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Fan C, Xing X, Murphy SJH, Poursine-Laurent J, Schmidt H, Parikh BA, Yoon J, Choudhary MNK, Saligrama N, Piersma SJ, Yokoyama WM, Wang T. Cis-regulatory evolution of the recently expanded Ly49 gene family. Nat Commun 2024; 15:4839. [PMID: 38844462 PMCID: PMC11156856 DOI: 10.1038/s41467-024-48990-y] [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: 11/13/2023] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Comparative genomics has revealed the rapid expansion of multiple gene families involved in immunity. Members within each gene family often evolved distinct roles in immunity. However, less is known about the evolution of their epigenome and cis-regulation. Here we systematically profile the epigenome of the recently expanded murine Ly49 gene family that mainly encode either inhibitory or activating surface receptors on natural killer cells. We identify a set of cis-regulatory elements (CREs) for activating Ly49 genes. In addition, we show that in mice, inhibitory and activating Ly49 genes are regulated by two separate sets of proximal CREs, likely resulting from lineage-specific losses of CRE activity. Furthermore, we find that some Ly49 genes are cross-regulated by the CREs of other Ly49 genes, suggesting that the Ly49 family has begun to evolve a concerted cis-regulatory mechanism. Collectively, we demonstrate the different modes of cis-regulatory evolution for a rapidly expanding gene family.
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Affiliation(s)
- Changxu Fan
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Samuel J H Murphy
- Department of Neurology, Washington University School of Medicine, St. Louis, 63110, USA
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, 63110, USA
| | - Jennifer Poursine-Laurent
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA
| | - Heather Schmidt
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Bijal A Parikh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Jeesang Yoon
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA
| | - Mayank N K Choudhary
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Naresha Saligrama
- Department of Neurology, Washington University School of Medicine, St. Louis, 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, 63110, USA
| | - Sytse J Piersma
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, 63110, USA.
| | - Wayne M Yokoyama
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA.
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA.
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63110, USA.
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Araúzo-Bravo MJ, Delic D, Gerovska D, Wunderlich F. Protective Vaccination Reshapes Hepatic Response to Blood-Stage Malaria of Genes Preferentially Expressed by NK Cells. Vaccines (Basel) 2020; 8:vaccines8040677. [PMID: 33202767 PMCID: PMC7712122 DOI: 10.3390/vaccines8040677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 02/04/2023] Open
Abstract
The role of natural killer (NK) cells in the liver as first-line post infectionem (p.i.) effectors against blood-stage malaria and their responsiveness to protective vaccination is poorly understood. Here, we investigate the effect of vaccination on NK cell-associated genes induced in the liver by blood-stage malaria of Plasmodium chabaudi. Female Balb/c mice were vaccinated at weeks 3 and 1 before being infected with 106P. chabaudi-parasitized erythrocytes. Genes preferentially expressed by NK cells were investigated in livers of vaccination-protected and non-protected mice on days 0, 1, 4, 8, and 11 p.i. using microarrays, qRT-PCR, and chromosome landscape analysis. Blood-stage malaria induces expression of specific genes in the liver at different phases of infection, i.e., Itga1 in expanding liver-resident NK (lrNK) cells, Itga2 in immigrating conventional NK (cNK) cells; Eomes and Tbx21 encoding transcription factors; Ncr1, Tnfsf10, Prf1, Gzma, Gzmb, Gzmc, Gzmm, and Gzmk encoding cytolytic effectors; natural killer gene complex (NKC)-localized genes encoding the NK cell receptors KLRG1, KLRK1, KLRAs1, 2, 5, 7, KLRD1, KLRC1, KLRC3, as well as the three receptors KLRB1A, KLRB1C, KLRB1F and their potential ligands CLEC2D and CLEC2I. Vaccination enhances this malaria-induced expression of genes, but impairs Gzmm expression, accelerates decline of Tnfsf10 and Clec2d expression, whereas it accelerates increased expression of Clec2i, taking a very similar time course as that of genes encoding plasma membrane proteins of erythroblasts, whose malaria-induced extramedullary generation in the liver is known to be accelerated by vaccination. Collectively, vaccination reshapes the response of the liver NK cell compartment to blood-stage malaria. Particularly, the malaria-induced expansion of lrNK cells peaking on day 4 p.i. is highly significantly (p < 0.0001) reduced by enhanced immigration of peripheral cNK cells, and KLRB1F:CLEC2I interactions between NK cells and erythroid cells facilitate extramedullary erythroblastosis in the liver, thus critically contributing to vaccination-induced survival of otherwise lethal blood-stage malaria of P. chabaudi.
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Affiliation(s)
- Marcos J. Araúzo-Bravo
- Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014 San Sebastián, Spain;
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
- TransBioNet Thematic Network of Excellence for Transitional Bioinformatics, Barcelona Supercomputing Center, 08034 Barcelona, Spain
- Correspondence: (M.J.A.-B.); (D.D.); Tel.: +34-943006108 (M.J.A.-B.); +49-735154143839 (D.D.)
| | - Denis Delic
- Boeringer Ingelheim Pharma, 88400 Biberach, Germany
- Correspondence: (M.J.A.-B.); (D.D.); Tel.: +34-943006108 (M.J.A.-B.); +49-735154143839 (D.D.)
| | - Daniela Gerovska
- Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014 San Sebastián, Spain;
| | - Frank Wunderlich
- Department of Biology, Heinrich-Heine-University, 40225 Düsseldorf, Germany;
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Lemay AM, Haston CK. A Chromosome 6, not Natural Killer Cell, Contribution to Radiation- and Bleomycin-Induced Lung Disease in Mice. Radiat Res 2018; 190:605-611. [DOI: 10.1667/rr15144.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Anne-Marie Lemay
- Departments of Human Genetics and Medicine and the Meakins-Christie Laboratories, McGill University, Montreal, Canada
| | - Christina K. Haston
- Departments of Human Genetics and Medicine and the Meakins-Christie Laboratories, McGill University, Montreal, Canada
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Foerster F, Boegel S, Heck R, Pickert G, Rüssel N, Rosigkeit S, Bros M, Strobl S, Kaps L, Aslam M, Diken M, Castle J, Sahin U, Tuettenberg A, Bockamp E, Schuppan D. Enhanced protection of C57 BL/6 vs Balb/c mice to melanoma liver metastasis is mediated by NK cells. Oncoimmunology 2017; 7:e1409929. [PMID: 29632723 PMCID: PMC5889278 DOI: 10.1080/2162402x.2017.1409929] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/07/2017] [Accepted: 11/21/2017] [Indexed: 01/26/2023] Open
Abstract
The B16F10 murine melanoma cell line displays a low expression of MHC class I molecules favoring immune evasion and metastases in immunocompetent C57 BL/6 wild-type mice. Here, we generated metastases to the liver, an organ that is skewed towards immune tolerance, by intrasplenic injection of B16F10 cells in syngeneic C57 BL/6 compared to allogeneic Balb/c mice. Surprisingly, Balb/c mice, which usually display a pronounced M2 macrophage and Th2 T cell polarization, were ∼3 times more susceptible to metastasis than C57 BL/6 mice, despite a much higher M1 and Th1 T cell immune response. The anti-metastatic advantage of C57 BL/6 mice could be attributed to a more potent NK-cell mediated cytotoxicity against B16F10 cells. Our findings highlight the role of NK cells in innate anti-tumor immunity in the context of the liver – particularly against highly aggressive MHC I-deficient cancer cells. Moreover, the B16F10 model of melanoma liver metastasis is suited for developing novel therapies targeting innate NK cell related immunity in liver metastases and liver cancer.
