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Železnjak J, Lisnić VJ, Popović B, Lisnić B, Babić M, Halenius A, L'Hernault A, Roviš TL, Hengel H, Erhard F, Redwood AJ, Vidal SM, Dölken L, Krmpotić A, Jonjić S. The complex of MCMV proteins and MHC class I evades NK cell control and drives the evolution of virus-specific activating Ly49 receptors. J Exp Med 2019; 216:1809-1827. [PMID: 31142589 PMCID: PMC6683999 DOI: 10.1084/jem.20182213] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/04/2019] [Accepted: 05/07/2019] [Indexed: 11/05/2022] Open
Abstract
Železnjak et al. demonstrate that two MCMV-encoded proteins interact with MHC I molecules, forming an altered-self complex that prevents missing self recognition by increasing specificity for inhibitory Ly49 receptors. This led to the evolution of CMV-specific activating Ly49s. CMVs efficiently target MHC I molecules to avoid recognition by cytotoxic T cells. However, the lack of MHC I on the cell surface renders the infected cell susceptible to NK cell killing upon missing self recognition. To counter this, mouse CMV (MCMV) rescues some MHC I molecules to engage inhibitory Ly49 receptors. Here we identify a new viral protein, MATp1, that is essential for MHC I surface rescue. Rescued altered-self MHC I molecules show increased affinity to inhibitory Ly49 receptors, resulting in inhibition of NK cells despite substantially reduced MHC I surface levels. This enables the virus to evade recognition by licensed NK cells. During evolution, this novel viral immune evasion mechanism could have prompted the development of activating NK cell receptors that are specific for MATp1-modified altered-self MHC I molecules. Our study solves a long-standing conundrum of how MCMV avoids recognition by NK cells, unravels a fundamental new viral immune evasion mechanism, and demonstrates how this forced the evolution of virus-specific activating MHC I–restricted Ly49 receptors.
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Affiliation(s)
- Jelena Železnjak
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.,Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Vanda Juranić Lisnić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.,Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Branka Popović
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Berislav Lisnić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.,Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Marina Babić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.,Innate Immunity, German Rheumatism Research Centre, a Leibniz Institute, Berlin, Germany
| | - Anne Halenius
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anne L'Hernault
- Precision Medicine and Genomics, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, UK
| | - Tihana Lenac Roviš
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.,Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Hartmut Hengel
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Florian Erhard
- Institute of Virology and Immunobiology, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Alec J Redwood
- Institute for Respiratory Health, University of Western Australia, Western Australia, Australia
| | - Silvia M Vidal
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Center for Complex Traits, McGill University, Montreal, Quebec, Canada
| | - Lars Dölken
- Institute of Virology and Immunobiology, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Astrid Krmpotić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Stipan Jonjić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia .,Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
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Goodier MR, Jonjić S, Riley EM, Juranić Lisnić V. CMV and natural killer cells: shaping the response to vaccination. Eur J Immunol 2017; 48:50-65. [PMID: 28960320 DOI: 10.1002/eji.201646762] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/14/2017] [Accepted: 09/22/2017] [Indexed: 12/14/2022]
Abstract
Cytomegaloviruses (CMVs) are highly prevalent, persistent human pathogens that not only evade but also shape our immune responses. Natural killer (NK) cells play an important role in the control of CMV and CMVs have in turn developed a plethora of immunoevasion mechanisms targeting NK cells. This complex interplay can leave a long-lasting imprint on the immune system in general and affect responses toward other pathogens and vaccines. This review aims to provide an overview of NK cell biology and development, the manipulation of NK cells by CMVs and the potential impact of these evasion strategies on responses to vaccination.
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Affiliation(s)
- Martin R Goodier
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK
| | - Stipan Jonjić
- Department for Histology and Embryology and Center for Proteomics, Faculty of Medicine, University of Rijeka, Croatia
| | - Eleanor M Riley
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK
| | - Vanda Juranić Lisnić
- Department for Histology and Embryology and Center for Proteomics, Faculty of Medicine, University of Rijeka, Croatia
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Detecting signatures of past pathogen selection on human HLA loci: are there needles in the haystack? Parasitology 2017; 145:731-739. [PMID: 28809135 DOI: 10.1017/s0031182017001159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human leucocyte antigens (HLAs) are responsible for the display of peptide fragments for recognition by T-cell receptors. The gene family encoding them is thus integral to human adaptive immunity, and likely to be under strong pathogen selection. Despite this, it has proved difficult to demonstrate specific examples of pathogen-HLA coevolution. Selection from multiple pathogens simultaneously could explain why the evolutionary signatures of particular pathogens on HLAs have proved elusive. Here, we present an individual-based model of HLA evolution in the presence of two mortality-causing pathogens. We demonstrate that it is likely that individual pathogen species causing high mortality have left recognizable signatures on the HLA genomic region, despite more than one pathogen being present. Such signatures are likely to exist at the whole-population level, and involve haplotypic combinations of HLA genes rather than single loci.
