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van der Wiel MKH, Le NG, de Groot N, de Groot NG, Bontrop RE, Bruijnesteijn J. Exploring the genetic mechanisms driving KIR diversification. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2025; 214:762-779. [PMID: 40096639 DOI: 10.1093/jimmun/vkae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Accepted: 11/21/2024] [Indexed: 03/19/2025]
Abstract
Killer cell immunoglobulin-like receptors (KIRs) are key modulators of natural killer cell activity, displaying either activating or inhibitory potential upon recognition of major histocompatibility complex (MHC) class I molecules. The genomic organization of KIR genes is complex, involving copy number variation and allelic polymorphism, which is probably due to their coevolution with highly polymorphic MHC ligands. The KIR diversity is reflected by more than 70 similar region configurations encountered in humans, generated through meiotic recombination events. Rhesus macaques happen to display even more diversity, and over 100 distinct configurations were identified in a relatively small cohort of animals. More than half of these region configurations feature hybrid KIR genes, suggesting a more pronounced mode of diversification in macaques. The molecular mechanism facilitating meiotic rearrangements in the KIR region is poorly understood. Examination of 21 rhesus macaque and 14 human KIR region configurations revealed the presence of long terminal repeats and PRDM9 binding motifs associated with recombination hotspots. The variable DNA recognition patterns of PRDM9 could potentially contribute to the differing recombination activities documented for the KIR region in humans and macaques. The diversification process of the KIR repertoire in natural killer cells is fundamentally distinct from the mechanisms generating T and B cell receptor diversity or MHC polymorphisms. This sophisticated recombination machinery preserves the functional integrity by the frequent generation of in-frame KIR genes. A diverse KIR repertoire contributes to the protection of individuals and populations against pathogen evasion and subversion.
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Affiliation(s)
- Marit K H van der Wiel
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, the Netherlands
| | - Ngoc Giang Le
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, the Netherlands
| | - Nanine de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, the Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, the Netherlands
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, the Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| | - Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, the Netherlands
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de Groot NG, de Vos‐Rouweler AJM, Heijmans CMC, Louwerse A, Massen JJM, Langermans JAM, Bontrop RE, Bruijnesteijn J. Genetic Conservation and Population Management of Non-Human Primates: Parentage Determination Using Seven Microsatellite-Based Multiplexes. Ecol Evol 2025; 15:e71216. [PMID: 40196407 PMCID: PMC11974450 DOI: 10.1002/ece3.71216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Revised: 03/07/2025] [Accepted: 03/21/2025] [Indexed: 04/09/2025] Open
Abstract
Conservation of non-human primates receives much attention, with nearly 350 of the more than 520 recorded primate species classified as threatened. To conduct effective population management, monitoring genetic diversity within species is of key importance, as it can offer insights into the levels of inbreeding within groups or populations. To examine kinship within the macaque breeding groups housed at the Biomedical Primate Research Centre, located in Rijswijk, The Netherlands, we have developed seven microsatellite-based multiplexes for parentage analysis. These multiplexes comprise a unique set of 23 short tandem repeats (STR) distributed across 15 chromosomes. Extensive validation has been conducted across 2217 Indian rhesus (Macaca mulatta) and 759 long-tailed macaques (M. fascicularis), demonstrating that these STR markers are highly polymorphic and segregate. Most markers exhibit a polymorphic information content (PIC) value above 0.5, illustrating that they are highly informative and valuable in providing us with a reliable parentage determination. Beyond macaques, we manifested that the multiplexes are also suitable for addressing parentage issues in apes and other Old World monkey species. Furthermore, this assay works on DNA isolated from both invasive and non-invasive derived material (e.g., hair follicles and potentially feces). Thus, we present here seven validated multiplexes suitable for parentage analysis in apes and Old World monkey species. These multiplexes support future colony management objectives for various captive populations and, given the applicability of non-invasive techniques, could also be valuable for monitoring free-ranging primate populations.
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Affiliation(s)
- Natasja G. de Groot
- Comparative Genetics and RefinementBiomedical Primate Research CentreRijswijkGJthe Netherlands
| | | | - Corrine M. C. Heijmans
- Comparative Genetics and RefinementBiomedical Primate Research CentreRijswijkGJthe Netherlands
| | - Annet Louwerse
- Animal Science DepartmentBiomedical Primate Research CentreRijswijkGJthe Netherlands
| | - Jorg J. M. Massen
- Animal Behaviour and Cognition, Department of BiologyUtrecht UniversityUtrechtCHthe Netherlands
| | - Jan A. M. Langermans
- Animal Science DepartmentBiomedical Primate Research CentreRijswijkGJthe Netherlands
- Population Health Sciences, Unit Animals in Science and Society, Faculty of Veterinary MedicineUtrecht UniversityUtrechtCMthe Netherlands
| | - Ronald E. Bontrop
- Comparative Genetics and RefinementBiomedical Primate Research CentreRijswijkGJthe Netherlands
- Theoretical Biology and BioinformaticsUtrecht UniversityUtrechtCHthe Netherlands
| | - Jesse Bruijnesteijn
- Comparative Genetics and RefinementBiomedical Primate Research CentreRijswijkGJthe Netherlands
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3
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Clain JA, Picard M, Rabezanahary H, André S, Boutrais S, Goma Matsetse E, Dewatines J, Dueymes Q, Thiboutot E, Racine G, Soundaramourty C, Mammano F, Corbeau P, Zghidi-Abouzid O, Estaquier J. Immune Alterations and Viral Reservoir Atlas in SIV-Infected Chinese Rhesus Macaques. Infect Dis Rep 2025; 17:12. [PMID: 39997464 PMCID: PMC11855486 DOI: 10.3390/idr17010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 01/24/2025] [Accepted: 01/26/2025] [Indexed: 02/26/2025] Open
Abstract
BACKGROUND/OBJECTIVES Over the last decades, our projects have been dedicated to clarifying immunopathological and virological events associated with Human Immunodeficiency Virus (HIV) infection. METHODS By using non-human primate models of pathogenic and non-pathogenic lentiviral infections, we aimed at identifying the cells and tissues in which the virus persists, despite antiretroviral therapy (ART). Indeed, the eradication of viral reservoirs is a major challenge for HIV cure. RESULTS We present a series of results performed in rhesus macaques of Chinese origin deciphering the virological and immunological events associated with ART that can be of interest for people living with HIV. CONCLUSIONS This model could be of interest for understanding in whole body the clinical alteration that persist despite ART.
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Affiliation(s)
- Julien A. Clain
- Centre Hospitalier Universitaire (CHU) de Québec Centre de Recherche, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (J.A.C.); (H.R.); (S.B.); (E.G.M.); (J.D.); (Q.D.); (E.T.); (G.R.); (O.Z.-A.)
| | - Morgane Picard
- Institut national de la santé et de la recherche médicale (INSERM) U1124, Université Paris Cité, 75006 Paris, France; (M.P.); (S.A.); (C.S.); (F.M.)
| | - Henintsoa Rabezanahary
- Centre Hospitalier Universitaire (CHU) de Québec Centre de Recherche, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (J.A.C.); (H.R.); (S.B.); (E.G.M.); (J.D.); (Q.D.); (E.T.); (G.R.); (O.Z.-A.)
| | - Sonia André
- Institut national de la santé et de la recherche médicale (INSERM) U1124, Université Paris Cité, 75006 Paris, France; (M.P.); (S.A.); (C.S.); (F.M.)
| | - Steven Boutrais
- Centre Hospitalier Universitaire (CHU) de Québec Centre de Recherche, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (J.A.C.); (H.R.); (S.B.); (E.G.M.); (J.D.); (Q.D.); (E.T.); (G.R.); (O.Z.-A.)
| | - Ella Goma Matsetse
- Centre Hospitalier Universitaire (CHU) de Québec Centre de Recherche, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (J.A.C.); (H.R.); (S.B.); (E.G.M.); (J.D.); (Q.D.); (E.T.); (G.R.); (O.Z.-A.)
| | - Juliette Dewatines
- Centre Hospitalier Universitaire (CHU) de Québec Centre de Recherche, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (J.A.C.); (H.R.); (S.B.); (E.G.M.); (J.D.); (Q.D.); (E.T.); (G.R.); (O.Z.-A.)
| | - Quentin Dueymes
- Centre Hospitalier Universitaire (CHU) de Québec Centre de Recherche, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (J.A.C.); (H.R.); (S.B.); (E.G.M.); (J.D.); (Q.D.); (E.T.); (G.R.); (O.Z.-A.)
| | - Elise Thiboutot
- Centre Hospitalier Universitaire (CHU) de Québec Centre de Recherche, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (J.A.C.); (H.R.); (S.B.); (E.G.M.); (J.D.); (Q.D.); (E.T.); (G.R.); (O.Z.-A.)
| | - Gina Racine
- Centre Hospitalier Universitaire (CHU) de Québec Centre de Recherche, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (J.A.C.); (H.R.); (S.B.); (E.G.M.); (J.D.); (Q.D.); (E.T.); (G.R.); (O.Z.-A.)
| | - Calaiselvy Soundaramourty
- Institut national de la santé et de la recherche médicale (INSERM) U1124, Université Paris Cité, 75006 Paris, France; (M.P.); (S.A.); (C.S.); (F.M.)
| | - Fabrizio Mammano
- Institut national de la santé et de la recherche médicale (INSERM) U1124, Université Paris Cité, 75006 Paris, France; (M.P.); (S.A.); (C.S.); (F.M.)
- Institut national de la santé et de la recherche médicale (Inserm) U1259 MAVIVHe, Université de Tours, 37032 Tours, France
| | - Pierre Corbeau
- Institut de Génétique Humaine, CNRS-Université de Montpellier UMR9002, 34094 Montpellier, France;
| | - Ouafa Zghidi-Abouzid
- Centre Hospitalier Universitaire (CHU) de Québec Centre de Recherche, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (J.A.C.); (H.R.); (S.B.); (E.G.M.); (J.D.); (Q.D.); (E.T.); (G.R.); (O.Z.-A.)
| | - Jérôme Estaquier
- Centre Hospitalier Universitaire (CHU) de Québec Centre de Recherche, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (J.A.C.); (H.R.); (S.B.); (E.G.M.); (J.D.); (Q.D.); (E.T.); (G.R.); (O.Z.-A.)
- Institut national de la santé et de la recherche médicale (INSERM) U1124, Université Paris Cité, 75006 Paris, France; (M.P.); (S.A.); (C.S.); (F.M.)