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Affiliation(s)
- Friedrich Foerster
- First Department of Medicine, University Medical Center Mainz, Mainz, Germany.,Institute of Translational Immunology and Research Center for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Sebastian Boegel
- TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Rosario Heck
- Institute of Translational Immunology and Research Center for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Geetha Pickert
- Institute of Translational Immunology and Research Center for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Nina Rüssel
- Institute of Translational Immunology and Research Center for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Sebastian Rosigkeit
- Institute of Translational Immunology and Research Center for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Matthias Bros
- Department of Dermatology, University Medical Center Mainz, Mainz, Germany
| | - Stephanie Strobl
- Institute of Translational Immunology and Research Center for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Leonard Kaps
- Institute of Translational Immunology and Research Center for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Misbah Aslam
- Institute of Translational Immunology and Research Center for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Mustafa Diken
- TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University gGmbH, Mainz, Germany
| | - John Castle
- TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Ugur Sahin
- TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Andrea Tuettenberg
- Department of Dermatology, University Medical Center Mainz, Mainz, Germany
| | - Ernesto Bockamp
- Institute of Translational Immunology and Research Center for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Detlef Schuppan
- Institute of Translational Immunology and Research Center for Immunotherapy, University Medical Center Mainz, Mainz, Germany.,Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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McCullen MV, Li H, Cam M, Sen SK, McVicar DW, Anderson SK. Analysis of Ly49 gene transcripts in mature NK cells supports a role for the Pro1 element in gene activation, not gene expression. Genes Immun 2016; 17:349-57. [PMID: 27467282 PMCID: PMC5008998 DOI: 10.1038/gene.2016.31] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/09/2016] [Accepted: 06/14/2016] [Indexed: 12/22/2022]
Abstract
The variegated expression of murine Ly49 loci has been associated with the probabilistic behavior of an upstream promoter active in immature cells, the Pro1 element. However, recent data suggest that Pro1 may be active in mature natural killer (NK) cells and function as an enhancer element. To assess directly if Pro1 transcripts are present in mature Ly49-expressing NK cells, RNA-sequencing of the total transcript pool was performed on freshly isolated splenic NK cells sorted for expression of either Ly49G or Ly49I. No Pro1 transcripts were detected from the Ly49a, Ly49c or Ly49i genes in mature Ly49(+) NK cells that contained high levels of Pro2 transcripts. Low levels of Ly49g Pro1 transcripts were found in both Ly49G(+) and Ly49G(-) populations, consistent with the presence of a small population of mature NK cells undergoing Ly49g gene activation, as previously demonstrated by culture of splenic NK cells in interleukin-2. Ly49 gene reporter constructs containing Pro1 failed to show any enhancer activity of Pro1 on Pro2 in a mature Ly49-expressing cell line. Taken together, the results are consistent with Pro1 transcription having a role in gene activation in developing NK, and argue against a role for Pro1 in Ly49 gene transcription by mature NK cells.
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Affiliation(s)
- Matthew V. McCullen
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Hongchuan Li
- Basic Science Program, Leidos Biomedical Research Inc., Frederick National Lab, Frederick MD 21702, USA
| | - Maggie Cam
- Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Shurjo K. Sen
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Daniel W. McVicar
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Stephen K. Anderson
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
- Basic Science Program, Leidos Biomedical Research Inc., Frederick National Lab, Frederick MD 21702, USA
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Rahim MMA, Makrigiannis AP. Ly49 receptors: evolution, genetic diversity, and impact on immunity. Immunol Rev 2016; 267:137-47. [PMID: 26284475 DOI: 10.1111/imr.12318] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Natural killer (NK) cells express cell surface receptors that recognize class I major histocompatibility complex (MHC-I) molecules to distinguish between healthy and unhealthy cells. The multigenic and polymorphic nature of the MHC-I genes has influenced the convergent evolution of similarly polymorphic and diversified NK cell receptor families: the C-type lectin-like Ly49 receptors in mice, and the killer cell immunoglobulin-like receptors (KIRs) in humans. Although structurally distinct, both receptor families have similar functions in terms of MHC-I recognition and downstream signal transduction, and they regulate multiple aspects of NK cell biology during development and after maturation as fully differentiated and functionally competent cells. The Ly49 gene locus has undergone rapid, lineage-specific expansions and contractions resulting in multiple distinct haplotypes of variable gene number, allelic diversity, and MHC-I ligand specificity. This in turn has influenced the type and degree of Ly49 receptor expression on NK cells, and their contribution to immunity in different mouse strains. In this review, we have attempted to describe the evolutionary processes that have shaped strain-specific Ly49 receptor repertoires, and their impact on NK cell functions during health and disease.
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Affiliation(s)
- Mir Munir A Rahim
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Andrew P Makrigiannis
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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Wight A, Yang D, Ioshikhes I, Makrigiannis AP. Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors. PLoS Comput Biol 2016; 12:e1004894. [PMID: 27124577 PMCID: PMC4849748 DOI: 10.1371/journal.pcbi.1004894] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/31/2016] [Indexed: 12/28/2022] Open
Abstract
Beyond its role in genomic organization and compaction, the nucleosome is believed to participate in the regulation of gene transcription. Here, we report a computational method to evaluate the nucleosome sensitivity for a transcription factor over a given stretch of the genome. Sensitive factors are predicted to be those with binding sites preferentially contained within nucleosome boundaries and lacking 10 bp periodicity. Based on these criteria, the Acute Myeloid Leukemia-1a (AML-1a) transcription factor, a regulator of immune gene expression, was identified as potentially sensitive to nucleosomal regulation within the mouse Ly49 gene family. This result was confirmed in RMA, a cell line with natural expression of Ly49, using MNase-Seq to generate a nucleosome map of chromosome 6, where the Ly49 gene family is located. Analysis of this map revealed a specific depletion of nucleosomes at AML-1a binding sites in the expressed Ly49A when compared to the other, silent Ly49 genes. Our data suggest that nucleosome-based regulation contributes to the expression of Ly49 genes, and we propose that this method of predicting nucleosome sensitivity could aid in dissecting the regulatory role of nucleosomes in general. The nucleosome—a large protein complex with DNA wound around it—is the fundamental unit of genomic organization in the eukaryotic cell. More than just a DNA organizer, however, nucleosomes may control gene expression by interfering with the cell’s ability to access the wound-up DNA, as shown by recent research. In this report, we demonstrate a computational method for predicting which elements of the genome are sensitive to regulation by nucleosomes. As a proof-of-concept, we identify AML-1a binding sites—important sequences in DNA regulation—as being specifically nucleosome sensitive. We then show that AML-1a sites are specifically depleted of nucleosomes when a gene is expressed, indicating the ability for nucleosomes to suppress the expression of that gene. This finding confirms that nucleosomes are likely involved in genome regulation, and provides a method for predicting which areas of the genome are probably affected most by nucleosomes. This paper also highlights the usefulness of the Ly49 gene family in testing computer-derived genomic predictions, and is of interest to anyone studying how gene expression is regulated from cell to cell.
