
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Affiliation(s)
- Zakia Djaoud
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA; ,
| | - Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA; ,
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11
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Deng Z, Zhen J, Harrison GF, Zhang G, Chen R, Sun G, Yu Q, Nemat-Gorgani N, Guethlein LA, He L, Tang M, Gao X, Cai S, Palmer WH, Shortt JA, Gignoux CR, Carrington M, Zou H, Parham P, Hong W, Norman PJ. Adaptive Admixture of HLA Class I Allotypes Enhanced Genetically Determined Strength of Natural Killer Cells in East Asians. Mol Biol Evol 2021; 38:2582-2596. [PMID: 33616658 PMCID: PMC8136484 DOI: 10.1093/molbev/msab053] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Human natural killer (NK) cells are essential for controlling infection, cancer, and fetal development. NK cell functions are modulated by interactions between polymorphic inhibitory killer cell immunoglobulin-like receptors (KIR) and polymorphic HLA-A, -B, and -C ligands expressed on tissue cells. All HLA-C alleles encode a KIR ligand and contribute to reproduction and immunity. In contrast, only some HLA-A and -B alleles encode KIR ligands and they focus on immunity. By high-resolution analysis of KIR and HLA-A, -B, and -C genes, we show that the Chinese Southern Han (CHS) are significantly enriched for interactions between inhibitory KIR and HLA-A and -B. This enrichment has had substantial input through population admixture with neighboring populations, who contributed HLA class I haplotypes expressing the KIR ligands B*46:01 and B*58:01, which subsequently rose to high frequency by natural selection. Consequently, over 80% of Southern Han HLA haplotypes encode more than one KIR ligand. Complementing the high number of KIR ligands, the CHS KIR locus combines a high frequency of genes expressing potent inhibitory KIR, with a low frequency of those expressing activating KIR. The Southern Han centromeric KIR region encodes strong, conserved, inhibitory HLA-C-specific receptors, and the telomeric region provides a high number and diversity of inhibitory HLA-A and -B-specific receptors. In all these characteristics, the CHS represent other East Asians, whose NK cell repertoires are thus enhanced in quantity, diversity, and effector strength, likely augmenting resistance to endemic viral infections.
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Affiliation(s)
- Zhihui Deng
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
- Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Jianxin Zhen
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
- Central Laboratory, Shenzhen Baoan Women’s and Children’s Hospital, Shenzhen, Guangdong, P. R. China
| | - Genelle F Harrison
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Guobin Zhang
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Rui Chen
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Ge Sun
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Qiong Yu
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Liumei He
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Mingzhong Tang
- Clinical Laboratory, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, P. R. China
| | - Xiaojiang Gao
- Inflammatory Cell Dynamics Section, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Siqi Cai
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - William H Palmer
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Jonathan A Shortt
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Christopher R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD21702, and Ragon Institute of MGH, Cambridge, MA, USA
| | - Hongyan Zou
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wenxu Hong
- Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Shenzhen, Guangdong, P. R. China
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
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12
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Structural plasticity of KIR2DL2 and KIR2DL3 enables altered docking geometries atop HLA-C. Nat Commun 2021; 12:2173. [PMID: 33846289 PMCID: PMC8041999 DOI: 10.1038/s41467-021-22359-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 03/12/2021] [Indexed: 01/07/2023] Open
Abstract
The closely related inhibitory killer-cell immunoglobulin-like receptors (KIR), KIR2DL2 and KIR2DL3, regulate the activation of natural killer cells (NK) by interacting with the human leukocyte antigen-C1 (HLA-C1) group of molecules. KIR2DL2, KIR2DL3 and HLA-C1 are highly polymorphic, with this variation being associated with differences in the onset and progression of some human diseases. However, the molecular bases underlying these associations remain unresolved. Here, we determined the crystal structures of KIR2DL2 and KIR2DL3 in complex with HLA-C*07:02 presenting a self-epitope. KIR2DL2 differed from KIR2DL3 in docking modality over HLA-C*07:02 that correlates with variabilty of recognition of HLA-C1 allotypes. Mutagenesis assays indicated differences in the mechanism of HLA-C1 allotype recognition by KIR2DL2 and KIR2DL3. Similarly, HLA-C1 allotypes differed markedly in their capacity to inhibit activation of primary NK cells. These functional differences derive, in part, from KIR2DS2 suggesting KIR2DL2 and KIR2DL3 binding geometries combine with other factors to distinguish HLA-C1 functional recognition.
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13
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Arima N. Dual effects of natural killer cells in transplantation for leukemia. Crit Rev Oncol Hematol 2020; 158:103206. [PMID: 33388454 DOI: 10.1016/j.critrevonc.2020.103206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 12/09/2020] [Accepted: 12/20/2020] [Indexed: 12/29/2022] Open
Abstract
Natural killer (NK) cells were originally considered to belong to the innate immune system to play a protective role against tumor cells and viral infections. In human, they can recognize self and non-self HLA class 1 as their ligand. So, analyzing the outcomes of allogeneic hematopoietic stem cell transplantation is a good opportunity to know the antitumor effects and regulatory effects of NK cells through HLA class 1 matching and mismatching of donor and recipient. In this review, I looked back on the main analysis results of the past transplants, summarized our reports consisting of many cases in a single ethnic, and showed that NK cells might work oppositely depending on the type of leukemia. New treatment strategies based on these concepts may offer individualized treatment options and ultimately increase offer the possibility of a cure for patients with leukemia.
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Affiliation(s)
- Nobuyoshi Arima
- Department of Hematology, Shinko Hospital, 1-4-47, Wakihamacho, Chuo-ku, Kobe, 651-0072, Hyogo, Japan.