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Agarwal D, Liu C, Bhoj V, Kearns J, Bharani T, Choe I, Vivek K, O'Connor DH, Wiseman RW, Duquesnoy RJ, Naji A, Kamoun M. Adaptation of HLA testing to characterize the cynomolgus macaque MHC polymorphisms and alloantibody signatures. HLA 2024; 103:e15239. [PMID: 37784210 DOI: 10.1111/tan.15239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/12/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]
Abstract
Nonhuman primates are the closest animal models to humans with respect to genetics and physiology. Consequently, a critical component of immunogenetics research relies on drawing inferences from the cynomolgus macaque to inform human trials. Despite the conserved organization of the Major Histocompatibility Complex (MHC) between cynomolgus macaques and humans, MHC genotyping of cynomolgus macaques is challenging due to high rates of copy number variants, duplications, and rearrangements, particularly at the MHC class I loci. Furthermore, the limited availability of commercial reagents specific to cynomolgus macaques that can be used to characterize anti-MHC class I and class II antibody (Ab) specificities in cynomolgus macaques presents a major bottleneck in translational research. Here we successfully characterized cynomolgus macaque Mafa class I and class II serologic specificities in 86 animals originating from various geographical regions using the complement dependent cytotoxicity (CDC) assay with human HLA class I and class II monoclonal antibody (mAb) typing trays. Further, we successfully induced and characterized anti-Mafa class I and class II alloantibody specificity using HLA single antigen bead assays. We also subsequently tracked the alloAb burden in the animals during treatment with anti-B lymphocyte stimulator (BLyS) treatment. Altogether, these methods can be easily used in translational research to serotype MHC class I and class II specificity in macaques, characterize their alloAb specificity, and evaluate the efficacy of novel therapeutic modalities in depleting circulating alloAbs in these animals.
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Affiliation(s)
- Divyansh Agarwal
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Chengyang Liu
- Division of Transplantation, Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Vijay Bhoj
- Center for Cellular Immunotherapies and the Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jane Kearns
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Tina Bharani
- Thomas Jefferson University Hospitals, Sidney Kimmel Medical College, Philadelphia, Pennsylvania, USA
| | - Insuk Choe
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kumar Vivek
- Department of Anesthesiology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - René J Duquesnoy
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Ali Naji
- Division of Transplantation, Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Malek Kamoun
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Grant NL, Kelly K, Maiello P, Abbott H, O’Connor S, Lin PL, Scanga CA, Flynn JL. Mycobacterium tuberculosis-Specific CD4 T Cells Expressing Transcription Factors T-Bet or RORγT Associate with Bacterial Control in Granulomas. mBio 2023; 14:e0047723. [PMID: 37039646 PMCID: PMC10294621 DOI: 10.1128/mbio.00477-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/16/2023] [Indexed: 04/12/2023] Open
Abstract
Despite the extensive research on CD4 T cells within the context of Mycobacterium tuberculosis (Mtb) infections, few studies have focused on identifying and investigating the profile of Mtb-specific T cells within lung granulomas. To facilitate the identification of Mtb-specific CD4 T cells, we identified immunodominant epitopes for two Mtb proteins, namely, Rv1196 and Rv0125, using a Mauritian cynomolgus macaque model of Mtb infection, thereby providing data for the synthesis of MHC class II tetramers. Using tetramers, we identified Mtb-specific cells within different immune compartments, postinfection. We found that granulomas were enriched sites for Mtb-specific cells and that tetramer+ cells had increased frequencies of the activation marker CD69 as well as the transcription factors T-bet and RORγT, compared to tetramer negative cells within the same sample. Our data revealed that while the frequency of Rv1196 tetramer+ cells was positively correlated with the granuloma bacterial burden, the frequency of RORγT or T-bet within tetramer+ cells was inversely correlated with the granuloma bacterial burden, thereby highlighting the importance of having activated, polarized, Mtb-specific cells for the control of Mtb in lung granulomas. IMPORTANCE Tuberculosis, caused by the bacterial pathogen Mycobacterium tuberculosis, kills 1.5 million people each year, despite the existence of effective drugs and a vaccine that is given to infants in most countries. Clearly, we need better vaccines against this disease. However, our understanding of the immune responses that are necessary to prevent tuberculosis is incomplete. This study seeks to understand the functions of T cells that are specific for M. tuberculosis at the site of the disease in the lungs. For this, we developed specialized tools called MHC class II tetramers to identify those T cells that can recognize M. tuberculosis and applied the tools to the study of this infection in nonhuman primate models that mimic human tuberculosis. We demonstrate that M. tuberculosis-specific T cells in lung lesions are associated with control of the bacteria only when those T cells are expressing certain functions, thereby highlighting the importance of combining the identification of specific T cells with functional analyses. Thus, we surmise that these functions of specific T cells are critical to the control of infection and should be considered as a part of the development of vaccines against tuberculosis.
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Affiliation(s)
- Nicole L. Grant
- Department of Infectious Disease and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Kristen Kelly
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Helena Abbott
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Shelby O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison Wisconsin, USA
| | - Philana Ling Lin
- Department of Pediatrics, Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Charles A. Scanga
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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6
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Anderson JL, Sandstrom K, Smith WR, Wetzel M, Klenchin VA, Evans DT. MHC Class I Ligands of Rhesus Macaque Killer Cell Ig-like Receptors. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1815-1826. [PMID: 37036309 PMCID: PMC10192222 DOI: 10.4049/jimmunol.2200954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/20/2023] [Indexed: 04/11/2023]
Abstract
Definition of MHC class I ligands of rhesus macaque killer cell Ig-like receptors (KIRs) is fundamental to NK cell biology in this species as an animal model for infectious diseases, reproductive biology, and transplantation. To provide a more complete foundation for studying NK cell responses, rhesus macaque KIRs representing common allotypes of lineage II KIR genes were tested for interactions with MHC class I molecules representing diverse Macaca mulatta (Mamu)-A, -B, -E, -F, -I, and -AG alleles. KIR-MHC class I interactions were identified by coincubating reporter cell lines bearing chimeric KIR-CD3ζ receptors with target cells expressing individual MHC class I molecules and were corroborated by staining with KIR IgG-Fc fusion proteins. Ligands for 12 KIRs of previously unknown specificity were identified that fell into three general categories: interactions with multiple Mamu-Bw4 molecules, interactions with Mamu-A-related molecules, including allotypes of Mamu-AG and the hybrid Mamu-B*045:03 molecule, or interactions with Mamu-A1*012:01. Whereas most KIRs found to interact with Mamu-Bw4 are inhibitory, most of the KIRs that interact with Mamu-AG are activating. The KIRs that recognize Mamu-A1*012:01 belong to a phylogenetically distinct group of macaque KIRs with a 3-aa deletion in the D0 domain that is also present in human KIR3DL1/S1 and KIR3DL2. This study more than doubles the number of rhesus macaque KIRs with defined MHC class I ligands and identifies interactions with Mamu-AG, -B*045, and -A1*012. These findings support overlapping, but nonredundant, patterns of ligand recognition that reflect extensive functional diversification of these receptors.
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Affiliation(s)
- Jennifer L. Anderson
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
| | - Kjell Sandstrom
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
| | - Willow R. Smith
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
| | - Molly Wetzel
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
| | - Vadim A. Klenchin
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
| | - David T. Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI
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7
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Karl JA, Prall TM, Bussan HE, Varghese JM, Pal A, Wiseman RW, O'Connor DH. Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype. Genome Res 2023; 33:448-462. [PMID: 36854669 PMCID: PMC10078292 DOI: 10.1101/gr.277429.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023]
Abstract
Macaques provide the most widely used nonhuman primate models for studying the immunology and pathogenesis of human diseases. Although the macaque major histocompatibility complex (MHC) region shares most features with the human leukocyte antigen (HLA) region, macaques have an expanded repertoire of MHC class I genes. Although a chimera of two rhesus macaque MHC haplotypes was first published in 2004, the structural diversity of MHC genomic organization in macaques remains poorly understood owing to a lack of adequate genomic reference sequences. We used ultralong Oxford Nanopore and high-accuracy Pacific Biosciences (PacBio) HiFi sequences to fully assemble the ∼5.2-Mb M3 haplotype of an MHC-homozygous, Mauritian-origin cynomolgus macaque (Macaca fascicularis). The MHC homozygosity allowed us to assemble a single MHC haplotype unambiguously and avoid chimeric assemblies that hampered previous efforts to characterize this exceptionally complex genomic region in macaques. The high quality of this new assembly is exemplified by the identification of an extended cluster of six Mafa-AG genes that contains a recent duplication with a highly similar ∼48.5-kb block of sequence. The MHC class II region of this M3 haplotype is similar to the previously sequenced rhesus macaque haplotype and HLA class II haplotypes. The MHC class I region, in contrast, contains 13 MHC-B genes, four MHC-A genes, and three MHC-E genes (vs. 19 MHC-B, two MHC-A, and one MHC-E in the previously sequenced haplotype). These results provide an unambiguously assembled single contiguous cynomolgus macaque MHC haplotype with fully curated gene annotations that will inform infectious disease and transplantation research.
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Affiliation(s)
- Julie A Karl
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Trent M Prall
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Hailey E Bussan
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Joshua M Varghese
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Aparna Pal
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA;
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
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8
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Li X, Liu T, Li A, Xiao Y, Sun K, Feng J. Diversifying selection and climatic effects on major histocompatibility complex class
II
gene diversity in the greater horseshoe bat. Evol Appl 2023; 16:688-704. [PMID: 36969140 PMCID: PMC10033860 DOI: 10.1111/eva.13528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
Heterogeneous pathogenic stress can shape major histocompatibility complex (MHC) diversity by influencing the functional plasticity of the immune response. Therefore, MHC diversity could reflect environmental stress, demonstrating its importance in uncovering the mechanisms of adaptive genetic variation. In this study, we combined neutral microsatellite loci, an immune-related MHC II-DRB locus, and climatic factors to unravel the mechanisms affecting the diversity and genetic differentiation of MHC genes in the greater horseshoe bat (Rhinolophus ferrumequinum), a species with a wide geographical distribution that has three distinct genetic lineages in China. First, increased genetic differentiation at the MHC locus among populations compared using microsatellites indicated diversifying selection. Second, the genetic differentiation of MHC and microsatellites were significantly correlated, suggesting that demographic processes exist. However, MHC genetic differentiation was significantly correlated with geographical distance among populations, even after controlling for the neutral markers, suggesting a major effect of selection. Third, although the MHC genetic differentiation was larger than that for microsatellites, there was no significant difference in the genetic differentiation between the two markers among genetic lineages, indicating the effect of balancing selection. Fourth, combined with climatic factors, MHC diversity and supertypes showed significant correlations with temperature and precipitation, but not with the phylogeographic structure of R. ferrumequinum, suggesting an effect of local adaptation driven by climate on MHC diversity. Moreover, the number of MHC supertypes varied between populations and lineages, suggesting regional characteristics and support for local adaptation. Taken together, the results of our study provide insights into the adaptive evolutionary driving forces at different geographic scales in R. ferrumequinum. In addition, climate factors may have played a vital role in driving adaptive evolution in this species.