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Affiliation(s)
- Andrew Wight
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Doo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ilya Ioshikhes
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
- * E-mail: (II); (APM)
| | - Andrew P. Makrigiannis
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail: (II); (APM)
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The activating Ly49W and inhibitory Ly49G NK cell receptors display similar affinities for identical MHC class I ligands. Immunogenetics 2014; 66:467-77. [DOI: 10.1007/s00251-014-0777-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 04/23/2014] [Indexed: 01/26/2023]
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9
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Rahim MMA, Tu MM, Mahmoud AB, Wight A, Abou-Samra E, Lima PDA, Makrigiannis AP. Ly49 receptors: innate and adaptive immune paradigms. Front Immunol 2014; 5:145. [PMID: 24765094 PMCID: PMC3980100 DOI: 10.3389/fimmu.2014.00145] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/20/2014] [Indexed: 11/13/2022] Open
Abstract
The Ly49 receptors are type II C-type lectin-like membrane glycoproteins encoded by a family of highly polymorphic and polygenic genes within the mouse natural killer (NK) gene complex. This gene family is designated Klra, and includes genes that encode both inhibitory and activating Ly49 receptors in mice. Ly49 receptors recognize class I major histocompatibility complex-I (MHC-I) and MHC-I-like proteins on normal as well as altered cells. Their functional homologs in humans are the killer cell immunoglobulin-like receptors, which recognize HLA class I molecules as ligands. Classically, Ly49 receptors are described as being expressed on both the developing and mature NK cells. The inhibitory Ly49 receptors are involved in NK cell education, a process in which NK cells acquire function and tolerance toward cells that express “self-MHC-I.” On the other hand, the activating Ly49 receptors recognize altered cells expressing activating ligands. New evidence shows a broader Ly49 expression pattern on both innate and adaptive immune cells. Ly49 receptors have been described on multiple NK cell subsets, such as uterine NK and memory NK cells, as well as NKT cells, dendritic cells, plasmacytoid dendritic cells, macrophages, neutrophils, and cells of the adaptive immune system, such as activated T cells and regulatory CD8+ T cells. In this review, we discuss the expression pattern and proposed functions of Ly49 receptors on various immune cells and their contribution to immunity.
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Affiliation(s)
- Mir Munir A Rahim
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa , Ottawa, ON , Canada
| | - Megan M Tu
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa , Ottawa, ON , Canada
| | - Ahmad Bakur Mahmoud
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa , Ottawa, ON , Canada ; College of Applied Medical Sciences, Taibah University , Madinah Munawwarah , Kingdom of Saudi Arabia
| | - Andrew Wight
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa , Ottawa, ON , Canada
| | - Elias Abou-Samra
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa , Ottawa, ON , Canada
| | - Patricia D A Lima
- Biomedical and Molecular Sciences, Queen's University , Kingston, ON , Canada
| | - Andrew P Makrigiannis
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa , Ottawa, ON , Canada
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McFall E, Tu MM, Al-Khattabi N, Tai LH, St-Laurent AS, Tzankova V, Hall CW, Belanger S, Troke AD, Wight A, Mahmoud AB, Zein HS, Rahim MMA, Carlyle JR, Makrigiannis AP. Optimized tetramer analysis reveals Ly49 promiscuity for MHC ligands. THE JOURNAL OF IMMUNOLOGY 2013; 191:5722-9. [PMID: 24154624 DOI: 10.4049/jimmunol.1300726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Murine Ly49 receptors, which are expressed mainly on NK and NKT cells, interact with MHC class I (MHC-I) molecules with varying specificity. Differing reports of Ly49/MHC binding affinities may be affected by multiple factors, including cis versus trans competition and species origin of the MHC-I L chain (β2-microglobulin). To determine the contribution of each of these factors, Ly49G, Ly49I, Ly49O, Ly49V, and Ly49Q receptors from the 129 mouse strain were expressed individually on human 293T cells or the mouse cell lines MHC-I-deficient C1498, H-2(b)-expressing MC57G, and H-2(k)-expressing L929. The capacity to bind to H-2D(b)- and H-2K(b)-soluble MHC-I tetramers containing either human or murine β2-microglobulin L chains was tested for all five Ly49 receptors in all four cell lines. We found that most of these five inhibitory Ly49 receptors show binding for one or both self-MHC-I molecules in soluble tetramer binding assays when three conditions are fulfilled: 1) lack of competing cis interactions, 2) tetramer L chain is of mouse origin, and 3) Ly49 is expressed in mouse and not human cell lines. Furthermore, Ly49Q, the single known MHC-I receptor on plasmacytoid dendritic cells, was shown to bind H-2D(b) in addition to H-2K(b) when the above conditions were met, suggesting that Ly49Q functions as a pan-MHC-Ia receptor on plasmacytoid dendritic cells. In this study, we have optimized the parameters for soluble tetramer binding analyses to enhance future Ly49 ligand identification and to better evaluate specific contributions by different Ly49/MHC-I pairs to NK cell education and function.
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Affiliation(s)
- Emily McFall
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
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11
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Corbett AJ, Coudert JD, Forbes CA, Scalzo AA. Functional consequences of natural sequence variation of murine cytomegalovirus m157 for Ly49 receptor specificity and NK cell activation. THE JOURNAL OF IMMUNOLOGY 2010; 186:1713-22. [PMID: 21187440 DOI: 10.4049/jimmunol.1003308] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Ly49H activating receptor on C57BL/6 (B6) NK cells plays a key role in early resistance to murine cytomegalovirus (MCMV) infection through specific recognition of the MCMV-encoded MHC class I-like molecule m157 expressed on infected cells. The m157 molecule is also recognized by the Ly49I inhibitory receptor from the 129/J mouse strain. The m157 gene is highly sequence variable among MCMV isolates, with many m157 variants unable to bind Ly49H(B6). In this study, we have sought to define if m157 variability leads to a wider spectrum of interactions with other Ly49 molecules and if this modifies host susceptibility to MCMV. We have identified novel m157-Ly49 receptor interactions, involving Ly49C inhibitory receptors from B6, BALB/c, and NZB mice, as well as the Ly49H(NZB) activation receptor. Using an MCMV recombinant virus in which m157(K181) was replaced with m157(G1F), which interacts with both Ly49H(B6) and Ly49C(B6), we show that the m157(G1F)-Ly49C interactions cause no apparent attenuating effect on viral clearance in B6 mice. Hence, when m157 can bind both inhibitory and activation NK cell receptors, the outcome is still activation. Thus, these data indicate that whereas m157 variants predominately interact with inhibitory Ly49 receptors, these interactions do not profoundly interfere with early NK cell responses.