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14
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Centromeric KIR AA Individuals Harbor Particular KIR Alleles Conferring Beneficial NK Cell Features with Implications in Haplo-Identical Hematopoietic Stem Cell Transplantation. Cancers (Basel) 2020; 12:cancers12123595. [PMID: 33271841 PMCID: PMC7760878 DOI: 10.3390/cancers12123595] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/25/2022] Open
Abstract
We have recently shown a broad disparity of Natural Killer (NK) cell responses against leukemia highlighting good and bad responders resting on the Killer cell Immunoglobulin-like Receptors (KIR) and HLA genetics. In this study, we deeply studied KIR2D allele expression, HLA-C recognition and functional effect on NK cells in 108 blood donors in combining high-resolution KIR allele typing and multicolor flow cytometry. The KIR2DL1*003 allotype is associated with centromeric (cen) AA motif and confers the highest NK cell frequency, expression level and strength of KIR/HLA-C interactions compared to the KIR2DL1*002 and KIR2DL1*004 allotypes respectively associated with cenAB and BB motifs. KIR2DL2*001 and *003 allotypes negatively affect the frequency of KIR2DL1+ and KIR2DL3+ NK cells. Altogether, our data suggest that cenAA individuals display more efficient KIR2DL alleles (L1*003 and L3*001) to mount a consistent frequency of KIR2DL+ NK cells and to confer an effective NK cell responsiveness. The transposition of our in vitro observations in the T-replete haplo-identical HSCT context led us to observe that cenAA HSC grafts limit significantly the incidence of relapse in patients with myeloid diseases after T-replete haplo-identical HSCT. As NK cells are crucial in HSCT reconstitution, one could expect that the consideration of KIR2DL1/2/3 allelic polymorphism could help to refine scores used for HSC donor selection.
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15
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Bruijnesteijn J, de Groot NG, Bontrop RE. The Genetic Mechanisms Driving Diversification of the KIR Gene Cluster in Primates. Front Immunol 2020; 11:582804. [PMID: 33013938 PMCID: PMC7516082 DOI: 10.3389/fimmu.2020.582804] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/18/2020] [Indexed: 12/26/2022] Open
Abstract
The activity and function of natural killer (NK) cells are modulated through the interactions of multiple receptor families, of which some recognize MHC class I molecules. The high level of MHC class I polymorphism requires their ligands either to interact with conserved epitopes, as is utilized by the NKG2A receptor family, or to co-evolve with the MHC class I allelic variation, which task is taken up by the killer cell immunoglobulin-like receptor (KIR) family. Multiple molecular mechanisms are responsible for the diversification of the KIR gene system, and include abundant chromosomal recombination, high mutation rates, alternative splicing, and variegated expression. The combination of these genetic mechanisms generates a compound array of diversity as is reflected by the contraction and expansion of KIR haplotypes, frequent birth of fusion genes, allelic polymorphism, structurally distinct isoforms, and variegated expression, which is in contrast to the mainly allelic nature of MHC class I polymorphism in humans. A comparison of the thoroughly studied human and macaque KIR gene repertoires demonstrates a similar evolutionarily conserved toolbox, through which selective forces drove and maintained the diversified nature of the KIR gene cluster. This hypothesis is further supported by the comparative genetics of KIR haplotypes and genes in other primate species. The complex nature of the KIR gene system has an impact upon the education, activity, and function of NK cells in coherence with an individual’s MHC class I repertoire and pathogenic encounters. Although selection operates on an individual, the continuous diversification of the KIR gene system in primates might protect populations against evolving pathogens.
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Affiliation(s)
- Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
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16
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Vargas LDB, Dourado RM, Amorim LM, Ho B, Calonga-Solís V, Issler HC, Marin WM, Beltrame MH, Petzl-Erler ML, Hollenbach JA, Augusto DG. Single Nucleotide Polymorphism in KIR2DL1 Is Associated With HLA-C Expression in Global Populations. Front Immunol 2020; 11:1881. [PMID: 32983108 PMCID: PMC7478174 DOI: 10.3389/fimmu.2020.01881] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022] Open
Abstract
Regulation of NK cell activity is mediated through killer-cell immunoglobulin-like receptors (KIR) ability to recognize human leukocyte antigen (HLA) class I molecules as ligands. Interaction of KIR and HLA is implicated in viral infections, autoimmunity, and reproduction and there is growing evidence of the coevolution of these two independently segregating gene families. By leveraging KIR and HLA-C data from 1000 Genomes consortium we observed that the KIR2DL1 variant rs2304224 * T is associated with lower expression of HLA-C in individuals carrying the ligand HLA-C2 (p = 0.0059). Using flow cytometry, we demonstrated that this variant is also associated with higher expression of KIR2DL1 on the NK cell surface (p = 0.0002). Next, we applied next generation sequencing to analyze KIR2DL1 sequence variation in 109 Euro and 75 Japanese descendants. Analyzing the extended haplotype homozygosity, we show signals of positive selection for rs4806553 * G and rs687000 * G, which are in linkage disequilibrium with rs2304224 * T. Our results suggest that lower expression of HLA-C2 ligands might be compensated for higher expression of the receptor KIR2DL1 and bring new insights into the coevolution of KIR and HLA.
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Affiliation(s)
- Luciana de Brito Vargas
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Renata M Dourado
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Leonardo M Amorim
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Brenda Ho
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Verónica Calonga-Solís
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Hellen C Issler
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Wesley M Marin
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Marcia H Beltrame
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Maria Luiza Petzl-Erler
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Jill A Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Danillo G Augusto
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil.,Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
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17
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Goodson-Gregg FJ, Krepel SA, Anderson SK. Tuning of human NK cells by endogenous HLA-C expression. Immunogenetics 2020; 72:205-215. [PMID: 32219494 PMCID: PMC7182622 DOI: 10.1007/s00251-020-01161-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/11/2020] [Indexed: 12/14/2022]
Abstract
NK cells are primarily responsible for detecting malignant or pathogen-infected cells, and their function is influenced both by stress-associated activating signals and opposing inhibitory signals from receptors that recognize self MHC. The receptors that produce this inhibitory signal shift from the NKG2A:HLA-E system to that of KIR:HLA as the NK cells mature. This maturation is associated with an increase in lytic activity, as well as an increase in HLA-C protein levels controlled by the NK-specific HLA-C promoter, NK-Pro. We propose that modulation of the translatability of HLA-C transcripts in NK cells constitutes an evolutionary mechanism to control cis inhibitory signaling by HLA-C, which fine tunes NK cell activity. Furthermore, the high degree of variability in KIR receptor affinity for HLA alleles, as well as the variable expression levels of both KIR and HLA, suggest an evolutionary requirement for the tuning of NK lytic activity. Various data have demonstrated that mature NK cells may gain or lose lytic activity when placed in different environments. This indicates that NK cell activity may be more a function of constant tuning by inhibitory signals, rather than a static, irreversible "license to kill" granted to mature NK cells. Inhibitory signaling controls the filling of the cytolytic granule reservoir, which becomes depleted if there are insufficient inhibitory signals, leading to a hyporesponsive NK cell. We propose a novel model for the tuning of human NK cell activity via cis interactions in the context of recent findings on the mechanism of NK education.