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Affiliation(s)
- Xiaolin Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- Key Laboratory of Vegetation Ecology, Ministry of Education Changchun China
| | - Tong Liu
- College of Life Science, Jilin Agricultural University Changchun China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- Key Laboratory of Vegetation Ecology, Ministry of Education Changchun China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- College of Life Science, Jilin Agricultural University Changchun China
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9
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Hu Q, Huang X, Jin Y, Zhang R, Zhao A, Wang Y, Zhou C, Liu W, Liu X, Li C, Fan G, Zhuo M, Wang X, Ling F, Luo W. Long-read assembly of major histocompatibility complex and killer cell immunoglobulin-like receptor genome regions in cynomolgus macaque. Biol Direct 2022; 17:36. [PMID: 36447238 PMCID: PMC9707422 DOI: 10.1186/s13062-022-00350-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) and the killer cell immunoglobulin-like receptors (KIR) are key regulators of immune responses. The cynomolgus macaque, an Old World monkey species, can be applied as an important preclinical model for studying human diseases, including coronavirus disease 2019 (COVID-19). Several MHC-KIR combinations have been associated with either a poor or good prognosis. Therefore, macaques with a well-characterized immunogenetic profile may improve drug evaluation and speed up vaccine development. At present, a complete overview of the MHC and KIR haplotype organizations in cynomolgus macaques is lacking, and characterization by conventional techniques is hampered by the extensive expansion of the macaque MHC-B region that complicates the discrimination between genes and alleles. METHODS We assembled complete MHC and KIR genomic regions of cynomolgus macaque using third-generation long-read sequencing approach. We identified functional Mafa-B loci at the transcriptome level using locus-specific amplification in a cohort of 33 Vietnamese cynomolgus macaques. RESULTS This is the first physical mapping of complete MHC and KIR gene regions in a Vietnamese cynomolgus macaque. Furthermore, we identified four functional Mafa-B loci (B2, B3, B5, and B6) and showed that alleles of the Mafa-I*01, -B*056, -B*034, and -B*001 functional lineages, respectively, are highly frequent in the Vietnamese cynomolgus macaque population. CONCLUSION The insights into the MHC and KIR haplotype organizations and the level of diversity may refine the selection of animals with specific genetic markers for future medical research.
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Affiliation(s)
- Qingxiu Hu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xiaoqi Huang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yabin Jin
- The First People's Hospital of Foshan, Sun Yat-sen University, Foshan, 528000, China
| | - Rui Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Aimin Zhao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yiping Wang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Chenyun Zhou
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Weixin Liu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xunwei Liu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Chunhua Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Min Zhuo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xiaoning Wang
- National Clinic Center of Geriatric, The Chinese PLA General Hospital, Beijing, 100853, China.
| | - Fei Ling
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
| | - Wei Luo
- The First People's Hospital of Foshan, Sun Yat-sen University, Foshan, 528000, China.
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10
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Malouli D, Gilbride RM, Wu HL, Hwang JM, Maier N, Hughes CM, Newhouse D, Morrow D, Ventura AB, Law L, Tisoncik-Go J, Whitmore L, Smith E, Golez I, Chang J, Reed JS, Waytashek C, Weber W, Taher H, Uebelhoer LS, Womack JL, McArdle MR, Gao J, Papen CR, Lifson JD, Burwitz BJ, Axthelm MK, Smedley J, Früh K, Gale M, Picker LJ, Hansen SG, Sacha JB. Cytomegalovirus-vaccine-induced unconventional T cell priming and control of SIV replication is conserved between primate species. Cell Host Microbe 2022; 30:1207-1218.e7. [PMID: 35981532 PMCID: PMC9927879 DOI: 10.1016/j.chom.2022.07.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/01/2022] [Accepted: 07/19/2022] [Indexed: 01/26/2023]
Abstract
Strain 68-1 rhesus cytomegalovirus expressing simian immunodeficiency virus (SIV) antigens (RhCMV/SIV) primes MHC-E-restricted CD8+ T cells that control SIV replication in 50%-60% of the vaccinated rhesus macaques. Whether this unconventional SIV-specific immunity and protection is unique to rhesus macaques or RhCMV or is intrinsic to CMV remains unknown. Here, using cynomolgus CMV vectors expressing SIV antigens (CyCMV/SIV) and Mauritian cynomolgus macaques, we demonstrate that the induction of MHC-E-restricted CD8+ T cells requires matching CMV to its host species. RhCMV does not elicit MHC-E-restricted CD8+ T cells in cynomolgus macaques. However, cynomolgus macaques vaccinated with species-matched 68-1-like CyCMV/SIV mounted MHC-E-restricted CD8+ T cells, and half of the vaccinees stringently controlled SIV post-challenge. Protected animals manifested a vaccine-induced IL-15 transcriptomic signature that is associated with efficacy in rhesus macaques. These findings demonstrate that the ability of species-matched CMV vectors to elicit MHC-E-restricted CD8+ T cells that are required for anti-SIV efficacy is conserved in nonhuman primates, and these data support the development of HCMV/HIV for a prophylactic HIV vaccine.
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Affiliation(s)
- Daniel Malouli
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Roxanne M Gilbride
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Helen L Wu
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Joseph M Hwang
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Nicholas Maier
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Colette M Hughes
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Daniel Newhouse
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - David Morrow
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Abigail B Ventura
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Lynn Law
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Jennifer Tisoncik-Go
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Leanne Whitmore
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Elise Smith
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Inah Golez
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Jean Chang
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Jason S Reed
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Courtney Waytashek
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Whitney Weber
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Husam Taher
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Luke S Uebelhoer
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jennie L Womack
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Matthew R McArdle
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Junwei Gao
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Courtney R Papen
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Benjamin J Burwitz
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Michael K Axthelm
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jeremy Smedley
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Klaus Früh
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Louis J Picker
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Scott G Hansen
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA.
| | - Jonah B Sacha
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA.
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11
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de Groot NG, de Groot N, de Vos-Rouweler AJM, Louwerse A, Bruijnesteijn J, Bontrop RE. Dynamic evolution of Mhc haplotypes in cynomolgus macaques of different geographic origins. Immunogenetics 2022; 74:409-429. [PMID: 35084546 PMCID: PMC8792142 DOI: 10.1007/s00251-021-01249-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/26/2021] [Indexed: 11/05/2022]
Abstract
The major histocompatibility complex (MHC) plays a key role in immune defense, and the Mhc genes of cynomolgus macaque display a high degree of polymorphism. Based on their geographic distribution, different populations of cynomolgus macaques are recognized. Here we present the characterization of the Mhc class I and II repertoire of a large pedigreed group of cynomolgus macaques originating from the mainland north of the isthmus of Kra (N = 42). Segregation analyses resulted in the definition of 81 unreported Mafa-A/B/DRB/DQ/DP haplotypes, which include 32 previously unknown DRB regions. In addition, we report 13 newly defined Mafa-A/B/DRB/DQ/DP haplotypes in a group of cynomolgus macaques originating from the mainland south of the isthmus of Kra/Maritime Southeast Asia (N = 16). A relatively high level of sharing of Mafa-A (51%) and Mafa-B (40%) lineage groups is observed between the populations native to the north and the south of isthmus of Kra. At the allelic level, however, the Mafa-A/B haplotypes seem to be characteristic of a population. An overall comparison of all currently known data revealed that each geographic population has its own specific combinations of Mhc class I and II haplotypes. This illustrates the dynamic evolution of the cynomolgus macaque Mhc region, which was most likely generated by recombination and maintained by selection due to the differential pathogenic pressures encountered in different geographic areas.
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Affiliation(s)
- Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, The Netherlands.
| | - Nanine de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, The Netherlands
| | | | - Annet Louwerse
- Animal Science Department, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, The Netherlands
| | - Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH, Utrecht, The Netherlands
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12
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Nicholas RE, Sandstrom K, Anderson JL, Smith WR, Wetzel M, Banerjee P, Janaka SK, Evans DT. KIR3DL05 and KIR3DS02 Recognition of a Nonclassical MHC Class I Molecule in the Rhesus Macaque Implicated in Pregnancy Success. Front Immunol 2022; 13:841136. [PMID: 35401580 PMCID: PMC8984097 DOI: 10.3389/fimmu.2022.841136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Knowledge of the MHC class I ligands of rhesus macaque killer-cell Ig-like receptors (KIRs) is fundamental to understanding the role of natural killer (NK) cells in this species as a nonhuman primate model for infectious diseases, transplantation and reproductive biology. We previously identified Mamu-AG as a ligand for KIR3DL05. Mamu-AG is a nonclassical MHC class I molecule that is expressed at the maternal-fetal interface of the placenta in rhesus macaques similar to HLA-G in humans. Although Mamu-AG and HLA-G share similar molecular features, including limited polymorphism and a short cytoplasmic tail, Mamu-AG is considerably more polymorphic. To determine which allotypes of Mamu-AG serve as ligands for KIR3DL05, we tested reporter cell lines expressing five different alleles of KIR3DL05 (KIR3DL05*001, KIR3DL05*004, KIR3DL05*005, KIR3DL05*008 and KIR3DL05*X) for responses to target cells expressing eight different alleles of Mamu-AG. All five allotypes of KIR3DL05 responded to Mamu-AG2*01:01, two exhibited dominant responses to Mamu-AG1*05:01, and three had low but detectable responses to Mamu-AG3*03:01, -AG3*03:02, -AG3*03:03 and -AG3*03:04. Since KIR3DL05*X is the product of recombination between KIR3DL05 and KIR3DS02, we also tested an allotype of KIR3DS02 (KIR3DS02*004) and found that this activating KIR also recognizes Mamu-AG2*01:01. Additional analysis of Mamu-AG variants with single amino acid substitutions identified residues in the α1-domain essential for recognition by KIR3DL05. These results reveal variation in KIR3DL05 and KIR3DS02 responses to Mamu-AG and define Mamu-AG polymorphisms that differentially affect KIR recognition.