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Affiliation(s)
- Alexandra J Corbett
- Centre for Ophthalmology and Vision Science, University of Western Australia, Crawley, Western Australia 6009, Australia
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Abstract
The natural killer gene complex (NKC) on chromosome 6 contains clusters of genes that encode both activation and inhibitory receptors expressed on mouse natural killer (NK) cells. NKC genes, particularly belonging to the Nkrp1 and Ly49 gene families, display haplotype differences between different mouse strains and allelic polymorphisms of individual genes, as previously revealed by conventional analysis in a small number of inbred mouse strains. Herein we used array-based comparative genomic hybridization (aCGH) to efficiently compare the NKC in 21 mouse strains to the reference C57BL/6 strain. By using unsupervised clustering methods, we could sort these variations into the same groups as determined by previous RFLP analyses of Nkrp1 and Ly49 genes. Prospective analyses of aCGH and RFLP data validated these relationships. Moreover, aCGH data predicted monoclonal antibody reactivity with an allospecific determinant on molecules expressed by NK cells. Taken together, these data demonstrate the structural variation in the NKC between mouse strains as well as the usefulness of aCGH in analysis of complex, polymorphic gene clusters.
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Rouhi A, Lai CB, Cheng TP, Takei F, Yokoyama WM, Mager DL. Evidence for high bi-allelic expression of activating Ly49 receptors. Nucleic Acids Res 2009; 37:5331-42. [PMID: 19605564 PMCID: PMC2760814 DOI: 10.1093/nar/gkp592] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Stochastic expression is a hallmark of the Ly49 family that encode the main MHC class-I-recognizing receptors of mouse natural killer (NK) cells. This highly polygenic and polymorphic family includes both activating and inhibitory receptor genes and is one of genome's fastest evolving loci. The inhibitory Ly49 genes are expressed in a stochastic mono-allelic manner, possibly under the control of an upstream bi-directional early promoter and show mono-allelic DNA methylation patterns. To date, no studies have directly addressed the transcriptional regulation of the activating Ly49 receptors. Our study shows differences in DNA methylation pattern between activating and inhibitory genes in C57BL/6 and F1 hybrid mouse strains. We also show a bias towards bi-allelic expression of the activating receptors based on allele-specific single-cell RT–PCR in F1 hybrid NK cells for Ly49d and Ly49H expression in Ly49h+/− mice. Furthermore, we have identified a region of high sequence identity with possible transcriptional regulatory capacity for the activating Ly49 genes. Our results also point to a likely difference between NK and T-cells in their ability to transcribe the activating Ly49 genes. These studies highlight the complex regulation of this rapidly evolving gene family of central importance in mouse NK cell function.
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Affiliation(s)
- Arefeh Rouhi
- The Terry Fox laboratory, British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, Canada
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14
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Cutler G, Kassner PD. Copy number variation in the mouse genome: implications for the mouse as a model organism for human disease. Cytogenet Genome Res 2009; 123:297-306. [PMID: 19287168 DOI: 10.1159/000184721] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2008] [Indexed: 11/19/2022] Open
Abstract
Individuals within a species have genetic differences which ultimately result in the spectrum of phenotypic variation that we observe. Genetic variation exists at the nucleotide level in the form of single nucleotide polymorphisms (SNPs), and at a structural level as inversions, deletions and amplifications of larger stretches of nucleotides. Profiling of human and mouse genomes has identified numerous genomic segmental copy number variations (CNVs) throughout these genomes. Since inbred mice are widely used laboratory models for the study of both normal and disease biology, it is crucial that we understand the full scope of genetic variation, including CNVs, within these animals. These genetic differences can inform us about the history of a population or species, enlighten us on gene function, and guide our selection of a model system for the study of human disease.
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Affiliation(s)
- G Cutler
- Lead Discovery, Amgen, South San Francisco, CA, USA.
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15
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Brown MG, Scalzo AA. NK gene complex dynamics and selection for NK cell receptors. Semin Immunol 2008; 20:361-8. [PMID: 18640056 DOI: 10.1016/j.smim.2008.06.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Accepted: 06/06/2008] [Indexed: 01/06/2023]
Abstract
Natural killer (NK) cells play important roles in innate defense against infectious agents particularly viruses and also tumors. They mediate their effects through direct cytolysis, release of cytokines and regulation of subsequent adaptive immune responses. NK cells are equipped with sophisticated arrays of inhibitory and activation receptors that regulate their function. In this review we illustrate some of the major evolutionary relationships between NK cell receptors among different animal species and what some of the major mechanisms are that give rise to this diversity in receptor families, including the potential roles of pathogens such as viruses in driving receptor evolution.
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Affiliation(s)
- Michael G Brown
- Center for Immunity, Inflammation and Regenerative Medicine, Department of Medicine, University of Virginia, Charlottesville, VA 22908, United States
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16
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Carlyle JR, Mesci A, Fine JH, Chen P, Bélanger S, Tai LH, Makrigiannis AP. Evolution of the Ly49 and Nkrp1 recognition systems. Semin Immunol 2008; 20:321-30. [PMID: 18595730 DOI: 10.1016/j.smim.2008.05.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Accepted: 05/21/2008] [Indexed: 11/29/2022]
Abstract
The Ly49 and Nkrp1 loci encode structurally and functionally related cell surface proteins that positively or negatively regulate natural killer (NK) cell-mediated cytotoxicity and cytokine production. Yet despite their clear relatedness and genetic linkage within the NK gene complex (NKC), these two multi-gene families have adopted dissimilar evolutionary strategies. The Ly49 genes are extremely polymorphic and evolutionarily dynamic, with distinct gene numbers, remarkable allelic diversity, and varying MHC-I-ligand specificities and affinities among different murine haplotypes. In contrast, the Nkrp1 genes have opted for overall conservation of genomic organization, sequences, and ligand specificities, with only limited and focused allelic polymorphism. Possible selection pressures driving such varied evolution of the two gene families may include disequilibrium from ligand co-inheritance, pathogen immunoevasin strategies, flexibility in host counter-evolution mechanisms, and the prevalence and dynamics of inherent repetitive elements.
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Affiliation(s)
- James R Carlyle
- Department of Immunology, University of Toronto & Sunnybrook Research Institute, 2075 Bayview Avenue (S-236), Toronto, ON M4N 3M5, Canada.
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17
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Ly49 cluster sequence analysis in a mouse model of diabetes: an expanded repertoire of activating receptors in the NOD genome. Genes Immun 2008; 9:509-21. [PMID: 18528402 PMCID: PMC2678550 DOI: 10.1038/gene.2008.43] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The mouse Ly49 and human killer cell immunoglobulin-like receptors (KIR) gene clusters encode activating and inhibitory class I MHC receptors on natural killer (NK) cells. A direct correlation between the presence of multiple activating KIR and various human autoimmune diseases including diabetes has been shown. Previous studies have implicated NK cell receptors in the development of diabetes in the non-obese diabetic (NOD) inbred mouse strain. To assess the contribution of Ly49 to NOD disease acceleration the Ly49 gene cluster of these mice was sequenced. Remarkably, the NOD Ly49 haplotype encodes the largest haplotype and the most functional activating Ly49 of any known mouse strain. These activating Ly49 include three Ly49p-related and two Ly49h-related genes. The NOD cluster contains large regions highly homologous to both C57BL/6 and 129 haplotypes, suggesting unequal crossing over as a mechanism of Ly49 haplotype evolution. Interestingly, the 129-like region has duplicated in the NOD genome. Thus, the NOD Ly49 cluster is a unique mix of elements seen in previously characterized Ly49 haplotypes resulting in a disproportionately large number of functional activating Ly49 genes. Finally, the functionality of activating Ly49 in NOD mice was confirmed in cytotoxicity assays.