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Affiliation(s)
- Frederick J Goodson-Gregg
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Stacey A Krepel
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Stephen K Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
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18
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Wright PA. Killer-cell immunoglobulin-like receptor assessment algorithms in haemopoietic progenitor cell transplantation: current perspectives and future opportunities. HLA 2020; 95:435-448. [PMID: 31999071 DOI: 10.1111/tan.13817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/13/2019] [Accepted: 01/22/2020] [Indexed: 12/27/2022]
Abstract
Natural killer cells preferentially target and kill malignant and virally infected cells. Both these properties present compelling clinical utility in the field of haemopoietic progenitor cell transplantation (HPCT), potentially promoting a graft vs leukaemia effect in the absence of graft vs host disease and protecting against cytomegalovirus activation. Killer Ig-like receptors (KIR) play a central role in the cytotoxic action of natural killer cells, providing opportunity for improving transplantation outcomes by prioritising potential donors with optimal characteristics. Numerous algorithms for assessing KIR gene content as part of HPCT donor selection protocols exist, but no single model has been found to be universally applicable in all transplant centres. This review summarises several of the predominant strategies in KIR assessment algorithms, discussing their basic scientific principles, clinical utility and benefits to post-transplant outcomes. Finally, the review will consider how future donor selection protocols could develop towards unifying the concepts of KIR proteomics and genetics for optimising patient care.
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Affiliation(s)
- Paul A Wright
- Transplantation Laboratory, Division of Surgery, Manchester University NHS Foundation Trust, Manchester, United Kingdom
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19
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Sim MJW, Rajagopalan S, Altmann DM, Boyton RJ, Sun PD, Long EO. Human NK cell receptor KIR2DS4 detects a conserved bacterial epitope presented by HLA-C. Proc Natl Acad Sci U S A 2019; 116:12964-12973. [PMID: 31138701 PMCID: PMC6601252 DOI: 10.1073/pnas.1903781116] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Natural killer (NK) cells have an important role in immune defense against viruses and cancer. Activation of human NK cell cytotoxicity toward infected or tumor cells is regulated by killer cell immunoglobulin-like receptors (KIRs) that bind to human leukocyte antigen class I (HLA-I). Combinations of KIR with HLA-I are genetically associated with susceptibility to disease. KIR2DS4, an activating member of the KIR family with poorly defined ligands, is a receptor of unknown function. Here, we show that KIR2DS4 has a strong preference for rare peptides carrying a Trp at position 8 (p8) of 9-mer peptides bound to HLA-C*05:01. The complex of a peptide bound to HLA-C*05:01 with a Trp at p8 was sufficient for activation of primary KIR2DS4+ NK cells, independent of activation by other receptors and of prior NK cell licensing. HLA-C*05:01+ cells that expressed the peptide epitope triggered KIR2DS4+ NK cell degranulation. We show an inverse correlation of the worldwide allele frequency of functional KIR2DS4 with that of HLA-C*05:01, indicative of functional interaction and balancing selection. We found a highly conserved peptide sequence motif for HLA-C*05:01-restricted activation of human KIR2DS4+ NK cells in bacterial recombinase A (RecA). KIR2DS4+ NK cells were stimulated by RecA epitopes from multiple human pathogens, including Helicobacter, Chlamydia, Brucella, and Campylobacter. We predict that over 1,000 bacterial species could activate NK cells through KIR2DS4, and propose that human NK cells also contribute to immune defense against bacteria through recognition of a conserved RecA epitope presented by HLA-C*05:01.
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Affiliation(s)
- Malcolm J W Sim
- Molecular and Cellular Immunology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
- Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - Sumati Rajagopalan
- Molecular and Cellular Immunology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - Daniel M Altmann
- Lung Immunology Group, Department of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Rosemary J Boyton
- Lung Immunology Group, Department of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Peter D Sun
- Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - Eric O Long
- Molecular and Cellular Immunology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852;
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20
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Pende D, Falco M, Vitale M, Cantoni C, Vitale C, Munari E, Bertaina A, Moretta F, Del Zotto G, Pietra G, Mingari MC, Locatelli F, Moretta L. Killer Ig-Like Receptors (KIRs): Their Role in NK Cell Modulation and Developments Leading to Their Clinical Exploitation. Front Immunol 2019; 10:1179. [PMID: 31231370 PMCID: PMC6558367 DOI: 10.3389/fimmu.2019.01179] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/09/2019] [Indexed: 12/19/2022] Open
Abstract
Natural killer (NK) cells contribute to the first line of defense against viruses and to the control of tumor growth and metastasis spread. The discovery of HLA class I specific inhibitory receptors, primarily of killer Ig-like receptors (KIRs), and of activating receptors has been fundamental to unravel NK cell function and the molecular mechanisms of tumor cell killing. Stemmed from the seminal discoveries in early '90s, in which Alessandro Moretta was the major actor, an extraordinary amount of research on KIR specificity, genetics, polymorphism, and repertoire has followed. These basic notions on NK cells and their receptors have been successfully translated to clinical applications, primarily to the haploidentical hematopoietic stem cell transplantation to cure otherwise fatal leukemia in patients with no HLA compatible donors. The finding that NK cells may express the PD-1 inhibitory checkpoint, particularly in cancer patients, may allow understanding how anti-PD-1 therapy could function also in case of HLA class Ineg tumors, usually susceptible to NK-mediated killing. This, together with the synergy of therapeutic anti-checkpoint monoclonal antibodies, including those directed against NKG2A or KIRs, emerging in recent or ongoing studies, opened new solid perspectives in cancer therapy.