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Affiliation(s)
- Rachel E. Nicholas
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Kjell Sandstrom
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Jennifer L. Anderson
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Willow R. Smith
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Molly Wetzel
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Priyankana Banerjee
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Sanath Kumar Janaka
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - David T. Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
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13
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Miyamae J, Okano M, Nishiya K, Katakura F, Kulski JK, Moritomo T, Shiina T. Haplotype structures and polymorphisms of dog leukocyte antigen (DLA) class I loci shaped by intralocus and interlocus recombination events. Immunogenetics 2022; 74:245-259. [PMID: 34993565 DOI: 10.1007/s00251-021-01234-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/10/2021] [Indexed: 11/26/2022]
Abstract
The dog leukocyte antigen (DLA) class I genomic region is located on chromosome 12, and the class I genomic region is composed of at least two distinct haplotypic gene structures, DLA-88-DLA-12 and DLA-88-DLA-88L. However, detailed information of the genomic differences among DLA-88, DLA-12, and DLA-88L are still lacking at the full-length gene level, and therefore, DLA allelic sequences classified for each of these loci are limited in number so far. In this study, we determined the DNA sequence of a 95-kb DLA class I genomic region including DLA-88, DLA-12/88L, and DLA-64 with three DLA homozygous dogs and of 37 full-length allelic gene sequences for DLA-88 and DLA-12/88L loci in 26 DLA class I homozygous dogs. Nucleotide diversity profiles of the 95-kb regions and sequence identity scores of the allelic sequences suggested that DLA-88L is a hybrid gene generated by interlocus and/or intralocus gene conversion between DLA-88 and DLA-12. The putative minimum conversion tract was estimated to be at least an 850-bp segment in length located from the 5´flanking untranslated region to the end of intron 2. In addition, at least one DLA-12 allele (DLA-12*004:01) was newly generated by interlocus gene conversion. In conclusion, the analysis for the occurrence of gene conversion within the dog DLA class I region revealed intralocus gene conversion tracts in 17 of 27 DLA-88 alleles and two of 10 DLA-12 alleles, suggesting that intralocus gene conversion has played an important role in expanding DLA allelic variations.
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Affiliation(s)
- Jiro Miyamae
- Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoino-oka, Imabari, Ehime, 794-8555, Japan.
| | - Masaharu Okano
- Department of Legal Medicine, Nihon University School of Dentistry, 1-8-13 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-8310, Japan
| | - Kohei Nishiya
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Fumihiko Katakura
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Jerzy K Kulski
- Discipline of Psychiatry, Medical School, The University of Western Australia, Crawley, WA, Australia
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1143, Japan
| | - Tadaaki Moritomo
- Department of Veterinary Medicine, College of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1143, Japan
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14
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de Groot NG, Heijmans CMC, Bezstarosti S, Bruijnesteijn J, Haasnoot GW, Mulder A, Claas FHJ, Heidt S, Bontrop RE. Two Human Monoclonal HLA-Reactive Antibodies Cross-React with Mamu-B*008, a Rhesus Macaque MHC Allotype Associated with Control of Simian Immunodeficiency Virus Replication. THE JOURNAL OF IMMUNOLOGY 2021; 206:1957-1965. [PMID: 33692147 DOI: 10.4049/jimmunol.2001405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/02/2021] [Indexed: 11/19/2022]
Abstract
MHC class I molecules play an important role in adaptive immune responses against intracellular pathogens. These molecules are highly polymorphic, and many allotypes have been characterized. In a transplantation setting, a mismatch between MHC allotypes may initiate an alloimmune response. Rhesus macaques (Macaca mulatta, Mamu) are valuable as a preclinical model species in transplantation research as well as to evaluate the safety and efficacy of vaccine candidates. In both lines of research, the availability of nonhuman primate MHC-reactive mAbs may enable in vitro monitoring and detection of presence of particular Mamu molecules. In this study, we screened a collection of thoroughly characterized HLA class I-specific human mAbs for cross-reactivity with rhesus macaque MHC class I allotypes. Two mAbs, OK4F9 and OK4F10, recognize an epitope that is defined by isoleucine (I) at amino acid position 142 that is present on the Indian rhesus macaque Mamu-B*008:01 allotype, which is an allotype known to be associated with elite control of SIV replication. The reactive pattern of a third mAb, MUS4H4, is more complex and includes an epitope shared on Mamu-A2*05:01 and -B*001:01-encoded Ags. This is the first description, to our knowledge, of human HLA-reactive mAbs that can recognize Mamu allotypes, and these can be useful tools for in vitro monitoring the presence of the relevant allelic products. Moreover, OK4F9 and OK4F10 can be powerful mAbs for application in SIV-related research.
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Affiliation(s)
- Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands;
| | - Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Suzanne Bezstarosti
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Geert W Haasnoot
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Arend Mulder
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Frans H J Claas
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Sebastiaan Heidt
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands
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15
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Development and evaluation of a rapid and cost-efficient NGS-based MHC class I genotyping method for macaques by using a prevalent short-read sequencer. Immunogenetics 2021; 73:175-186. [PMID: 33447871 DOI: 10.1007/s00251-020-01199-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/02/2020] [Indexed: 10/22/2022]
Abstract
Rhesus macaque is one of the most widely used primate model animals for immunological research of infectious diseases including human immunodeficiency virus (HIV) infection. It is well known that major histocompatibility complex (MHC) class I genotypes affect the susceptibility and disease progression to simian immunodeficiency virus (SIV) in rhesus macaques, which is resembling to HIV in humans. It is required to convincingly determine the MHC genotypes in the immunological investigations, that is why several next-generation sequencing (NGS)-based methods have been established. In general, NGS-based genotyping methods using short amplicons are not often applied to MHC because of increasing number of alleles and inevitable ambiguity in allele detection, although there is an advantage of short read sequencing systems that are commonly used today. In this study, we developed a new high-throughput NGS-based genotyping method for MHC class I alleles in rhesus macaques and cynomolgus macaques. By using our method, 95% and 100% of alleles identified by PCR cloning-based method were detected in rhesus macaques and cynomolgus macaques, respectively, which were highly correlated with their expression levels. It was noted that the simulation of new-allele detection step using artificial alleles differing by a few nucleotide sequences from a known allele could be identified with high accuracy and that we could detect a real novel allele from a rhesus macaque sample. These findings supported that our method could be adapted for primate animal models such as macaques to reduce the cost and labor of previous NGS-based MHC genotyping.
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16
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D'Souza SS, Bennett S, Kumar A, Kelnhofer LE, Weinfurter J, Suknuntha K, Coonen J, Mejia A, Simmons H, Golos T, Hematti P, Capitini CM, Reynolds MR, Slukvin II. Transplantation of T-cell receptor α/β-depleted allogeneic bone marrow in nonhuman primates. Exp Hematol 2021; 93:44-51. [PMID: 33176119 PMCID: PMC7855119 DOI: 10.1016/j.exphem.2020.09.198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/24/2020] [Accepted: 09/26/2020] [Indexed: 10/23/2022]
Abstract
Allogeneic hematopoietic stem cell transplantation (alloHSCT) is a potentially curative treatment for hematologic cancers and chronic infections such as human immunodeficiency virus (HIV). Its success in these settings is attributed to the ability of engrafting immune cells to eliminate cancer cells or deplete the HIV reservoir (graft-versus-host effect [GvHE]). However, alloHSCT is commonly associated with graft-versus-host diseases (GvHDs) causing significant morbidity and mortality, thereby requiring development of novel allogeneic HSCT protocols and therapies promoting GvHE without GvHD using physiologically relevant preclinical models. Here we evaluated the outcomes of major histocompatibility complex-matched T-cell receptor α/β-depleted alloHSCT in Mauritian cynomolgus macaques (MCMs). Following T-cell receptor α/β depletion, bone marrow cells were transplanted into major histocompatibility complex-identical MCMs conditioned with total body irradiation. GvHD prophylaxis included sirolimus alone in two animals or tacrolimus with cyclophosphamide in another two animals. Posttransplant chimerism was determined by sequencing diagnostic single-nucleotide polymorphisms to quantify the amounts of donor and recipient cells present in blood. Animals treated posttransplant with sirolimus developed nearly complete chimerism with acute GvHD. In the cyclophosphamide and tacrolimus treatment group, animals developed mixed chimerism without GvHD, with long-term engraftment observed in one animal. None of the animals developed cytomegalovirus infection. These studies indicate the feasibility of alloHSCT engraftment without GvHD in an MHC-identical MCM model following complete myeloablative conditioning and anti-GvHD prophylaxis with posttransplant cyclophosphamide and tacrolimus. Further exploration of this model will provide a platform for elucidating the mechanisms of GvHD and GvHE and for testing novel alloHSCT modalities for HIV infection.
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Affiliation(s)
- Saritha S D'Souza
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI
| | - Sarah Bennett
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI
| | - Akhilesh Kumar
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI
| | - Laurel E Kelnhofer
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI
| | - Jason Weinfurter
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI
| | - Kran Suknuntha
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Wisconsin-Madison, Madison, WI; Chakri Naruebodindra Medical Institute, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Samut Prakan, Thailand
| | - Jennifer Coonen
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI
| | - Andres Mejia
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI
| | - Heather Simmons
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI
| | - Thaddeus Golos
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI; Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI; Department of Obstetrics and Gynecology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
| | - Peiman Hematti
- Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI; Division of Hematology/Oncology/Bone Marrow Transplantation, Department of Medicine, University of Wisconsin Hospital and Clinics, Madison, WI
| | - Christian M Capitini
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
| | - Matthew R Reynolds
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI; Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI
| | - Igor I Slukvin
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI; Department of Pathology and Laboratory Medicine, School of Medicine, University of Wisconsin-Madison, Madison, WI; Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Madison, WI.
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17
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Bruijnesteijn J, de Groot NG, Bontrop RE. The Genetic Mechanisms Driving Diversification of the KIR Gene Cluster in Primates. Front Immunol 2020; 11:582804. [PMID: 33013938 PMCID: PMC7516082 DOI: 10.3389/fimmu.2020.582804] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/18/2020] [Indexed: 12/26/2022] Open
Abstract
The activity and function of natural killer (NK) cells are modulated through the interactions of multiple receptor families, of which some recognize MHC class I molecules. The high level of MHC class I polymorphism requires their ligands either to interact with conserved epitopes, as is utilized by the NKG2A receptor family, or to co-evolve with the MHC class I allelic variation, which task is taken up by the killer cell immunoglobulin-like receptor (KIR) family. Multiple molecular mechanisms are responsible for the diversification of the KIR gene system, and include abundant chromosomal recombination, high mutation rates, alternative splicing, and variegated expression. The combination of these genetic mechanisms generates a compound array of diversity as is reflected by the contraction and expansion of KIR haplotypes, frequent birth of fusion genes, allelic polymorphism, structurally distinct isoforms, and variegated expression, which is in contrast to the mainly allelic nature of MHC class I polymorphism in humans. A comparison of the thoroughly studied human and macaque KIR gene repertoires demonstrates a similar evolutionarily conserved toolbox, through which selective forces drove and maintained the diversified nature of the KIR gene cluster. This hypothesis is further supported by the comparative genetics of KIR haplotypes and genes in other primate species. The complex nature of the KIR gene system has an impact upon the education, activity, and function of NK cells in coherence with an individual’s MHC class I repertoire and pathogenic encounters. Although selection operates on an individual, the continuous diversification of the KIR gene system in primates might protect populations against evolving pathogens.