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18
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Pascal V, Nathan NR, Claudio E, Siebenlist U, Anderson SK. NF-kappa B p50/p65 affects the frequency of Ly49 gene expression by NK cells. THE JOURNAL OF IMMUNOLOGY 2007; 179:1751-9. [PMID: 17641041 DOI: 10.4049/jimmunol.179.3.1751] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In mice, acquisition of Ly49 receptors characterizes one of the developmental stages of NK cells. We previously described a novel Ly49 promoter, Pro1, involved in Ly49 gene regulation in immature NK cells. Pro1 transcriptional activity requires a NF-kappaB binding site; however, only NF-kappaB/p50 binding to this element was observed. Cotransfection of NF-kappaB/p65 with Ly49g Pro1 in LNK cells induced a decrease in the transcriptional activity of the core promoter. Moreover, decreasing NF-kappaB/p65 protein expression by RNA interference increases Pro1 transcriptional activity. A high rate of NF-kappaB/p65 degradation in LNK cells correlates with Pro1 activity, since treatment with the proteasome inhibitor MG132 increased levels of NF-kappaB/p65 protein and decreased Pro1 activity. In addition, analysis of the Ly49 repertoire in NF-kappaB/p50 null mice reveals a decrease in the proportion of NK cells expressing a given Ly49 molecule. The defect in Ly49 expression is observed in the bone marrow and the spleen with a similar altered pattern of developmental stages in each tissue. The frequency of Ly49 expression in NF-kappaB/p52 null mice is slightly increased, indicating the specific role of NF-kappaB/p50 in Ly49 gene activation. These results suggest that NF-kappaB p50/p65 plays a major role in the initiation of Ly49 gene expression in NK cells.
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MESH Headings
- Animals
- Antigens, Ly/biosynthesis
- Antigens, Ly/genetics
- Cell Aggregation/genetics
- Cell Aggregation/immunology
- Cell Line
- Cell Line, Tumor
- Cytotoxicity, Immunologic/genetics
- Down-Regulation/genetics
- Down-Regulation/immunology
- Gene Expression Regulation/immunology
- Gene Frequency/immunology
- Interferon-gamma/biosynthesis
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lectins, C-Type/antagonists & inhibitors
- Lectins, C-Type/biosynthesis
- Lectins, C-Type/genetics
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- NF-kappa B p50 Subunit/deficiency
- NF-kappa B p50 Subunit/genetics
- NF-kappa B p50 Subunit/physiology
- NF-kappa B p52 Subunit/biosynthesis
- NF-kappa B p52 Subunit/genetics
- NK Cell Lectin-Like Receptor Subfamily A
- Promoter Regions, Genetic/immunology
- Receptors, NK Cell Lectin-Like
- Transcription Factor RelA/physiology
- Transcriptional Activation/immunology
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Affiliation(s)
- Véronique Pascal
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA
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19
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Tai LH, Goulet ML, Belanger S, Troke AD, St-Laurent AG, Mesci A, Toyama-Sorimachi N, Carlyle JR, Makrigiannis AP. Recognition of H-2Kb by Ly49Q suggests a role for class Ia MHC regulation of plasmacytoid dendritic cell function. Mol Immunol 2007; 44:2638-46. [PMID: 17240452 DOI: 10.1016/j.molimm.2006.12.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 12/12/2006] [Accepted: 12/13/2006] [Indexed: 12/30/2022]
Abstract
Ly49Q is a member of the polymorphic Ly49 family of NK cell receptors that displays both a high degree of conservation and a unique expression pattern restricted to myeloid lineage cells, including plasmacytoid dendritic cells (pDC). The function and ligand specificity of Ly49Q are unknown. Here, we use reporter cell analysis to demonstrate that a high-affinity ligand for Ly49Q is present on H-2(b), but not H-2(d), H-2(k), H-2(q), or H-2(a)-derived tumor cells and normal cells ex vivo. The ligand is peptide-dependent and MHC Ia-like, as revealed by its functional absence on cells deficient in TAP-1, beta(2)m, or H-2K(b)D(b) expression. Furthermore, Ly49Q is specific for H-2K(b), as the receptor binds peptide-loaded H-2K(b) but not H-2D(b) complexes, and Ly49Q recognition can be blocked using anti-K(b) but not anti-D(b) mAb. Greater soluble H-2K(b) binding to ligand-deficient pDC also suggests cis interactions of Ly49Q and H-2K(b). These results demonstrate that Ly49Q efficiently binds H-2K(b) ligand, and suggest that pDC function, like that of NK cells, is regulated by classical MHC Ia molecules. MHC recognition capability by pDC has important implications for the role of this cell type during innate immune responses.
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Affiliation(s)
- Lee-Hwa Tai
- Institut de Recherches Cliniques de Montréal (IRCM), Laboratory of Molecular Immunology, Université de Montréal, Montréal, Quebec, Canada
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20
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Davies GE, Locke SM, Wright PW, Li H, Hanson RJ, Miller JS, Anderson SK. Identification of bidirectional promoters in the human KIR genes. Genes Immun 2007; 8:245-53. [PMID: 17315044 DOI: 10.1038/sj.gene.6364381] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Although the class I MHC receptors expressed by human and mouse natural killer (NK) cells have distinct molecular origins, they are functional analogues that are expressed in a variegated pattern. The murine Ly49 class I receptors contain bidirectional promoters that have been proposed to control the probabilistic expression of these genes. Whether similar elements are present in the human killer Ig-like receptor (KIR) genes is a fundamental question. A detailed analysis of the 2 kb intergenic region separating the KIR2DL4 gene and the adjacent KIR3DL1 gene revealed that additional promoter elements exist in the human KIR genes. Remarkably, the previously characterized KIR3DL1 proximal promoter possesses bidirectional promoter activity that maps to an 88 bp DNA fragment containing CREB, AML, Sp1 and Ets transcription factor binding sites. Individual KIR genes and alleles possess bidirectional promoters with distinct properties. Analysis of KIR(+)and KIR(-) NK cells and NK precursors indicates that reverse transcripts from the bidirectional promoter are found in cells that lack KIR protein expression, but are not present in mature KIR-expressing NK cells, suggesting that reverse transcription from the proximal promoter blocks gene activation in immature NK and precursor cells.