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Affiliation(s)
- Daniela Pende
- Laboratory of Immunology, Department of Integrated Oncological Therapies, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Michela Falco
- Laboratory of Clinical and Experimental Immunology, Integrated Department of Services and Laboratories, IRCCS Istituto G. Gaslini, Genoa, Italy
| | - Massimo Vitale
- Laboratory of Immunology, Department of Integrated Oncological Therapies, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Claudia Cantoni
- Laboratory of Clinical and Experimental Immunology, Integrated Department of Services and Laboratories, IRCCS Istituto G. Gaslini, Genoa, Italy
- Department of Experimental Medicine (DIMES), Center of Excellence for Biomedical Research, Università di Genova, Genoa, Italy
| | - Chiara Vitale
- Laboratory of Immunology, Department of Integrated Oncological Therapies, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Experimental Medicine (DIMES), Università di Genova, Genoa, Italy
| | - Enrico Munari
- Department of Pathology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Italy
| | - Alice Bertaina
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics Stanford School of Medicine, Stanford, CA, United States
| | - Francesca Moretta
- Department of Laboratory Medicine, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Italy
| | - Genny Del Zotto
- Core Facilities, Integrated Department of Services and Laboratories, IRCCS Istituto G. Gaslini, Genoa, Italy
| | - Gabriella Pietra
- Laboratory of Immunology, Department of Integrated Oncological Therapies, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Experimental Medicine (DIMES), Università di Genova, Genoa, Italy
| | - Maria Cristina Mingari
- Laboratory of Immunology, Department of Integrated Oncological Therapies, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Experimental Medicine (DIMES), Center of Excellence for Biomedical Research, Università di Genova, Genoa, Italy
| | - Franco Locatelli
- Department of Oncohematology and Cell and Gene Therapy, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Lorenzo Moretta
- Laboratory of Tumor Immunology, Department of Immunology, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
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21
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Nemat-Gorgani N, Guethlein LA, Henn BM, Norberg SJ, Chiaroni J, Sikora M, Quintana-Murci L, Mountain JL, Norman PJ, Parham P. Diversity of KIR, HLA Class I, and Their Interactions in Seven Populations of Sub-Saharan Africans. THE JOURNAL OF IMMUNOLOGY 2019; 202:2636-2647. [PMID: 30918042 DOI: 10.4049/jimmunol.1801586] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/13/2019] [Indexed: 12/21/2022]
Abstract
HLA class I and KIR sequences were determined for Dogon, Fulani, and Baka populations of western Africa, Mbuti of central Africa, and Datooga, Iraqw, and Hadza of eastern Africa. Study of 162 individuals identified 134 HLA class I alleles (41 HLA-A, 60 HLA-B, and 33 HLA-C). Common to all populations are three HLA-C alleles (C1+C*07:01, C1+C*07:02, and C2+C*06:02) but no HLA-A or -B Unexpectedly, no novel HLA class I was identified in these previously unstudied and anthropologically distinctive populations. In contrast, of 227 KIR detected, 22 are present in all seven populations and 28 are novel. A high diversity of HLA A-C-B haplotypes was observed. In six populations, most haplotypes are represented just once. But in the Hadza, a majority of haplotypes occur more than once, with 2 having high frequencies and 10 having intermediate frequencies. The centromeric (cen) part of the KIR locus exhibits an even balance between cenA and cenB in all seven populations. The telomeric (tel) part has an even balance of telA to telB in East Africa, but this changes across the continent to where telB is vestigial in West Africa. All four KIR ligands (A3/11, Bw4, C1, and C2) are present in six of the populations. HLA haplotypes of the Iraqw and Hadza encode two KIR ligands, whereas the other populations have an even balance between haplotypes encoding one and two KIR ligands. Individuals in these African populations have a mean of 6.8-8.4 different interactions between KIR and HLA class I, compared with 2.9-6.5 for non-Africans.
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Affiliation(s)
- Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, NY 11794
| | | | - Jacques Chiaroni
- UMR 7268-Anthropologie Bio-Culturelle, Droit, Éthique et Santé, Aix-Marseille Université, l'Etablissement Français du Sang, Centre National de la Recherche Scientifique, 13344 Marseille, France
| | - Martin Sikora
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark
| | | | | | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO 80045; and.,Department of Immunology, University of Colorado, Denver, CO 80045
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305;
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22
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Wroblewski EE, Parham P, Guethlein LA. Two to Tango: Co-evolution of Hominid Natural Killer Cell Receptors and MHC. Front Immunol 2019; 10:177. [PMID: 30837985 PMCID: PMC6389700 DOI: 10.3389/fimmu.2019.00177] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/21/2019] [Indexed: 12/16/2022] Open
Abstract
Natural killer (NK) cells have diverse roles in hominid immunity and reproduction. Modulating these functions are the interactions between major histocompatibility complex (MHC) class I molecules that are ligands for two NK cell surface receptor types. Diverse killer cell immunoglobulin-like receptors (KIR) bind specific motifs encoded within the polymorphic MHC class I cell surface glycoproteins, while, in more conserved interactions, CD94:NKG2A receptors recognize MHC-E with bound peptides derived from MHC class I leader sequences. The hominid lineage presents a choreographed co-evolution of KIR with their MHC class I ligands. MHC-A, -B, and -C are present in all great apes with species-specific haplotypic variation in gene content. The Bw4 epitope recognized by lineage II KIR is restricted to MHC-B but also present on some gorilla and human MHC-A. Common to great apes, but rare in humans, are MHC-B possessing a C1 epitope recognized by lineage III KIR. MHC-C arose from duplication of MHC-B and is fixed in all great apes except orangutan, where it exists on approximately 50% of haplotypes and all allotypes are C1-bearing. Recent study showed that gorillas possess yet another intermediate MHC organization compared to humans. Like orangutans, but unlike the Pan-Homo species, duplication of MHC-B occurred. However, MHC-C is fixed, and the MHC-C C2 epitope (absent in orangutans) emerges. The evolution of MHC-C drove expansion of its cognate lineage III KIR. Recently, position −21 of the MHC-B leader sequence has been shown to be critical in determining NK cell educational outcome. In humans, methionine (−21M) results in CD94:NKG2A-focused education whereas threonine (−21T) produces KIR-focused education. This is another dynamic position among hominids. Orangutans have exclusively −21M, consistent with their intermediate stage in lineage III KIR-focused evolution. Gorillas have both −21M and −21T, like humans, but they are unequally encoded by their duplicated B genes. Chimpanzees have near-fixed −21T, indicative of KIR-focused NK education. Harmonious with this observation, chimpanzee KIR exhibit strong binding and, compared to humans, smaller differences between binding levels of activating and inhibitory KIR. Consistent between these MHC-NK cell receptor systems over the course of hominid evolution is the evolution of polymorphism favoring the more novel and dynamic KIR system.