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Affiliation(s)
- Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
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18
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Na HS, Lee SY, Min HK, Park WJ, Lee JH, Cho KH, Hong SH, Kim DH, Jhun J, Choi JW, Kim SM, Kwok SK, Cho ML, Park SH. The establishment of a rheumatoid arthritis primate model in Macaca fascicularis. J Transl Med 2020; 18:264. [PMID: 32605610 PMCID: PMC7329448 DOI: 10.1186/s12967-020-02402-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/03/2020] [Indexed: 12/29/2022] Open
Abstract
Background Rheumatoid arthritis (RA) is a long-term autoimmune disorder that mostly affects the joints and leads to the destruction of cartilage. An RA model in non-human primates is especially useful because of their close phylogenetic relationship to humans in terms of cross-reactivity to compounds developed using modern drug technologies. Methods We used a collagen-induced arthritis (CIA) model in Macaca fascicularis. CIA was induced by the immunization of chicken type II collagen. Swelling was measured as the longitudinal and transverse axes of 16 proximal interphalangeal joints. Results A new system for visual evaluation was created, with a perfect score of 16. Individual behavioral analysis was also conducted. Serum was collected once a week after the first immunization. Blood chemistry and inflammatory cytokine parameters were higher in the CIA group than in the wild type group. Conclusion In conclusion, we established CIA in M. fascicularis, and the results can be used for drug evaluation models.
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Affiliation(s)
- Hyun Sik Na
- Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea.,Laboratory of Immune Network, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seon-Yeong Lee
- Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea.,Laboratory of Immune Network, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hong Ki Min
- Division of Rheumatology, Department of Internal Medicine, Konkuk University Medical Center, Seoul, Republic of Korea
| | - Wan-Je Park
- Haeeun Biomedical Research Institute, Genia Inc, Sungnam, Korea
| | - Jung-Hwan Lee
- Haeeun Biomedical Research Institute, Genia Inc, Sungnam, Korea
| | - Ka-Hee Cho
- Division of Rheumatology, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Shin-Hee Hong
- Haeeun Biomedical Research Institute, Genia Inc, Sungnam, Korea
| | - Dae-Hoon Kim
- Haeeun Biomedical Research Institute, Genia Inc, Sungnam, Korea
| | - Jooyeon Jhun
- Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea.,Laboratory of Immune Network, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jeong-Won Choi
- Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea.,Laboratory of Immune Network, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sung-Min Kim
- Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea.,Laboratory of Immune Network, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung-Ki Kwok
- Division of Rheumatology, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Mi-La Cho
- Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea. .,Laboratory of Immune Network, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea. .,Department of Medical Lifescience, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea. .,Conversant Research Consortium in Immunologic Disease, College of Medicine, The Catholic University of Korea, 505 Banpo-Dong, Seocho-Ku, 137-040, Seoul, Korea.
| | - Sung-Hwan Park
- Division of Rheumatology, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea.
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19
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Bruijnesteijn J, de Groot N, van der Wiel MKH, Otting N, de Vos-Rouweler AJM, de Groot NG, Bontrop RE. Unparalleled Rapid Evolution of KIR Genes in Rhesus and Cynomolgus Macaque Populations. THE JOURNAL OF IMMUNOLOGY 2020; 204:1770-1786. [PMID: 32111732 DOI: 10.4049/jimmunol.1901140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/21/2020] [Indexed: 12/19/2022]
Abstract
The killer cell Ig-like receptors (KIR) modulate immune responses through interactions with MHC class I molecules. The KIR region in large cohorts of rhesus and cynomolgus macaque populations were characterized, and the experimental design enabled the definition of a considerable number of alleles (n = 576) and haplotypes, which are highly variable with regard to architecture. Although high levels of polymorphism were recorded, only a few alleles are shared between species and populations. The rapid evolution of allelic polymorphism, accumulated by point mutations, was further confirmed by the emergence of a novel KIR allele in a rhesus macaque family. In addition to allelic variation, abundant orthologous and species-specific KIR genes were identified, the latter of which are frequently generated by fusion events. The concerted action of both genetic mechanisms, in combination with differential selective pressures at the population level, resulted in the unparalleled rapid evolution of the KIR gene region in two closely related macaque species. The variation of the KIR gene repertoire at the species and population level might have an impact on the outcome of preclinical studies with macaque models.
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Affiliation(s)
- Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Marit K H van der Wiel
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Annemiek J M de Vos-Rouweler
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and .,Theoretical Biology and Bioinformatics Group, Utrecht University, 3527 Utrecht, the Netherlands
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20
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Nomenclature report 2019: major histocompatibility complex genes and alleles of Great and Small Ape and Old and New World monkey species. Immunogenetics 2019; 72:25-36. [PMID: 31624862 DOI: 10.1007/s00251-019-01132-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 12/27/2022]
Abstract
The major histocompatibility complex (MHC) is central to the innate and adaptive immune responses of jawed vertebrates. Characteristic of the MHC are high gene density, gene copy number variation, and allelic polymorphism. Because apes and monkeys are the closest living relatives of humans, the MHCs of these non-human primates (NHP) are studied in depth in the context of evolution, biomedicine, and conservation biology. The Immuno Polymorphism Database (IPD)-MHC NHP Database (IPD-MHC NHP), which curates MHC data of great and small apes, as well as Old and New World monkeys, has been upgraded. The curators of the database are responsible for providing official designations for newly discovered alleles. This nomenclature report updates the 2012 report, and summarizes important nomenclature issues and relevant novel features of the IPD-MHC NHP Database.
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21
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Vaccine Vectors Harnessing the Power of Cytomegaloviruses. Vaccines (Basel) 2019; 7:vaccines7040152. [PMID: 31627457 PMCID: PMC6963789 DOI: 10.3390/vaccines7040152] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 02/05/2023] Open
Abstract
Cytomegalovirus (CMV) species have been gaining attention as experimental vaccine vectors inducing cellular immune responses of unparalleled strength and protection. This review outline the strengths and the restrictions of CMV-based vectors, in light of the known aspects of CMV infection, pathogenicity and immunity. We discuss aspects to be considered when optimizing CMV based vaccines, including the innate immune response, the adaptive humoral immunity and the T-cell responses. We also discuss the antigenic epitopes presented by unconventional major histocompatibility complex (MHC) molecules in some CMV delivery systems and considerations about routes for delivery for the induction of systemic or mucosal immune responses. With the first clinical trials initiating, CMV-based vaccine vectors are entering a mature phase of development. This impetus needs to be maintained by scientific advances that feed the progress of this technological platform.
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22
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Qurkhuli T, Schwensow N, Brändel SD, Tschapka M, Sommer S. Can extreme MHC class I diversity be a feature of a wide geographic range? The example of Seba's short-tailed bat (Carollia perspicillata). Immunogenetics 2019; 71:575-587. [PMID: 31520134 PMCID: PMC7079943 DOI: 10.1007/s00251-019-01128-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/14/2019] [Indexed: 12/19/2022]
Abstract
The major histocompatibility complex (MHC) is one of the most diverse genetic regions under pathogen-driven selection because of its central role in antigen binding and immunity. The highest MHC variability, both in terms of the number of individual alleles and gene copies, has so far been found in passerine birds; this is probably attributable to passerine adaptation to both a wide geographic range and a diverse array of habitats. If extraordinary high MHC variation and duplication rates are adaptive features under selection during the evolution of ecologically and taxonomically diverse species, then similarly diverse MHC architectures should be found in bats. Bats are an extremely species-rich mammalian group that is globally widely distributed. Many bat species roost in multitudinous groups and have high contact rates with pathogens, conspecifics, and allospecifics. We have characterized the MHC class I diversity in 116 Panamanian Seba's short-tailed bats (Carollia perspicillata), a widely distributed, generalist, neotropical species. We have detected a remarkable individual and population-level diversity of MHC class I genes, with between seven and 22 alleles and a unique genotype in each individual. This diversity is comparable with that reported in passerine birds and, in both taxonomic groups, further variability has evolved through length polymorphisms. Our findings support the hypothesis that, for species with a geographically broader range, high MHC class I variability is particularly adaptive. Investigation of the details of the underlying adaptive processes and the role of the high MHC diversity in pathogen resistance are important next steps for a better understanding of the role of bats in viral evolution and as carriers of several deadly zoonotic viruses.
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Affiliation(s)
- Tamar Qurkhuli
- Institute for Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, 89081, Ulm, Germany
| | - Nina Schwensow
- Institute for Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, 89081, Ulm, Germany
| | - Stefan Dominik Brändel
- Institute for Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, 89081, Ulm, Germany
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Panamá, República de Panamá
| | - Marco Tschapka
- Institute for Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, 89081, Ulm, Germany
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Panamá, República de Panamá
| | - Simone Sommer
- Institute for Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, 89081, Ulm, Germany.
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23
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Abstract
Viruses of wild and domestic animals can infect humans in a process called zoonosis, and these events can give rise to explosive epidemics such as those caused by the HIV and Ebola viruses. While humans are constantly exposed to animal viruses, those that can successfully infect and transmit between humans are exceedingly rare. The key event in zoonosis is when an animal virus begins to replicate (one virion making many) in the first human subject. Only at this point will the animal virus first experience the selective environment of the human body, rendering possible viral adaptation and refinement for humans. In addition, appreciable viral titers in this first human may enable infection of a second, thus initiating selection for viral variants with increased capacity for spread. We assert that host genetics plays a critical role in defining which animal viruses in nature will achieve this key event of replication in a first human host. This is because animal viruses that pose the greatest risk to humans will have few (or no) genetic barriers to replicating themselves in human cells, thus requiring minimal mutations to make this jump. Only experimental virology provides a path to identifying animal viruses with the potential to replicate themselves in humans because this information will not be evident from viral sequencing data alone.