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Carrillo-Bustamante P, de Boer RJ, Keşmir C. Specificity of inhibitory KIRs enables NK cells to detect changes in an altered peptide environment. Immunogenetics 2017; 70:87-97. [PMID: 28695292 PMCID: PMC5775373 DOI: 10.1007/s00251-017-1019-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 06/20/2017] [Indexed: 12/12/2022]
Abstract
The activity of natural killer (NK) cells is tightly regulated by inhibitory and activating receptors. Inhibitory killer immunoglobulin-like receptors (iKIRs) survey the surface of target cells by monitoring the expression of human leukocyte antigen (HLA) class I. The binding of iKIRs has been shown to be sensitive to the peptides presented by HLA class I, implying that iKIRs have the ability to detect the changes in the repertoire of peptide-HLA class I complexes (pHLA), a process occurring during viral infection and in tumor cells. To study how the pHLA repertoire changes upon infection, and whether an iKIR is able to detect these changes, we study peptides eluted from cells prior and after infection with measles virus (MV). Remarkably, most changes in the repertoire of potential iKIR ligands are predicted to be caused by the altered expression of self-peptides. We show that an iKIR can detect these changes in the presented peptides only if it is sufficiently specific, e.g., if iKIRs can distinguish between different amino acids in the contact residues (e.g., position 7 and 8). Our analysis further indicates that one single iKIR per host is not sufficient to detect changes in the peptide repertoire, suggesting that a multigene family encoding for different iKIRs is required for successful peptide recognition.
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Affiliation(s)
- Paola Carrillo-Bustamante
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands. .,Center for Modeling and Simulation in the Biosciences (BIOMS/IWR), Max Planck Institute, Heidelberg, Germany.
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Can Keşmir
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
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Penman BS, Moffett A, Chazara O, Gupta S, Parham P. Reproduction, infection and killer-cell immunoglobulin-like receptor haplotype evolution. Immunogenetics 2016; 68:755-764. [PMID: 27517293 PMCID: PMC5056949 DOI: 10.1007/s00251-016-0935-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/24/2016] [Indexed: 12/20/2022]
Abstract
Killer-cell immunoglobulin-like receptors (KIRs) are encoded by one of the most polymorphic families in the human genome. KIRs are expressed on natural killer (NK) cells, which have dual roles: (1) in fighting infection and (2) in reproduction, regulating hemochorial placentation. Uniquely among primates, human KIR genes are arranged into two haplotypic combinations: KIR A and KIR B. It has been proposed that KIR A is specialized to fight infection, whilst KIR B evolved to help ensure successful reproduction. Here we demonstrate that a combination of infectious disease selection and reproductive selection can drive the evolution of KIR B-like haplotypes from a KIR A-like founder haplotype. Continued selection to survive and to reproduce maintains a balance between KIR A and KIR B.
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Affiliation(s)
- Bridget S Penman
- Department of Zoology, University of Oxford, Tinbergen Building, South Parks Road, Oxford, OX13PS, UK.
| | - Ashley Moffett
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Olympe Chazara
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, Tinbergen Building, South Parks Road, Oxford, OX13PS, UK
| | - Peter Parham
- Department of Structural Biology, Stanford University, Stanford, CA, 94035, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94035, USA
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Abstract
Natural killer (NK) cells are immune cells that play a crucial role against viral infections and tumors. To be tolerant against healthy tissue and simultaneously attack infected cells, the activity of NK cells is tightly regulated by a sophisticated array of germline-encoded activating and inhibiting receptors. The best characterized mechanism of NK cell activation is “missing self” detection, i.e., the recognition of virally infected or transformed cells that reduce their MHC expression to evade cytotoxic T cells. To monitor the expression of MHC-I on target cells, NK cells have monomorphic inhibitory receptors which interact with conserved MHC molecules. However, there are other NK cell receptors (NKRs) encoded by gene families showing a remarkable genetic diversity. Thus, NKR haplotypes contain several genes encoding for receptors with activating and inhibiting signaling, and that vary in gene content and allelic polymorphism. But if missing-self detection can be achieved by a monomorphic NKR system why have these polygenic and polymorphic receptors evolved? Here, we review the expansion of NKR receptor families in different mammal species, and we discuss several hypotheses that possibly underlie the diversification of the NK cell receptor complex, including the evolution of viral decoys, peptide sensitivity, and selective MHC-downregulation.