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Affiliation(s)
- G E Davies
- 1Basic Research Program, SAIC-Frederick Inc., National Cancer Institute-Frederick, Frederick, MD, USA
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21
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Natural killer cell subsets in allograft rejection and tolerance. Curr Opin Organ Transplant 2007; 12:10-16. [PMID: 27792083 DOI: 10.1097/mot.0b013e3280129f2a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW To discuss the role of natural killer cells in regulating the survival of transplanted organs. RECENT FINDINGS Natural killer cells have been found to have the dual capacity to promote rejection of transplanted organs and be required for the induction of transplantation tolerance. In murine recipients of bone marrow transplants, or in CD28 recipients of cardiac allografts, different natural killer cell subsets have been shown to promote or delay rejection, depending on their major histocompatibility complex class I specificity. In mouse models of skin and islet allograft acceptance mediated by costimulation-targeting therapies, the presence of natural killer cells was found to be essential for long-term graft acceptance, perhaps due to their ability to eliminate donor or recipient immune cells. SUMMARY Natural killer cells can either accelerate or avert rejection in a manner that is influenced by both donor-recipient major histocompatibility complex disparity as well as the milieu created by costimulation-targeting therapies. In clinical settings, alloreactivity by defined natural killer cell subsets may be important in achieving tolerance, and the outcome of natural killer cell activity may be influenced by specific immunosuppressive regimens.
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22
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Pascal V, Stulberg MJ, Anderson SK. Regulation of class I major histocompatibility complex receptor expression in natural killer cells: one promoter is not enough! Immunol Rev 2007; 214:9-21. [PMID: 17100872 DOI: 10.1111/j.1600-065x.2006.00452.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The class I major histocompatibility complex (MHC) receptors expressed by natural killer (NK) cells play an important role in regulating their function. The number and type of inhibitory receptors expressed by NK cells must be tightly controlled in order to avoid the generation of dominantly inhibited NK cells. The selective stochastic expression of the class I MHC receptors generates a variegated NK cell population capable of discriminating subtle changes in MHC expression on potential target cells. The molecular mechanisms controlling the cell-specific and probabilistic expression of these receptors are without doubt very complex. The traditional approach of considering a core promoter modulated by upstream enhancer elements is likely too simplistic a paradigm to adequately explain the regulation of these genes, as well as other gene clusters that are not expressed in an 'all or none' fashion. Our studies on the regulation of the mouse Ly49 and human killer immunoglobulin-like receptor (KIR) clusters of class I MHC receptor genes have revealed the presence of multiple transcripts in both sense and antisense orientations. In both systems, an antisense promoter overlaps a promoter that produces sense transcripts, creating a bidirectional element. In the Ly49 genes, the competing promoters behave as probabilistic switches, and it is likely that the human bidirectional promoters will have a similar property. The antisense transcripts generated in the Ly49 genes are far removed from the promoter responsible for Ly49 expression in mature NK cells, whereas the antisense KIR transcripts detected are within the adult promoter region. This finding suggests that the mechanism of promoter regulation in the KIR genes may be quite different from that of the Ly49 genes. This review summarizes the current state of knowledge regarding class I MHC receptor gene regulation. The models proposed for the control of the probabilistic expression of the Ly49 and KIR genes are discussed in the context of current knowledge regarding the complex control of other well-studied gene clusters such as the beta-globin and cytokine clusters.
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MESH Headings
- Animals
- Antigens, Ly/biosynthesis
- Antigens, Ly/genetics
- Antigens, Ly/metabolism
- Gene Expression Regulation/immunology
- Histocompatibility Antigens Class I/biosynthesis
- Histocompatibility Antigens Class I/genetics
- Histocompatibility Antigens Class I/metabolism
- Humans
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lectins, C-Type/biosynthesis
- Lectins, C-Type/genetics
- Lectins, C-Type/metabolism
- Promoter Regions, Genetic
- Receptors, Immunologic/biosynthesis
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Receptors, KIR
- Receptors, NK Cell Lectin-Like
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Affiliation(s)
- Véronique Pascal
- Laboratory of Experimental Immunology, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA
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23
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Scalzo AA, Corbett AJ, Rawlinson WD, Scott GM, Degli-Esposti MA. The interplay between host and viral factors in shaping the outcome of cytomegalovirus infection. Immunol Cell Biol 2006; 85:46-54. [PMID: 17146464 DOI: 10.1038/sj.icb.7100013] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cytomegalovirus (CMV) remains a major human pathogen causing significant morbidity and mortality in immunosuppressed or immunoimmature individuals. Although significant advances have been made in dissecting out certain features of the host response to human CMV (HCMV) infection, the strict species specificity of CMVs means that most aspects of antiviral immunity are best assessed in animal models. The mouse model of murine CMV (MCMV) infection is an important tool for analysis of in vivo features of host-virus interactions and responses to antiviral drugs that are difficult to assess in humans. Important studies of the contribution of host resistance genes to infection outcome, interplays between innate and adaptive host immune responses, the contribution of virus immune evasion genes and genetic variation in these genes to the establishment of persistence and in vivo studies of resistance to antiviral drugs have benefited from the well-developed MCMV model. In this review, we discuss recent advances in the immunobiology of host-CMV interactions that provide intriguing insights into the complex interplay between host and virus that ultimately facilitates viral persistence. We also discuss recent studies of genetic responses to antiviral therapy, particularly changes in DNA polymerase and protein kinase genes of MCMV and HCMV.
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Affiliation(s)
- Anthony A Scalzo
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, Western Australia, Australia.
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24
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Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, Eis PS, Shannon WD, Li X, McLeod HL, Cheverud JM, Ley TJ. A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet 2006; 3:e3. [PMID: 17206864 PMCID: PMC1761046 DOI: 10.1371/journal.pgen.0030003] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Accepted: 11/21/2006] [Indexed: 11/18/2022] Open
Abstract
Submicroscopic (less than 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study 21 well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. We performed comparative genomic hybridization using long oligomer arrays to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies. The CNVs range in size from 21 to 2,002 kb. Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains. Most of the CNVs (77.5%) contain annotated genes, and many (47.5%) colocalize with previously mapped segmental duplications in the mouse genome. We demonstrate that this technique can identify copy number differences associated with known polymorphic traits. The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci. Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits.
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Affiliation(s)
- Timothy A Graubert
- Department of Medicine, Division of Oncology, Stem Cell Biology Section, Washington University, St. Louis, Missouri, United States of America.
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25
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Mesci A, Ljutic B, Makrigiannis AP, Carlyle JR. NKR-P1 biology: from prototype to missing self. Immunol Res 2006; 35:13-26. [PMID: 17003506 DOI: 10.1385/ir:35:1:13] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 11/11/2022]
Abstract
Natural killer (NK) cells represent lymphocytes of the innate immune system capable of recognizing and destroying a broad array of target cells, including tumors, virus-infected cells, antibodycoated cells, foreign transplants, and "stressed" cells. NK cells eliminate their targets through two main effector mechanisms, cytokine secretion and cell-mediated cytotoxicity, which in turn depend on detection of target cells through a complex integration of stimulatory and inhibitory receptor-ligand interactions. The NKR-P1 molecules were the first family of NK cell receptors identified, yet they have remained enigmatic in their contribution to self-nonself discrimination until recently. Here, we outline a brief history of the NKR-P1 receptor family, then examine recent data providing insight into their genetic regulation, signaling function, cognate ligands, and gene organization and diversity.