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Affiliation(s)
- Cody J. Warren
- BioFrontiers Institute and Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute and Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
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24
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Abstract
PURPOSE OF REVIEW CMV-vectored vaccines expressing SIV antigens have mediated unprecedented levels of virus control following SIV challenge in rhesus macaques. Remarkably, protection was dependent on nonclassically restricted CD8 T cells. Here, we review the latest research in CMV-vectored vaccines in both humans and nonhuman primates as well as recent advances in the understanding nonclassically restricted T cells, particularly MHC-E-restricted CD8 T cells. RECENT FINDINGS Recent studies have investigated human translation of CMV-vectored vaccines including studies to ensure vaccine vector safety. Other work has focused on testing of animal models to investigate the relative contribution of MHC diversity and CMV strain on T-cell induction. Lastly, several groups have investigated MHC-E peptide binding, including HLA-E, have found that MHC-E can accommodate different peptide motifs, consistent with the original observations in CMV-vaccinated macaques. SUMMARY CMV remains a promising vaccine vector with the potential to be protective against multiple diseases, including HIV. However, CMV is highly species-specific and in humans, congenital infection can lead to serious birth defects. To ensure safe translation to humans, further clinical and animal studies are needed to better understand CMV-vectored immunity as well as more basic immunological questions relating to the induction of classical vs. nonclassical T cells.
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Affiliation(s)
- Maria Abad-Fernandez
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nilu Goonetilleke
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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25
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Abstract
Most studies of T lymphocytes focus on recognition of classical major histocompatibility complex (MHC) class I or II molecules presenting oligopeptides, yet there are numerous variations and exceptions of biological significance based on recognition of a wide variety of nonclassical MHC molecules. These include αβ and γδ T cells that recognize different class Ib molecules (CD1, MR-1, HLA-E, G, F, et al.) that are nearly monomorphic within a given species. Collectively, these T cells can be considered “unconventional,” in part because they recognize lipids, metabolites, and modified peptides. Unlike classical MHC-specific cells, unconventional T cells generally exhibit limited T-cell antigen receptor (TCR) repertoires and often produce innate immune cell-like rapid effector responses. Exploiting this system in new generation vaccines for human immunodeficiency virus (HIV), tuberculosis (TB), other infectious agents, and cancer was the focus of a recent workshop, “Immune Surveillance by Non-classical MHC Molecules: Improving Diversity for Antigens,” sponsored by the National Institute of Allergy and Infectious Diseases. Here, we summarize salient points presented regarding the basic immunobiology of unconventional T cells, recent advances in methodologies to measure unconventional T-cell activity in diseases, and approaches to harness their considerable clinical potential.
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26
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KANTHASWAMY SREETHARAN, OLDT ROBERTF, NG JILLIAN, SMITH DAVIDGLENN, MARTÍNEZ MELWEENI, SARIOL CARLOSA. Determination of major histocompatibility class I and class II genetic composition of the Caribbean Primate Center specific pathogen-free rhesus macaque (Macaca mulatta) colony based on massively parallel sequencing. J Med Primatol 2018; 47:379-387. [PMID: 29971797 PMCID: PMC6234078 DOI: 10.1111/jmp.12353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2018] [Indexed: 11/27/2022]
Abstract
BACKGROUND Knowledge of major histocompatibility complex (MHC) composition and distribution in rhesus macaque colonies is critical for management strategies that maximize the utility of this model for biomedical research. METHODS Variation within the Mamu-A and Mamu-B (class I) and DRB, DQA/B, and DPA/B (class II) regions of 379 animals from the Caribbean Primate Research Center's (CPRC) specific pathogen free (SPF) colony was examined using massively parallel sequencing. RESULTS Analyses of the 7 MHC loci revealed a background of Indian origin with high levels of variation despite past genetic bottlenecks. All loci exhibited mutual linkage disequilibria while conforming to Hardy-Weinberg expectations suggesting the achievement of mutation-selection balance. CONCLUSION The CPRC's SPF colony is a significant resource for research on AIDS and other infectious agents. Characterizing colony-wide MHC variability facilitates the breeding and selection of animals bearing desired haplotypes and increases the investigator's ability to understand the immune responses mounted by these animals.
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Affiliation(s)
- SREETHARAN KANTHASWAMY
- California National Primate Research Center, University of
California, Davis, CA, USA
- School of Mathematics and Natural Sciences, Arizona State University
(ASU) at the West Campus, Glendale, AZ, USA
| | - ROBERT F. OLDT
- School of Mathematics and Natural Sciences, Arizona State University
(ASU) at the West Campus, Glendale, AZ, USA
| | - JILLIAN NG
- California National Primate Research Center, University of
California, Davis, CA, USA
| | - DAVID GLENN SMITH
- California National Primate Research Center, University of
California, Davis, CA, USA
| | - MELWEEN I. MARTÍNEZ
- Caribbean Primate Research Center, University of Puerto Rico-Medical
Sciences Campus, San Juan, Puerto Rico
| | - CARLOS A. SARIOL
- Caribbean Primate Research Center, University of Puerto Rico-Medical
Sciences Campus, San Juan, Puerto Rico
- Department of Microbiology and Medical Zoology, University of Puerto
Rico-Medical Sciences Campus, San Juan, Puerto Rico
- Department of Medicine, University of Puerto Rico-Medical Sciences
Campus, San Juan, Puerto Rico
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27
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Banerjee P, Ries M, Janaka SK, Grandea AG, Wiseman R, O'Connor DH, Golos TG, Evans DT. Diversification of Bw4 Specificity and Recognition of a Nonclassical MHC Class I Molecule Implicated in Maternal-Fetal Tolerance by Killer Cell Ig-like Receptors of the Rhesus Macaque. THE JOURNAL OF IMMUNOLOGY 2018; 201:2776-2786. [PMID: 30232137 DOI: 10.4049/jimmunol.1800494] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 08/20/2018] [Indexed: 12/21/2022]
Abstract
The rhesus macaque is an important animal model for AIDS and other infectious diseases; however, studies to address NK cell function in this species have been limited by the lack of defined ligands for killer cell Ig-like receptors (KIRs). To identify ligands for rhesus macaque KIRs, we adopted a novel approach based on a pair of stable cell lines. NFAT-responsive luciferase reporter cell lines expressing the extracellular domains of macaque KIRs fused to the transmembrane and cytoplasmic domains of CD28 and CD3ζ were incubated with target cells expressing individual MHC class I molecules, and ligand recognition was detected by the MHC class I-dependent upregulation of luciferase. Using this approach, we found that Mamu-KIR3DL01, -KIR3DL06, -KIR3DL08, and -KIR3DSw08 all recognize Mamu-Bw4 molecules but with differing allotype specificity. In contrast, Mamu-KIR3DL05 recognizes Mamu-A and Mamu-A-related molecules, including Mamu-A1*002 and -A3*13, Mamu-B*036, the product of a recombinant Mamu-B allele with α1 and α2 domain sequences derived from a MHC-A gene, and Mamu-AG*01, a nonclassical molecule expressed on placental trophoblasts that originated from an ancestral duplication of a MHC-A gene. These results reveal an expansion of the lineage II KIRs in macaques that recognize Bw4 ligands and identify a nonclassical molecule implicated in placental development and pregnancy as a ligand for Mamu-KIR3DL05. In addition to offering new insights into KIR-MHC class I coevolution, these findings provide an important foundation for investigating the role of NK cells in the rhesus macaque as an animal model for infectious diseases and reproductive biology.
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Affiliation(s)
- Priyankana Banerjee
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Moritz Ries
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Sanath Kumar Janaka
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Andres G Grandea
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Roger Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705.,Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715
| | - Thaddeus G Golos
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715.,Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53706; and.,Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI 53705
| | - David T Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705; .,Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715
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28
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MHC class I diversity of olive baboons (Papio anubis) unravelled by next-generation sequencing. Immunogenetics 2018; 70:439-448. [PMID: 29478145 PMCID: PMC6006219 DOI: 10.1007/s00251-018-1053-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 01/30/2018] [Indexed: 12/26/2022]
Abstract
The olive baboon represents an important model system to study various aspects of human biology and health, including the origin and diversity of the major histocompatibility complex. After screening of a group of related animals for polymorphisms associated with a well-defined microsatellite marker, subsequent MHC class I typing of a selected population of 24 animals was performed on two distinct next-generation sequencing (NGS) platforms. A substantial number of 21 A and 80 B transcripts were discovered, about half of which had not been previously reported. Per animal, from one to four highly transcribed A alleles (majors) were observed, in addition to ones characterised by low transcripion levels (minors), such as members of the A*14 lineage. Furthermore, in one animal, up to 13 B alleles with differential transcription level profiles may be present. Based on segregation profiles, 16 Paan-AB haplotypes were defined. A haplotype encodes in general one or two major A and three to seven B transcripts, respectively. A further peculiarity is the presence of at least one copy of a B*02 lineage on nearly every haplotype, which indicates that B*02 represents a separate locus with probably a specialistic function. Haplotypes appear to be generated by recombination-like events, and the breakpoints map not only between the A and B regions but also within the B region itself. Therefore, the genetic makeup of the olive baboon MHC class I region appears to have been subject to a similar or even more complex expansion process than the one documented for macaque species.
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29
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Hill AB. The immune response to CMV infection and vaccination in mice, monkeys and humans: recent developments. Curr Opin Virol 2018; 28:161-166. [PMID: 29459261 DOI: 10.1016/j.coviro.2018.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/16/2018] [Indexed: 11/24/2022]
Abstract
The immune response to CMV is characterized by extremely large T cell and antibody responses that persist for a lifetime, but do not prevent superinfection with other CMV strains. This makes generation of a vaccine against CMV very difficult, but has facilitated development of CMV-vectored vaccines, which have shown promise in mouse tumor models and in monkey models of infectious disease. The serendipitous use of a mutant rhesus CMV vector for the SIV vaccine elicited extraordinary, CD8 T cell responses restricted by MHCII and non-classical MHCI molecules which apparently provide protection against SIV. CMV-specific CD8 T cell responses in the mouse model are driven by antigen and live out their lives primarily within the intravascular compartment.
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Affiliation(s)
- Ann B Hill
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, United States.