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Affiliation(s)
- Emily E Wroblewski
- Department of Anthropology, Washington University, St. Louis, MO, United States
| | - Peter Parham
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Lisbeth A Guethlein
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, United States
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23
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Huhn O, Chazara O, Ivarsson MA, Retière C, Venkatesan TC, Norman PJ, Hilton HG, Jayaraman J, Traherne JA, Trowsdale J, Ito M, Kling C, Parham P, Ghadially H, Moffett A, Sharkey AM, Colucci F. High-Resolution Genetic and Phenotypic Analysis of KIR2DL1 Alleles and Their Association with Pre-Eclampsia. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2018; 201:2593-2601. [PMID: 30249807 PMCID: PMC6258046 DOI: 10.4049/jimmunol.1800860] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/22/2018] [Indexed: 12/29/2022]
Abstract
Killer-cell Ig-like receptor (KIR) genes are inherited as haplotypes. They are expressed by NK cells and linked to outcomes of infectious diseases and pregnancy in humans. Understanding how genotype relates to phenotype is difficult because of the extensive diversity of the KIR family. Indeed, high-resolution KIR genotyping and phenotyping in single NK cells in the context of disease association is lacking. In this article, we describe a new method to separate NK cells expressing allotypes of the KIR2DL1 gene carried by the KIR A haplotype (KIR2DL1A) from those expressing KIR2DL1 alleles carried by the KIR B haplotype (KIR2DL1B). We find that in KIR AB heterozygous individuals, different KIR2DL1 allotypes can be detected in both peripheral blood and uterine NK cells. Using this new method, we demonstrate that both blood and uterine NK cells codominantly express KIR2DL1A and KIR2DL1B allotypes but with a predominance of KIR2DL1A variants, which associate with enhanced NK cell function. In a case-control study of pre-eclampsia, we show that KIR2DL1A, not KIR2DL1B, associates with increased disease risk. This method will facilitate our understanding of how individual KIR2DL1 allelic variants affect NK cell function and contribute to disease risk.
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Affiliation(s)
- Oisín Huhn
- Department of Obstetrics and Gynaecology, University of Cambridge School of Clinical Medicine, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0SW, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- MedImmune Ltd., Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Olympe Chazara
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Martin A Ivarsson
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Christelle Retière
- Etablissement Français du Sang, Université de Nantes, 44011 Nantes, France
- Centre de Recherche en Cancérologie et Immunologie Nantes Angers, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
- Centre de Recherche en Cancérologie et Immunologie Nantes Angers, INSERM U1232, CNRS, Université d'Angers, 49035 Angers, France
| | - Timothy C Venkatesan
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Hugo G Hilton
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Jyothi Jayaraman
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - James A Traherne
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - John Trowsdale
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Mitsutero Ito
- Department of Genetics, University of Cambridge, Cambridge CB2 3DY, United Kingdom; and
| | | | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | | | - Ashley Moffett
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Andrew M Sharkey
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom;
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Francesco Colucci
- Department of Obstetrics and Gynaecology, University of Cambridge School of Clinical Medicine, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0SW, United Kingdom;
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
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24
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Nemat-Gorgani N, Hilton HG, Henn BM, Lin M, Gignoux CR, Myrick JW, Werely CJ, Granka JM, Möller M, Hoal EG, Yawata M, Yawata N, Boelen L, Asquith B, Parham P, Norman PJ. Different Selected Mechanisms Attenuated the Inhibitory Interaction of KIR2DL1 with C2 + HLA-C in Two Indigenous Human Populations in Southern Africa. THE JOURNAL OF IMMUNOLOGY 2018; 200:2640-2655. [PMID: 29549179 DOI: 10.4049/jimmunol.1701780] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 02/21/2018] [Indexed: 01/03/2023]
Abstract
The functions of human NK cells in defense against pathogens and placental development during reproduction are modulated by interactions of killer cell Ig-like receptors (KIRs) with HLA-A, -B and -C class I ligands. Both receptors and ligands are highly polymorphic and exhibit extensive differences between human populations. Indigenous to southern Africa are the KhoeSan, the most ancient group of modern human populations, who have highest genomic diversity worldwide. We studied two KhoeSan populations, the Nama pastoralists and the ≠Khomani San hunter-gatherers. Comprehensive next-generation sequence analysis of HLA-A, -B, and -C and all KIR genes identified 248 different KIR and 137 HLA class I, which assort into ∼200 haplotypes for each gene family. All 74 Nama and 78 ≠Khomani San studied have different genotypes. Numerous novel KIR alleles were identified, including three arising by intergenic recombination. On average, KhoeSan individuals have seven to eight pairs of interacting KIR and HLA class I ligands, the highest diversity and divergence of polymorphic NK cell receptors and ligands observed to date. In this context of high genetic diversity, both the Nama and the ≠Khomani San have an unusually conserved, centromeric KIR haplotype that has arisen to high frequency and is different in the two KhoeSan populations. Distinguishing these haplotypes are independent mutations in KIR2DL1, which both prevent KIR2DL1 from functioning as an inhibitory receptor for C2+ HLA-C. The relatively high frequency of C2+ HLA-C in the Nama and the ≠Khomani San appears to have led to natural selection against strong inhibitory C2-specific KIR.
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Affiliation(s)
- Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Hugo G Hilton
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
| | - Meng Lin
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado, Denver, CO 80045.,Department of Biostatistics, University of Colorado, Denver, CO 80045
| | - Justin W Myrick
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
| | - Cedric J Werely
- South African Medical Research Council Centre for Tuberculosis Research, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Julie M Granka
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Marlo Möller
- South African Medical Research Council Centre for Tuberculosis Research, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Eileen G Hoal
- South African Medical Research Council Centre for Tuberculosis Research, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Makoto Yawata
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, National University of Singapore, Singapore 119077, Singapore.,Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore 117609, Singapore
| | - Nobuyo Yawata
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305.,Section of Ophthalmology, Department of Medicine, Fukuoka Dental College, Fukuoka 814-0193, Japan; and
| | - Lies Boelen
- Section of Immunology, Imperial College London, London SW7 2BX, United Kingdom
| | - Becca Asquith
- Section of Immunology, Imperial College London, London SW7 2BX, United Kingdom
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
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25
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Hilton HG, McMurtrey CP, Han AS, Djaoud Z, Guethlein LA, Blokhuis JH, Pugh JL, Goyos A, Horowitz A, Buchli R, Jackson KW, Bardet W, Bushnell DA, Robinson PJ, Mendoza JL, Birnbaum ME, Nielsen M, Garcia KC, Hildebrand WH, Parham P. The Intergenic Recombinant HLA-B∗46:01 Has a Distinctive Peptidome that Includes KIR2DL3 Ligands. Cell Rep 2018; 19:1394-1405. [PMID: 28514659 PMCID: PMC5510751 DOI: 10.1016/j.celrep.2017.04.059] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/07/2017] [Accepted: 04/20/2017] [Indexed: 01/26/2023] Open
Abstract