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Affiliation(s)
- Aruz Mesci
- Department of Immunology, University of Toronto, Sunnybrook & Women's Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
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26
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Vilches C, Parham P. Do NK-cell receptors and alloreactivity affect solid organ transplantation? Transpl Immunol 2006; 17:27-30. [PMID: 17157210 DOI: 10.1016/j.trim.2006.09.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2006] [Accepted: 09/13/2006] [Indexed: 01/09/2023]
Abstract
Although natural killer cells lyse targets without pre-sensitization, and in an MHC-unrestricted manner, they can also respond to healthy allogeneic cells of different MHC type. Such alloreactivity is a consequence of NK cells using clonally distributed, inhibitory MHC class I receptors to achieve tolerance to healthy autologous cells. Absence of an appropriate MHC class I ligand on an allogeneic cell erroneously informs the NK cell that the allogeneic cell has lost MHC class I expression and should be killed. Potential NK-cell allo-reactivities are common in non-HLA-identical hematopoietic cell transplants and can have both beneficial and detrimental effects. Less is known of NK-cell allo-reactivities in solid organ transplantation. In animal models NK cells are neither necessary nor sufficient for acute transplant rejection, but they can make a contribution by helping activate T cells. Genes encoding NK-cell receptors for polymorphic MHC class I molecules are also highly polymorphic, contributing to variability of the NK-cell repertoire and response in the human population. These receptors could represent intrinsic patient factors that influence the success of their transplanted solid organs.
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Affiliation(s)
- Carlos Vilches
- Servicio de Inmunología, Hospital Universitario Puerta de Hierro, San Martín de Porres 4, 28035 Madrid, Spain.
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27
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Kielczewska A, Vidal SM. Enemy at the gates: forward genetics of the mouse antiviral response. Curr Opin Immunol 2006; 18:617-26. [PMID: 16879955 DOI: 10.1016/j.coi.2006.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Accepted: 07/20/2006] [Indexed: 01/20/2023]
Abstract
The environment and the genetic constitution of both the pathogen and the host influence the severity and the outcome of viral infections. Whereas identification of the host component in humans remains challenging, recent progress in defining genes through analysis of mouse models of infection presenting natural or chemically induced variation in host susceptibility mark a fruitful period of gene discovery. This includes recognition that UNC93B1, which encodes an endocytic protein, is a susceptibility gene, providing an unexpected entry point to our understanding of the response against herpesvirus infection. By contrast, elucidation of alternative mechanisms of host resistance against mouse cytomegalovirus in inbred mouse strains has led to new insights regarding molecular recognition of the infected cells by natural killer cell MHC class I receptors. In addition, the conservation of genetic and functional aspects between mouse and human is enabling a rational pursuit of potential cures. With the continuous development of resources for experimental investigation of the genome, the production of new mutant alleles, and the phenotypic characterization of new models of infection, we predict that mouse genetic models will make an increasing contribution to our understanding of the genetic puzzle of host response to virus infection.
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Affiliation(s)
- Agnieszka Kielczewska
- McGill Centre for the Study of Host Resistance, Department of Human Genetics, McGill University, Montreal, Quebec, H3A 2B4, Canada
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28
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Carlyle JR, Mesci A, Ljutic B, Belanger S, Tai LH, Rousselle E, Troke AD, Proteau MF, Makrigiannis AP. Molecular and genetic basis for strain-dependent NK1.1 alloreactivity of mouse NK cells. THE JOURNAL OF IMMUNOLOGY 2006; 176:7511-24. [PMID: 16751398 DOI: 10.4049/jimmunol.176.12.7511] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
NK1.1 alloantigen expression can be used to define NK cells in certain mouse strains, such as B6 (NKR-P1C) and SJL (NKR-P1B). However, BALB/c NK cells do not react with the anti-NK1.1 mAb, PK136. To investigate the NK1.1(-) phenotype of BALB/c NK cells, we have undertaken NK1.1 epitope mapping and genomic analysis of the BALB/c Nkrp1 region. Bacterial artificial chromosome library analysis reveals that, unlike the Ly49 region, the Nkrp1-Ocil/Clr region displays limited genetic divergence between B6 and BALB/c mice. In fact, significant divergence is confined to the Nkrp1b and Nkrp1c genes. Strikingly, the B6 Nkrp1d gene appears to represent a divergent allele of the Nkrp1b gene in BALB/c mice and other strains. Importantly, BALB/c NK cells express abundant and functional Nkrp1 transcripts, and the BALB/c NKR-P1B receptor functionally binds Ocil/Clr-b ligand. However, the BALB/c NKR-P1B/C sequences differ from those of the known NK1.1 alloantigens, and epitope mapping demonstrates that directed mutation of a single amino acid in the NKR-P1B(BALB) protein confers NK1.1 reactivity. Thus, PK136 mAb recognizes, in part, a distal C-terminal epitope present in NKR-P1B(Sw/SJL) and NKR-P1C(B6), but absent in NKR-P1A/D/F(B6) and NKR-P1B/C(BALB). Allelic divergence of the Nkrp1b/c gene products and limited divergence of the BALB/c Nkrp1-Ocil/Clr region explain a longstanding confusion regarding the strain-specific NK1.1 alloantigen reactivity of mouse NK cells.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Animals
- Antigens, Ly
- Antigens, Surface/biosynthesis
- Antigens, Surface/genetics
- Cell Line
- Gene Library
- Gene Order
- Haplotypes
- Humans
- Killer Cells, Lymphokine-Activated/immunology
- Killer Cells, Lymphokine-Activated/metabolism
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lectins, C-Type/biosynthesis
- Lectins, C-Type/genetics
- Membrane Proteins/biosynthesis
- Membrane Proteins/genetics
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, SCID
- Molecular Sequence Data
- Multigene Family
- Mutagenesis, Insertional
- NK Cell Lectin-Like Receptor Subfamily B
- Physical Chromosome Mapping
- Species Specificity
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Affiliation(s)
- James R Carlyle
- Department of Immunology, University of Toronto, Sunnybrook and Women's Research Institute, ON, Canada.
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29
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Rouhi A, Gagnier L, Takei F, Mager DL. Evidence for epigenetic maintenance of Ly49a monoallelic gene expression. THE JOURNAL OF IMMUNOLOGY 2006; 176:2991-9. [PMID: 16493057 DOI: 10.4049/jimmunol.176.5.2991] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Although structurally unrelated, the human killer cell Ig-like (KIR) genes and the rodent lectin-like Ly49 genes serve similar functional roles in NK cells. Moreover, both gene families display variegated, monoallelic expression patterns established at the transcriptional level. DNA methylation has been shown to play an important role in maintenance of expression patterns of KIR genes, which have CpG island promoters. The potential role of DNA methylation in expression of Ly49 genes, which have CpG-poor promoters, is unknown. In this study, we show that hypomethylation of the region encompassing the Pro-2 promoter of Ly49a and Ly49c in primary C57BL/6 NK cells correlates with expression of the gene. Using C57BL/6 x BALB/c F1 hybrid mice, we demonstrate that the expressed allele of Ly49a is hypomethylated while the nonexpressed allele is heavily methylated, indicating a role for epigenetics in maintaining monoallelic Ly49 gene expression. Furthermore, the Ly49a Pro-2 region is heavily methylated in fetal NK cells but variably methylated in nonlymphoid tissues. Finally, in apparent contrast to the KIR genes, we show that DNA methylation and the histone acetylation state of the Pro-2 region are strictly linked with Ly49a expression status.