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30
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Wu HL, Wiseman RW, Hughes CM, Webb GM, Abdulhaqq SA, Bimber BN, Hammond KB, Reed JS, Gao L, Burwitz BJ, Greene JM, Ferrer F, Legasse AW, Axthelm MK, Park BS, Brackenridge S, Maness NJ, McMichael AJ, Picker LJ, O'Connor DH, Hansen SG, Sacha JB. The Role of MHC-E in T Cell Immunity Is Conserved among Humans, Rhesus Macaques, and Cynomolgus Macaques. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2018; 200:49-60. [PMID: 29150562 PMCID: PMC5736429 DOI: 10.4049/jimmunol.1700841] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/23/2017] [Indexed: 11/19/2022]
Abstract
MHC-E is a highly conserved nonclassical MHC class Ib molecule that predominantly binds and presents MHC class Ia leader sequence-derived peptides for NK cell regulation. However, MHC-E also binds pathogen-derived peptide Ags for presentation to CD8+ T cells. Given this role in adaptive immunity and its highly monomorphic nature in the human population, HLA-E is an attractive target for novel vaccine and immunotherapeutic modalities. Development of HLA-E-targeted therapies will require a physiologically relevant animal model that recapitulates HLA-E-restricted T cell biology. In this study, we investigated MHC-E immunobiology in two common nonhuman primate species, Indian-origin rhesus macaques (RM) and Mauritian-origin cynomolgus macaques (MCM). Compared to humans and MCM, RM expressed a greater number of MHC-E alleles at both the population and individual level. Despite this difference, human, RM, and MCM MHC-E molecules were expressed at similar levels across immune cell subsets, equivalently upregulated by viral pathogens, and bound and presented identical peptides to CD8+ T cells. Indeed, SIV-specific, Mamu-E-restricted CD8+ T cells from RM recognized antigenic peptides presented by all MHC-E molecules tested, including cross-species recognition of human and MCM SIV-infected CD4+ T cells. Thus, MHC-E is functionally conserved among humans, RM, and MCM, and both RM and MCM represent physiologically relevant animal models of HLA-E-restricted T cell immunobiology.
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Affiliation(s)
- Helen L Wu
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53706
| | - Colette M Hughes
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Gabriela M Webb
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Shaheed A Abdulhaqq
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Benjamin N Bimber
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
| | - Katherine B Hammond
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Jason S Reed
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Lina Gao
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239
| | - Benjamin J Burwitz
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
| | - Justin M Greene
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Fidel Ferrer
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Alfred W Legasse
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
| | - Michael K Axthelm
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
| | - Byung S Park
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
- School of Public Health, Oregon Health and Science University, Portland, OR 97239
| | - Simon Brackenridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Nicholas J Maness
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433
- Department of Microbiology and Immunology, School of Medicine, Tulane University Health Sciences Center, New Orleans, LA 70118; and
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 2JD, United Kingdom
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53706
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006
| | - Jonah B Sacha
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006;
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006
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Abstract
Since the discovery of acquired immunodeficiency syndrome (AIDS) in 1981, it has been extremely difficult to develop an effective vaccine or a therapeutic cure despite over 36 years of global efforts. One of the major reasons is due to the lack of an immune-competent animal model that supports live human immunodeficiency virus (HIV) infection and disease progression such that vaccine-induced correlates of protection and efficacy can be determined clearly before human trials. Nevertheless, rhesus macaques infected with simian immunodeficiency virus (SIV) and chimeric simian human immunodeficiency virus (SHIV) have served as invaluable models not only for understanding AIDS pathogenesis but also for studying HIV vaccine and cure. In this chapter, therefore, we summarize major scientific evidence generated in these models since the beginning of the AIDS pandemic. Hopefully, the accumulated knowledge and lessons contributed by thousands of scientists will be useful in promoting the search of an ultimate solution to end HIV/AIDS.
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32
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Burwitz BJ, Wu HL, Abdulhaqq S, Shriver-Munsch C, Swanson T, Legasse AW, Hammond KB, Junell SL, Reed JS, Bimber BN, Greene JM, Webb GM, Northrup M, Laub W, Kievit P, MacAllister R, Axthelm MK, Ducore R, Lewis A, Colgin LMA, Hobbs T, Martin LD, Ferguson B, Thomas CR, Panoskaltsis-Mortari A, Meyers G, Stanton JJ, Maziarz RT, Sacha JB. Allogeneic stem cell transplantation in fully MHC-matched Mauritian cynomolgus macaques recapitulates diverse human clinical outcomes. Nat Commun 2017; 8:1418. [PMID: 29127275 PMCID: PMC5681693 DOI: 10.1038/s41467-017-01631-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/04/2017] [Indexed: 12/31/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplantation (HSCT) is a critically important therapy for hematological malignancies, inborn errors of metabolism, and immunodeficiency disorders, yet complications such as graft-vs.-host disease (GvHD) limit survival. Development of anti-GvHD therapies that do not adversely affect susceptibility to infection or graft-vs.-tumor immunity are hampered by the lack of a physiologically relevant, preclinical model of allogeneic HSCT. Here we show a spectrum of diverse clinical HSCT outcomes including primary and secondary graft failure, lethal GvHD, and stable, disease-free full donor engraftment using reduced intensity conditioning and mobilized peripheral blood HSCT in unrelated, fully MHC-matched Mauritian-origin cynomolgus macaques. Anti-GvHD prophylaxis of tacrolimus, post-transplant cyclophosphamide, and CD28 blockade induces multi-lineage, full donor chimerism and recipient-specific tolerance while maintaining pathogen-specific immunity. These results establish a new preclinical allogeneic HSCT model for evaluation of GvHD prophylaxis and next-generation HSCT-mediated therapies for solid organ tolerance, cure of non-malignant hematological disease, and HIV reservoir clearance.
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Affiliation(s)
- Benjamin J Burwitz
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Helen L Wu
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Shaheed Abdulhaqq
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Christine Shriver-Munsch
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Tonya Swanson
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Alfred W Legasse
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Katherine B Hammond
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Stephanie L Junell
- Division of Medical Physics, Department of Radiation Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Jason S Reed
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Benjamin N Bimber
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Justin M Greene
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Gabriela M Webb
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Mina Northrup
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Wolfram Laub
- Division of Medical Physics, Department of Radiation Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Paul Kievit
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Rhonda MacAllister
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Michael K Axthelm
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Rebecca Ducore
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Anne Lewis
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Lois M A Colgin
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Theodore Hobbs
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Lauren D Martin
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Betsy Ferguson
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Charles R Thomas
- Division of Medical Physics, Department of Radiation Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Angela Panoskaltsis-Mortari
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, 2450 Riverside Avenue, Minneapolis, MN, 55454, USA
| | - Gabrielle Meyers
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Jeffrey J Stanton
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA
| | - Richard T Maziarz
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Jonah B Sacha
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA.
- Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR, 97006, USA.
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de Groot NG, Heijmans CMC, de Ru AH, Janssen GMC, Drijfhout JW, Otting N, Vangenot C, Doxiadis GGM, Koning F, van Veelen PA, Bontrop RE. A Specialist Macaque MHC Class I Molecule with HLA-B*27-like Peptide-Binding Characteristics. THE JOURNAL OF IMMUNOLOGY 2017; 199:3679-3690. [PMID: 29021373 DOI: 10.4049/jimmunol.1700502] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 09/15/2017] [Indexed: 11/19/2022]
Abstract
In different macaque species, the MHC A2*05 gene is present in abundance, and its gene products are characterized by low cell-surface expression and a highly conserved peptide-binding cleft. We have characterized the peptide-binding motif of Mamu-A2*05:01, and elucidated the binding capacity for virus-derived peptides. The macaque A2*05 allotype prefers the basic amino acid arginine at the second position of the peptide, and hydrophobic and polar amino acids at the C-terminal end. These preferences are shared with HLA-B*27 and Mamu-B*008, molecules shown to be involved in elite control in human HIV type 1 and macaque SIV infections, respectively. In contrast, however, Mamu-A2*05 preferentially binds 8-mer peptides. Retention in the endoplasmic reticulum seems to be the cause of the lower cell-surface expression. Subsequent peptide-binding studies have illustrated that Mamu-A2*05:01 is able to bind SIV-epitopes known to evoke a strong CD8+ T cell response in the context of the Mamu-B*008 allotype in SIV-infected rhesus macaques. Thus, the macaque A2*05 gene encodes a specialized MHC class I molecule, and is most likely transported to the cell surface only when suitable peptides become available.
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Affiliation(s)
- Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands;
| | - Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - George M C Janssen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Jan W Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Christelle Vangenot
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland; and
| | - Gaby G M Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands
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34
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Zens TJ, Danobeitia JS, Chlebeck PJ, Zitur LJ, Odorico S, Brunner K, Coonen J, Capuano S, D’Alessandro AM, Matkowskyj K, Zhong W, Torrealba J, Fernandez L. Guidelines for the management of a brain death donor in the rhesus macaque: A translational transplant model. PLoS One 2017; 12:e0182552. [PMID: 28926566 PMCID: PMC5604963 DOI: 10.1371/journal.pone.0182552] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 07/20/2017] [Indexed: 01/08/2023] Open
Abstract
Introduction The development of a translatable brain death animal model has significant potential to advance not only transplant research, but also the understanding of the pathophysiologic changes that occur in brain death and severe traumatic brain injury. The aim of this paper is to describe a rhesus macaque model of brain death designed to simulate the average time and medical management described in the human literature. Methods Following approval by the Institutional Animal Care and Use Committee, a brain death model was developed. Non-human primates were monitored and maintained for 20 hours after brain death induction. Vasoactive agents and fluid boluses were administered to maintain hemodynamic stability. Endocrine derangements, particularly diabetes insipidus, were aggressively managed. Results A total of 9 rhesus macaque animals were included in the study. The expected hemodynamic instability of brain death in a rostral to caudal fashion was documented in terms of blood pressure and heart rate changes. During the maintenance phase of brain death, the animal’s temperature and hemodynamics were maintained with goals of mean arterial pressure greater than 60mmHg and heart rate within 20 beats per minute of baseline. Resuscitation protocols are described so that future investigators may reproduce this model. Conclusion We have developed a reproducible large animal primate model of brain death which simulates clinical scenarios and treatment. Our model offers the opportunity for researchers to have translational model to test the efficacy of therapeutic strategies prior to human clinical trials.