HLA-B∗46:01 was formed by an intergenic mini-conversion, between HLA-B∗15:01 and HLA-C∗01:02, in Southeast Asia during the last 50,000 years, and it has since become the most common HLA-B allele in the region. A functional effect of the mini-conversion was introduction of the C1 epitope into HLA-B∗46:01, making it an exceptional HLA-B allotype that is recognized by the C1-specific natural killer (NK) cell receptor KIR2DL3. High-resolution mass spectrometry showed that HLA-B∗46:01 has a low-diversity peptidome that is distinct from those of its parents. A minority (21%) of HLA-B∗46:01 peptides, with common C-terminal characteristics, form ligands for KIR2DL3. The HLA-B∗46:01 peptidome is predicted to be enriched for peptide antigens derived from Mycobacterium leprae. Overall, the results indicate that the distinctive peptidome and functions of HLA-B∗46:01 provide carriers with resistance to leprosy, which drove its rapid rise in frequency in Southeast Asia. The interlocus recombinant HLA-B∗46:01 is found at high frequency in Southeast Asia HLA-B∗46:01 has a low-diversity peptidome that is distinct from both its parents A subset of HLA-B∗46:01 peptides provides ligands for the NK cell receptor KIR2DL3 The unique features of HLA-B∗46:01 correlate with protection against leprosy
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Affiliation(s)
- Hugo G Hilton
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Curtis P McMurtrey
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Alex S Han
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Zakia Djaoud
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lisbeth A Guethlein
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jeroen H Blokhuis
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jason L Pugh
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ana Goyos
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Amir Horowitz
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Rico Buchli
- Pure Protein LLC, Oklahoma City, OK 73104, USA
| | - Ken W Jackson
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Wilfred Bardet
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - David A Bushnell
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Philip J Robinson
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Juan L Mendoza
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michael E Birnbaum
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - K Christopher Garcia
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - William H Hildebrand
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Peter Parham
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
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26
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Parham P, Guethlein LA. Genetics of Natural Killer Cells in Human Health, Disease, and Survival. Annu Rev Immunol 2018; 36:519-548. [PMID: 29394121 DOI: 10.1146/annurev-immunol-042617-053149] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Natural killer (NK) cells have vital functions in human immunity and reproduction. In the innate and adaptive immune responses to infection, particularly by viruses, NK cells respond by secreting inflammatory cytokines and killing infected cells. In reproduction, NK cells are critical for genesis of the placenta, the organ that controls the supply of oxygen and nutrients to the growing fetus. Controlling NK cell functions are interactions of HLA class I with inhibitory NK cell receptors. First evolved was the conserved interaction of HLA-E with CD94:NKG2A; later established were diverse interactions of HLA-A, -B, and -C with killer cell immunoglobulin-like receptors. Characterizing the latter interactions is rapid evolution, which distinguishes human populations and all species of higher primate. Driving this evolution are the different and competing selections imposed by pathogens on NK cell-mediated immunity and by the constraints of human reproduction on NK cell-mediated placentation. Promoting rapid evolution is independent segregation of polymorphic receptors and ligands throughout human populations.
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Affiliation(s)
- Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, California 94305, USA; ,
| | - Lisbeth A Guethlein
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, California 94305, USA; ,
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27
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Owers KA, Sjödin P, Schlebusch CM, Skoglund P, Soodyall H, Jakobsson M. Adaptation to infectious disease exposure in indigenous Southern African populations. Proc Biol Sci 2018; 284:rspb.2017.0226. [PMID: 28381615 DOI: 10.1098/rspb.2017.0226] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/08/2017] [Indexed: 02/04/2023] Open
Abstract
Genetic analyses can provide information about human evolutionary history that cannot always be gleaned from other sources. We evaluated evidence of selective pressure due to introduced infectious diseases in the genomes of two indigenous southern African San groups-the ‡Khomani who had abundant contact with other people migrating into the region and the more isolated Ju|'hoansi. We used a dual approach to test for increased selection on immune genes compared with the rest of the genome in these groups. First, we calculated summary values of statistics that measure genomic signatures of adaptation to contrast selection signatures in immune genes and all genes. Second, we located regions of the genome with extreme values of three selection statistics and examined these regions for enrichment of immune genes. We found stronger and more abundant signals of selection in immune genes in the ‡Khomani than in the Ju|'hoansi. We confirm this finding within each population to avoid effects of different demographic histories of the two populations. We identified eight immune genes that have potentially been targets of strong selection in the ‡Khomani, whereas in the Ju|'hoansi, no immune genes were found in the genomic regions with the strongest signals of selection. We suggest that the more abundant signatures of selection at immune genes in the ‡Khomani could be explained by their more frequent contact with immigrant groups, which likely led to increased exposure and adaptation to introduced infectious diseases.
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Affiliation(s)
- Katharine A Owers
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden.,Department of Epidemiology of Microbial Diseases, Yale University School of Public Health, New Haven, CT, USA
| | - Per Sjödin
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Carina M Schlebusch
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Pontus Skoglund
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Himla Soodyall
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
| | - Mattias Jakobsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden .,Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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28
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Meyer D, C Aguiar VR, Bitarello BD, C Brandt DY, Nunes K. A genomic perspective on HLA evolution. Immunogenetics 2018; 70:5-27. [PMID: 28687858 PMCID: PMC5748415 DOI: 10.1007/s00251-017-1017-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 06/16/2017] [Indexed: 12/20/2022]
Abstract
Several decades of research have convincingly shown that classical human leukocyte antigen (HLA) loci bear signatures of natural selection. Despite this conclusion, many questions remain regarding the type of selective regime acting on these loci, the time frame at which selection acts, and the functional connections between genetic variability and natural selection. In this review, we argue that genomic datasets, in particular those generated by next-generation sequencing (NGS) at the population scale, are transforming our understanding of HLA evolution. We show that genomewide data can be used to perform robust and powerful tests for selection, capable of identifying both positive and balancing selection at HLA genes. Importantly, these tests have shown that natural selection can be identified at both recent and ancient timescales. We discuss how findings from genomewide association studies impact the evolutionary study of HLA genes, and how genomic data can be used to survey adaptive change involving interaction at multiple loci. We discuss the methodological developments which are necessary to correctly interpret genomic analyses involving the HLA region. These developments include adapting the NGS analysis framework so as to deal with the highly polymorphic HLA data, as well as developing tools and theory to search for signatures of selection, quantify differentiation, and measure admixture within the HLA region. Finally, we show that high throughput analysis of molecular phenotypes for HLA genes-namely transcription levels-is now a feasible approach and can add another dimension to the study of genetic variation.