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MESH Headings
- Acetylation
- Alleles
- Animals
- Antigens, Ly/biosynthesis
- Antigens, Ly/genetics
- Antigens, Ly/metabolism
- Base Sequence
- Cells, Cultured
- CpG Islands/immunology
- DNA Methylation
- Epigenesis, Genetic/immunology
- Female
- Gene Expression Regulation/immunology
- Histones/metabolism
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lectins, C-Type/biosynthesis
- Lectins, C-Type/genetics
- Lectins, C-Type/metabolism
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Molecular Sequence Data
- NK Cell Lectin-Like Receptor Subfamily A
- Promoter Regions, Genetic/immunology
- Receptors, Immunologic/biosynthesis
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Receptors, KIR
- Receptors, NK Cell Lectin-Like
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Affiliation(s)
- Arefeh Rouhi
- The Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
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30
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Kveberg L, Bäck CJ, Dai KZ, Inngjerdingen M, Rolstad B, Ryan JC, Vaage JT, Naper C. The Novel Inhibitory NKR-P1C Receptor and Ly49s3 Identify Two Complementary, Functionally Distinct NK Cell Subsets in Rats. THE JOURNAL OF IMMUNOLOGY 2006; 176:4133-40. [PMID: 16547249 DOI: 10.4049/jimmunol.176.7.4133] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The proximal region of the NK gene complex encodes the NKR-P1 family of killer cell lectin-like receptors which in mice bind members of the genetically linked C-type lectin-related family, while the distal region encodes Ly49 receptors for polymorphic MHC class I molecules. Although certain members of the NKR-P1 family are expressed by all NK cells, we have identified a novel inhibitory rat NKR-P1 molecule termed NKR-P1C that is selectively expressed by a Ly49-negative NK subset with unique functional characteristics. NKR-P1C(+) NK cells efficiently lyse certain tumor target cells, secrete cytokines upon stimulation, and functionally recognize a nonpolymorphic ligand on Con A-activated lymphoblasts. However, they specifically fail to kill MHC-mismatched lymphoblast target cells. The NKR-P1C(+) NK cell subset also appears earlier during development and shows a tissue distribution distinct from its complementary Ly49s3(+) subset, which expresses a wide range of Ly49 receptors. These data suggest the existence of two major, functionally distinct populations of rat NK cells possessing very different killer cell lectin-like receptor repertoires.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal/immunology
- Antigens, Ly/genetics
- Antigens, Ly/immunology
- Antigens, Ly/metabolism
- Antigens, Surface/chemistry
- Antigens, Surface/immunology
- Antigens, Surface/metabolism
- Cells, Cultured
- Concanavalin A/pharmacology
- Cytokines/metabolism
- Gene Expression Regulation
- Humans
- Killer Cells, Natural/cytology
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lectins, C-Type/chemistry
- Lectins, C-Type/immunology
- Lectins, C-Type/metabolism
- Ligands
- Molecular Sequence Data
- NK Cell Lectin-Like Receptor Subfamily B
- Phylogeny
- Rats
- Sequence Alignment
- Sequence Homology, Amino Acid
- Time Factors
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Affiliation(s)
- Lise Kveberg
- Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Norway
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31
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Yawata M, Yawata N, Draghi M, Little AM, Partheniou F, Parham P. Roles for HLA and KIR polymorphisms in natural killer cell repertoire selection and modulation of effector function. ACTA ACUST UNITED AC 2006; 203:633-45. [PMID: 16533882 PMCID: PMC2118260 DOI: 10.1084/jem.20051884] [Citation(s) in RCA: 436] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Interactions between killer cell immunoglobulin-like receptors (KIRs) and human leukocyte antigen (HLA) class I ligands regulate the development and response of human natural killer (NK) cells. Natural selection drove an allele-level group A KIR haplotype and the HLA-C1 ligand to unusually high frequency in the Japanese, who provide a particularly informative population for investigating the mechanisms by which KIR and HLA polymorphism influence NK cell repertoire and function. HLA class I ligands increase the frequencies of NK cells expressing cognate KIR, an effect modified by gene dose, KIR polymorphism, and the presence of other cognate ligand-receptor pairs. The five common Japanese KIR3DLI allotypes have distinguishable inhibitory capacity, frequency of cellular expression, and level of cell surface expression as measured by antibody binding. Although KIR haplotypes encoding 3DL1*001 or 3DL1*005, the strongest inhibitors, have no activating KIR, the dominant haplotype encodes a moderate inhibitor, 3DL1*01502, plus functional forms of the activating receptors 2DL4 and 2DS4. In the population, certain combinations of KIR and HLA class I ligand are overrepresented or underrepresented in women, but not men, and thus influence female fitness and survival. These findings show how KIR-HLA interactions shape the genetic and phenotypic KIR repertoires for both individual humans and the population.
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Affiliation(s)
- Makoto Yawata
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA, and Department of Haematology, The Royal Free Hospital, London, UK.
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32
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Abstract
Natural killer (NK) cells were identified 30 years ago based on their ability to "spontaneously" kill tumor cells. The basis for NK cell recognition and activation is due to a variety of receptors that bind to specific ligands on tumor cells and normal cells. Some of these receptors have the ability to inhibit NK cell function, and other receptors activate NK cell function. Therapeutic strategies for cancer therapy are being developed based on preventing NK cell inhibition or using NK cell receptors to activate NK cells or T cells. There are intriguing clinical data from studies of bone marrow transplantation that support the idea that preventing NK cell inhibition by human leukocyte antigen (HLA) class I molecules can be a means to promote graft-versus-leukemia (GvL) effects and limit graft-versus-host disease (GvHD) in acute myeloid leukemia (AML) and chronic myeloid leukemia (CML) patients. Experimental findings also support the blockade of NK cell inhibitory receptors as a way to protect against leukemia relapse. It may be possible to use our knowledge of NK cell activating receptors and their ligands to immunize patients with modified tumor cells to promote beneficial NK cell responses and development of host antitumor cytotoxic T lymphocytes (CTLs). Finally, new data support the idea of using modified NK cell receptors as a means to target patients' T cells against their own tumor cells and induce long-term immunity against them. Tumors are essentially tissues that have overcome normal regulation mechanisms, and therefore the ability to distinguish normal cells from abnormal cells is a key part of selectively attacking tumor cells. NK cells have various receptor systems designed to recognize infected and abnormal cells. Understanding NK cell receptors and their recognition mechanisms provides new tools for the development of immunotherapies against cancer.
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Affiliation(s)
- Charles L Sentman
- Department of Microbiology and Immunology, Dartmouth Medical School, Lebanon, New Hampshire 03756, USA
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