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Carrillo-Bustamante P, Kesmir C, de Boer RJ. Can Selective MHC Downregulation Explain the Specificity and Genetic Diversity of NK Cell Receptors? Front Immunol 2015; 6:311. [PMID: 26136746 PMCID: PMC4468891 DOI: 10.3389/fimmu.2015.00311] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 06/01/2015] [Indexed: 11/26/2022] Open
Abstract
Natural killer (NK) cells express inhibiting receptors (iNKRs), which specifically bind MHC-I molecules on the surface of healthy cells. When the expression of MHC-I on the cell surface decreases, which might occur during certain viral infections and cancer, iNKRs lose inhibiting signals and the infected cells become target for NK cell activation (missing-self detection). Although the detection of MHC-I deficient cells can be achieved by conserved receptor-ligand interactions, several iNKRs are encoded by gene families with a remarkable genetic diversity, containing many haplotypes varying in gene content and allelic polymorphism. So far, the biological function of this expansion within the NKR cluster has remained poorly understood. Here, we investigate whether the evolution of diverse iNKRs genes can be driven by a specific viral immunoevasive mechanism: selective MHC downregulation. Several viruses, including EBV, CMV, and HIV, decrease the expression of MHC-I to escape from T cell responses. This downregulation does not always affect all MHC loci in the same way, as viruses target particular MHC molecules. To study the selection pressure of selective MHC downregulation on iNKRs, we have developed an agent-based model simulating an evolutionary scenario of hosts infected with herpes-like viruses, which are able to selectively downregulate the expression of MHC-I molecules on the cell surface. We show that iNKRs evolve specificity and, depending on the similarity of MHC alleles within each locus and the differences between the loci, they can specialize to a particular MHC-I locus. The easier it is to classify an MHC allele to its locus, the lower the required diversity of the NKRs. Thus, the diversification of the iNKR cluster depends on the locus specific MHC structure.
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Affiliation(s)
- Paola Carrillo-Bustamante
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University , Utrecht , Netherlands
| | - Can Kesmir
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University , Utrecht , Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University , Utrecht , Netherlands
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Carrillo-Bustamante P, Keşmir C, de Boer RJ. A Coevolutionary Arms Race between Hosts and Viruses Drives Polymorphism and Polygenicity of NK Cell Receptors. Mol Biol Evol 2015; 32:2149-60. [PMID: 25911231 PMCID: PMC4833080 DOI: 10.1093/molbev/msv096] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Natural killer cell receptors (NKRs) monitor the expression of major histocompatibility class I (MHC-I) and stress molecules to detect unhealthy tissue, such as infected or tumor cells. The NKR gene family shows a remarkable genetic diversity, containing several genes encoding receptors with activating and inhibiting signaling, and varying in gene content and allelic polymorphism. The expansion of the NKR genes is species-specific, with different species evolving alternative expanded NKR genes, which encode structurally different proteins, yet perform comparable functions. So far, the biological function of this expansion within the NKR cluster has remained poorly understood. To study the evolution of NKRs, we have developed an agent-based model implementing a coevolutionary scenario between hosts and herpes-like viruses that are able to evade the immune response by downregulating the expression of MHC-I on the cell surface. We show that hosts evolve specific inhibitory NKRs, specialized to particular MHC-I alleles in the population. Viruses in our simulations readily evolve proteins mimicking the MHC molecules of their host, even in the absence of MHC-I downregulation. As a result, the NKR locus becomes polygenic and polymorphic, encoding both specific inhibiting and activating receptors to optimally protect the hosts from coevolving viruses.
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Affiliation(s)
- Paola Carrillo-Bustamante
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Can Keşmir
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Rob J de Boer
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
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Affiliation(s)
- Ramit Mehr
- Computational Immunology Lab, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan , Israel
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