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Affiliation(s)
- Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil.
| | - Vitor R C Aguiar
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Bárbara D Bitarello
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Débora Y C Brandt
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
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29
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Hilton HG, Parham P. Missing or altered self: human NK cell receptors that recognize HLA-C. Immunogenetics 2017; 69:567-579. [PMID: 28695291 DOI: 10.1007/s00251-017-1001-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 05/10/2017] [Indexed: 12/11/2022]
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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Affiliation(s)
- Hugo G Hilton
- Departments of Structural Biology and Microbiology & Immunology, Stanford University, Fairchild D-159, 299 Campus Drive West, Stanford, CA, 94305, USA
| | - Peter Parham
- Departments of Structural Biology and Microbiology & Immunology, Stanford University, Fairchild D-159, 299 Campus Drive West, Stanford, CA, 94305, USA.
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30
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Chapel A, Garcia-Beltran WF, Hölzemer A, Ziegler M, Lunemann S, Martrus G, Altfeld M. Peptide-specific engagement of the activating NK cell receptor KIR2DS1. Sci Rep 2017; 7:2414. [PMID: 28546555 PMCID: PMC5445099 DOI: 10.1038/s41598-017-02449-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/11/2017] [Indexed: 01/10/2023] Open
Abstract
The activating NK cell receptor KIR2DS1 has been shown to be involved in many disorders including autoimmune diseases, malignancies and pregnancy outcomes. However, the precise ligands and functions of this receptor remain unclear. We aimed to gain a better understanding of the factors involved in the binding of KIR2DS1 and its inhibitory counterpart KIR2DL1 to HLA class I molecules, and the consequences for KIR2DS1+ NK-cell function. A systematic screen that assessed binding to 97 HLA-I proteins confirmed that KIR2DS1-binding was narrowly restricted to HLA-C group 2 complexes, while KIR2DL1 showed a broader binding specificity. Using KIR2DS1ζ+ Jurkat reporter-cells and peptide-pulsed 721.221.TAP1KO-HLA-C*06:02 cells, we identified the synthetic peptide SRGPVHHLL presented by HLA-C*06:02 that strongly engaged KIR2DS1- and KIR2DL1-binding. Functional analysis showed that this HLA-C*06:02-presented peptide can furthermore activate primary KIR2DS1(+) NK cell clones. Thus, we demonstrated peptide-dependent binding of the activating NK cell receptor KIR2DS1, providing new insights into the underlying mechanisms involved in KIR2DS1-related disorders.
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Affiliation(s)
- Anaïs Chapel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Angelique Hölzemer
- Department of Internal Medicine, University Hospital Eppendorf (UKE), Hamburg, Germany
| | - Maja Ziegler
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sebastian Lunemann
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Gloria Martrus
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Marcus Altfeld
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.
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31
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Wroblewski EE, Guethlein LA, Norman PJ, Li Y, Shaw CM, Han AS, Ndjango JBN, Ahuka-Mundeke S, Georgiev AV, Peeters M, Hahn BH, Parham P. Bonobos Maintain Immune System Diversity with Three Functional Types of MHC-B. THE JOURNAL OF IMMUNOLOGY 2017; 198:3480-3493. [PMID: 28348269 PMCID: PMC5469624 DOI: 10.4049/jimmunol.1601955] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/01/2017] [Indexed: 11/19/2022]
Abstract
Fast-evolving MHC class I polymorphism serves to diversify NK cell and CD8 T cell responses in individuals, families, and populations. Because only chimpanzee and bonobo have strict orthologs of all HLA class I, their study gives unique perspectives on the human condition. We defined polymorphism of Papa-B, the bonobo ortholog of HLA-B, for six wild bonobo populations. Sequences for Papa-B exon 2 and 3 were determined from the genomic DNA in 255 fecal samples, minimally representing 110 individuals. Twenty-two Papa-B alleles were defined, each encoding a different Papa-B protein. No Papa-B is identical to any chimpanzee Patr-B, human HLA-B, or gorilla Gogo-B. Phylogenetic analysis identified a clade of MHC-B, defined by residues 45-74 of the α1 domain, which is broadly conserved among bonobo, chimpanzee, and gorilla. Bonobo populations have 3-14 Papa-B allotypes. Three Papa-B are in all populations, and they are each of a different functional type: allotypes having the Bw4 epitope recognized by killer cell Ig-like receptors of NK cells, allotypes having the C1 epitope also recognized by killer cell Ig-like receptors, and allotypes having neither epitope. For population Malebo, these three Papa-B are the only Papa-B allotypes. Although small in number, their sequence divergence is such that the nucleotide diversity (mean proportional distance) of Papa-B in Malebo is greater than in the other populations and is also greater than expected for random combinations of three Papa-B Overall, Papa-B has substantially less diversity than Patr-B in chimpanzee subspecies and HLA-B in indigenous human populations, consistent with bonobo having experienced narrower population bottlenecks.
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Affiliation(s)
- Emily E Wroblewski
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Christiana M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alex S Han
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Jean-Bosco N Ndjango
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, 2012 Kisangani, Democratic Republic of the Congo
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomédicales, 1197 Kinshasa, Democratic Republic of the Congo.,University of Kinshasa, 190 Kinshasa, Democratic Republic of the Congo.,Institut de Recherche pour le Développement, Université de Montpellier, 34394 Montpellier, France; and
| | - Alexander V Georgiev
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Martine Peeters
- Institut de Recherche pour le Développement, Université de Montpellier, 34394 Montpellier, France; and
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
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32
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Hilton HG, Blokhuis JH, Guethlein LA, Norman PJ, Parham P. Resurrecting KIR2DP1: A Key Intermediate in the Evolution of Human Inhibitory NK Cell Receptors That Recognize HLA-C. THE JOURNAL OF IMMUNOLOGY 2017; 198:1961-1973. [PMID: 28122963 DOI: 10.4049/jimmunol.1601835] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/28/2016] [Indexed: 12/14/2022]
Abstract
KIR2DP1 is an inactive member of the human lineage III KIR family, which includes all HLA-C-specific receptor genes. The lethal, and only, defect in KIR2DP1 is a nucleotide deletion in codon 88. Fixed in modern humans, the deletion is also in archaic human genomes. KIR2DP1 is polymorphic, with dimorphism at specificity-determining position 44. By repairing the deletion, we resurrected 11 alleles of KIR2DP1F , the functional antecedent of KIR2DP1 We demonstrate how K44-KIR2DP1F with lysine 44 recognized C1+HLA-C, whereas T44-KIR2DP1F recognized C2+HLA-C. Dimorphisms at 12 other KIR2DP1F residues modulate receptor avidity or signaling. KIR2DP1 and KIR2DL1 are neighbors in the centromeric KIR region and are in tight linkage disequilibrium. Like KIR2DL1, KIR2DP1 contributed to CenA and CenB KIR haplotype differences. Encoded on CenA, C1-specific K44-KIR2DP1F were stronger receptors than the attenuated C2-specific T44-KIR2DP1F encoded on CenB The last common ancestor of humans and chimpanzees had diverse lineage III KIR that passed on to chimpanzees but not to humans. Early humans inherited activating KIR2DS4 and an inhibitory lineage III KIR, likely encoding a C1-specific receptor. The latter spawned the modern family of HLA-C receptors. KIR2DP1F has properties consistent with KIR2DP1F having been the founder gene. The first KIR2DP1F alleles encoded K44-C1 receptors; subsequently KIR2DP1F alleles encoding T44-C2 receptors evolved. The emergence of dedicated KIR2DL2/3 and KIR2DL1 genes encoding C1 and C2 receptors, respectively, could have led to obsolescence of KIR2DP1F Alternatively, pathogen subversion caused its demise. Preservation of KIR2DP1F functional polymorphism was a side effect of fixation of the deletion in KIR2DP1F by micro gene conversion.
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Affiliation(s)
- Hugo G Hilton
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305; and .,Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94305
| | - Jeroen H Blokhuis
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305; and.,Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94305
| | - Lisbeth A Guethlein
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305; and.,Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94305
| | - Paul J Norman
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305; and.,Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94305
| | - Peter Parham
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305; and .,Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94305
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33
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Béziat V, Hilton HG, Norman PJ, Traherne JA. Deciphering the killer-cell immunoglobulin-like receptor system at super-resolution for natural killer and T-cell biology. Immunology 2016; 150:248-264. [PMID: 27779741 PMCID: PMC5290243 DOI: 10.1111/imm.12684] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/12/2016] [Accepted: 10/17/2016] [Indexed: 12/13/2022] Open
Abstract
Killer-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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Affiliation(s)
- Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,Imagine Institute, Paris Descartes University, Paris, France
| | - Hugo G Hilton
- Departments of Structural Biology and Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | - Paul J Norman
- Departments of Structural Biology and Microbiology & Immunology, Stanford University, Stanford, CA, USA
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34
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Guethlein LA, Norman PJ, Hilton HG, Parham P. Co-evolution of MHC class I and variable NK cell receptors in placental mammals. Immunol Rev 2016; 267:259-82. [PMID: 26284483 DOI: 10.1111/imr.12326] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Shaping natural killer (NK) cell functions in human immunity and reproduction are diverse killer cell immunoglobulin-like receptors (KIRs) that recognize polymorphic MHC class I determinants. A survey of placental mammals suggests that KIRs serve as variable NK cell receptors only in certain primates and artiodactyls. Divergence of the functional and variable KIRs in primates and artiodactyls predates placental reproduction. Among artiodactyls, cattle but not pigs have diverse KIRs. Catarrhine (humans, apes, and Old World monkeys) and platyrrhine (New World monkeys) primates, but not prosimians, have diverse KIRs. Platyrrhine and catarrhine systems of KIR and MHC class I are highly diverged, but within the catarrhines, a stepwise co-evolution of MHC class I and KIR is discerned. In Old World monkeys, diversification focuses on MHC-A and MHC-B and their cognate lineage II KIR. With evolution of C1-bearing MHC-C from MHC-B, as informed by orangutan, the focus changes to MHC-C and its cognate lineage III KIR. Evolution of C2 from C1 and fixation of MHC-C drove further elaboration of MHC-C-specific KIR, as exemplified by chimpanzee. In humans, the evolutionary trajectory changes again. Emerging from reorganization of the KIR locus and selective attenuation of KIR avidity for MHC class I are the functionally distinctive KIR A and KIR B haplotypes.
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Affiliation(s)
- Lisbeth A Guethlein
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul J Norman
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Hugo G Hilton
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
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35
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Abstract
Natural killer cells are a diverse group of innate lymphocytes that are specialized to rapidly respond to cancerous or virus-infected cells. NK cell function is controlled by the integration of signals from activating and inhibitory receptors expressed at the cell surface. Variegated expression patterns of these activating and inhibitory receptors at the single cell level leads to a highly diverse NK cell repertoire. Here I review the factors that influence NK cell repertoire diversity and its functional consequences for our ability to fight viruses.
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Affiliation(s)
- Catherine A. Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine
- Immunology Program, Stanford University School of Medicine, Stanford, California
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36
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Hilton HG, Guethlein LA, Goyos A, Nemat-Gorgani N, Bushnell DA, Norman PJ, Parham P. Polymorphic HLA-C Receptors Balance the Functional Characteristics of KIR Haplotypes. THE JOURNAL OF IMMUNOLOGY 2015; 195:3160-70. [PMID: 26311903 DOI: 10.4049/jimmunol.1501358] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/22/2015] [Indexed: 01/04/2023]
Abstract
The human killer cell Ig-like receptor (KIR) locus comprises two groups of KIR haplotypes, termed A and B. These are present in all human populations but with different relative frequencies, suggesting they have different functional properties that underlie their balancing selection. We studied the genomic organization and functional properties of the alleles of the inhibitory and activating HLA-C receptors encoded by KIR haplotypes. Because every HLA-C allotype functions as a ligand for KIR, the interactions between KIR and HLA-C dominate the HLA class I-mediated regulation of human NK cells. The C2 epitope is recognized by inhibitory KIR2DL1 and activating KIR2DS1, whereas the C1 epitope is recognized by inhibitory KIR2DL2 and KIR2DL3. This study shows that the KIR2DL1, KIR2DS1, and KIR2DL2/3 alleles form distinctive phylogenetic clades that associate with specific KIR haplotypes. KIR A haplotypes are characterized by KIR2DL1 alleles that encode strong inhibitory C2 receptors and KIR2DL3 alleles encoding weak inhibitory C1 receptors. In striking contrast, KIR B haplotypes are characterized by KIR2DL1 alleles that encode weak inhibitory C2 receptors and KIR2DL2 alleles encoding strong inhibitory C1 receptors. The wide-ranging properties of KIR allotypes arise from substitutions throughout the KIR molecule. Such substitutions can influence cell surface expression, as well as the avidity and specificity for HLA-C ligands. Consistent with the crucial role of inhibitory HLA-C receptors in self-recognition, as well as NK cell education and response, most KIR haplotypes have both a functional C1 and C2 receptor, despite the considerable variation that occurs in ligand recognition and surface expression.
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Affiliation(s)
- Hugo G Hilton
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Ana Goyos
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - David A Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
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