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Affiliation(s)
- Tiffany J. Zens
- University of Wisconsin Department of Surgery, Division of Transplantation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Juan S. Danobeitia
- University of Wisconsin Department of Surgery, Division of Transplantation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Peter J. Chlebeck
- University of Wisconsin Department of Surgery, Division of Transplantation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Laura J. Zitur
- University of Wisconsin Department of Surgery, Division of Transplantation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Scott Odorico
- University of Wisconsin Department of Surgery, Division of Transplantation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Kevin Brunner
- Wisconsin Primate Research Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Jennifer Coonen
- Wisconsin Primate Research Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Saverio Capuano
- Wisconsin Primate Research Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Anthony M. D’Alessandro
- University of Wisconsin Department of Surgery, Division of Transplantation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Kristina Matkowskyj
- University of Wisconsin Department of Pathology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Weixiong Zhong
- University of Wisconsin Department of Pathology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Jose Torrealba
- University of Texas Southwestern Medical Center Department of Pathology, Dallas, Texas, United States of America
| | - Luis Fernandez
- University of Wisconsin Department of Surgery, Division of Transplantation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- * E-mail:
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Ries M, Reynolds MR, Bashkueva K, Crosno K, Capuano S, Prall TM, Wiseman R, O’Connor DH, Rakasz EG, Uno H, Lifson JD, Evans DT. KIR3DL01 upregulation on gut natural killer cells in response to SIV infection of KIR- and MHC class I-defined rhesus macaques. PLoS Pathog 2017; 13:e1006506. [PMID: 28708886 PMCID: PMC5529027 DOI: 10.1371/journal.ppat.1006506] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/26/2017] [Accepted: 07/02/2017] [Indexed: 01/29/2023] Open
Abstract
Natural killer cells provide an important early defense against viral pathogens and are regulated in part by interactions between highly polymorphic killer-cell immunoglobulin-like receptors (KIRs) on NK cells and their MHC class I ligands on target cells. We previously identified MHC class I ligands for two rhesus macaque KIRs: KIR3DL01 recognizes Mamu-Bw4 molecules and KIR3DL05 recognizes Mamu-A1*002. To determine how these interactions influence NK cell responses, we infected KIR3DL01+ and KIR3DL05+ macaques with and without defined ligands for these receptors with SIVmac239, and monitored NK cell responses in peripheral blood and lymphoid tissues. NK cell responses in blood were broadly stimulated, as indicated by rapid increases in the CD16+ population during acute infection and sustained increases in the CD16+ and CD16-CD56- populations during chronic infection. Markers of proliferation (Ki-67), activation (CD69 & HLA-DR) and antiviral activity (CD107a & TNFα) were also widely expressed, but began to diverge during chronic infection, as reflected by sustained CD107a and TNFα upregulation by KIR3DL01+, but not by KIR3DL05+ NK cells. Significant increases in the frequency of KIR3DL01+ (but not KIR3DL05+) NK cells were also observed in tissues, particularly in the gut-associated lymphoid tissues, where this receptor was preferentially upregulated on CD56+ and CD16-CD56- subsets. These results reveal broad NK cell activation and dynamic changes in the phenotypic properties of NK cells in response to SIV infection, including the enrichment of KIR3DL01+ NK cells in tissues that support high levels of virus replication.
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Affiliation(s)
- Moritz Ries
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Matthew R. Reynolds
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ksenia Bashkueva
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kristin Crosno
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Saverio Capuano
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Trent M. Prall
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Roger Wiseman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Eva G. Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Hajime Uno
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - David T. Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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36
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Kondova I, Braskamp G, Heidt PJ, Collignon W, Haaksma T, de Groot N, Otting N, Doxiadis G, Westmoreland SV, Vallender EJ, Bontrop RE. Spontaneous endometriosis in rhesus macaques: evidence for a genetic association with specific Mamu-A1 alleles. Primate Biol 2017; 4:117-125. [PMID: 32110699 PMCID: PMC7041536 DOI: 10.5194/pb-4-117-2017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/28/2017] [Indexed: 11/11/2022] Open
Abstract
Endometriosis is a poorly understood common debilitating women's
reproductive disorder resulting from proliferative and ectopic endometrial
tissue associated with variable clinical symptoms including dysmenorrhea
(painful menstrual periods), dyspareunia (pain on intercourse), female
infertility, and an increased risk of malignant transformation. The rhesus
macaque (Macaca mulatta) develops a spontaneous endometriosis that is very
similar to that seen in women. We hypothesized that specific major
histocompatibility complex (MHC) alleles may contribute to the pathogenesis
of endometriosis. As part of a collaboration between the Biomedical Primate
Research Centre (BPRC) in the Netherlands and the New England Primate
Research Center (NEPRC) in the United States, we analyzed DNA sequences of
MHC class I (Macaca mulatta, Mamu-A1) and class II
(Mamu-DRB) alleles from rhesus macaques with endometriosis and
compared the allele frequencies with those of age-matched healthy macaques.
We demonstrate that two MHC class I alleles are overrepresented in diseased
macaques compared to controls: Mamu-A1*001, 33.3 % in BPRC
animals with endometriosis vs. 11.6 % in healthy macaques (p= 0.007),
and Mamu-A1*007, 21.9 % NEPRC rhesus macaques vs.
6.7 %, (p= 0.003). We provide evidence that select MHC class I alleles
are associated with endometriosis in rhesus macaques and suggest that the
disease pathogenesis contribution of MHC class I warrants further research.
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Affiliation(s)
- Ivanela Kondova
- Animal Science Department, Division of Pathology and Microbiology, Division of Veterinary care, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Gerco Braskamp
- Animal Science Department, Division of Pathology and Microbiology, Division of Veterinary care, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands.,deceased
| | - Peter J Heidt
- Animal Science Department, Division of Pathology and Microbiology, Division of Veterinary care, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Wim Collignon
- Animal Science Department, Division of Pathology and Microbiology, Division of Veterinary care, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Tom Haaksma
- Animal Science Department, Division of Pathology and Microbiology, Division of Veterinary care, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Nanine de Groot
- Department of Comparative Genetics, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Nel Otting
- Department of Comparative Genetics, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Gaby Doxiadis
- Department of Comparative Genetics, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Susan V Westmoreland
- AbbVie Bioresearch Center, Immunology, Pharmacology, Pathology and Exploratory Toxicology, Worcester, MA 01605, USA
| | - Eric J Vallender
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS 39216, USA.,Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Ronald E Bontrop
- Department of Comparative Genetics, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
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Sterck EHM, Bontrop RE, de Groot N, de Vos-Rouweler AJM, Doxiadis GGM. No postcopulatory selection against MHC-homozygous offspring: Evidence from a pedigreed captive rhesus macaque colony. Mol Ecol 2017; 26:3785-3793. [PMID: 28437562 DOI: 10.1111/mec.14153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/18/2017] [Indexed: 02/06/2023]
Abstract
The heterozygosity status of polymorphic elements of the immune system, such as the major histocompatibility complex (MHC), is known to increase the potential to cope with a wider variety of pathogens. Pre- and postcopulatory processes may regulate MHC heterozygosity. In a population where mating occurs among individuals that share identical MHC haplotypes, postcopulatory selection may disfavour homozygous offspring or ones with two MHC haplotypes identical to its mother. We tested these ideas by determining the incidence of MHC-heterozygous and MHC-homozygous individuals in a pedigreed, partially consanguineous captive rhesus monkey colony. Bayesian statistics showed that when parents share MHC haplotypes, the distribution of MHC-heterozygous and MHC-homozygous individuals significantly fitted the expected Mendelian distribution, both for the complete MHC haplotypes, and for MHC class I or II genes separately. Altogether, we found in this captive colony no evidence for postcopulatory selection against MHC-homozygous individuals. However, the distribution of paternally and maternally inherited MHC haplotypes tended to differ significantly from expected. Individuals with two MHC haplotypes identical to their mother were underrepresented and offspring with MHC haplotypes identical to their father tended to be overrepresented. This suggests that postcopulatory processes affect MHC haplotype combination in offspring, but do not prevent low MHC heterozygosity.
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Affiliation(s)
- E H M Sterck
- Department of Animal Ecology, Utrecht University, Utrecht, The Netherlands.,Department of Animal Science, Ethology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - R E Bontrop
- Department of Comparative Genetics & Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,Department of Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - N de Groot
- Department of Comparative Genetics & Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - A J M de Vos-Rouweler
- Department of Comparative Genetics & Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - G G M Doxiadis
- Department of Comparative Genetics & Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
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38
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Murray SE, Nesterenko PA, Vanarsdall AL, Munks MW, Smart SM, Veziroglu EM, Sagario LC, Lee R, Claas FHJ, Doxiadis IIN, McVoy MA, Adler SP, Hill AB. Fibroblast-adapted human CMV vaccines elicit predominantly conventional CD8 T cell responses in humans. J Exp Med 2017; 214:1889-1899. [PMID: 28566275 PMCID: PMC5502433 DOI: 10.1084/jem.20161988] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/11/2017] [Accepted: 04/13/2017] [Indexed: 01/26/2023] Open
Abstract
Fibroblast-adapted rhesus CMV–vectored vaccines protect macaques from SIV challenge and elicit unconventional CD8 T cell responses. In contrast, Murray et al. show that humans vaccinated with fibroblast-adapted human CMV vaccines generate conventional CD8 T cell responses. Cytomegalovirus (CMV)-based vaccines have shown remarkable efficacy in the rhesus macaque model of acquired immune deficiency syndrome, enabling 50% of vaccinated monkeys to clear a subsequent virulent simian immunodeficiency virus challenge. The protective vaccine elicited unconventional CD8 T cell responses that were entirely restricted by MHC II or the nonclassical MHC I molecule, MHC-E. These unconventional responses were only elicited by a fibroblast-adapted rhesus CMV vector with limited tissue tropism; a repaired vector with normal tropism elicited conventional responses. Testing whether these unusual protective CD8 T responses could be elicited in humans requires vaccinating human subjects with a fibroblast-adapted mutant of human CMV (HCMV). In this study, we describe the CD8 T cell responses of human subjects vaccinated with two fibroblast-adapted HCMV vaccines. Most responses were identified as conventional classically MHC I restricted, and we found no evidence for MHC II or HLA-E restriction. These results indicate that fibroblast adaptation alone is unlikely to explain the unconventional responses observed in macaques.
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Affiliation(s)
- Susan E Murray
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR.,Department of Biology, University of Portland, Portland, OR
| | - Pavlo A Nesterenko
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR
| | - Adam L Vanarsdall
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR
| | - Michael W Munks
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR
| | - Savannah M Smart
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR
| | - Eren M Veziroglu
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR
| | - Lavinia C Sagario
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR
| | - Ronzo Lee
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA
| | - Frans H J Claas
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Ilias I N Doxiadis
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Michael A McVoy
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA
| | | | - Ann B Hill
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR
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39
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Karl JA, Graham ME, Wiseman RW, Heimbruch KE, Gieger SM, Doxiadis GGM, Bontrop RE, O'Connor DH. Major histocompatibility complex haplotyping and long-amplicon allele discovery in cynomolgus macaques from Chinese breeding facilities. Immunogenetics 2017; 69:211-229. [PMID: 28078358 PMCID: PMC5352482 DOI: 10.1007/s00251-017-0969-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/03/2017] [Indexed: 10/20/2022]
Abstract
Very little is currently known about the major histocompatibility complex (MHC) region of cynomolgus macaques (Macaca fascicularis; Mafa) from Chinese breeding centers. We performed comprehensive MHC class I haplotype analysis of 100 cynomolgus macaques from two different centers, with animals from different reported original geographic origins (Vietnamese, Cambodian, and Cambodian/Indonesian mixed-origin). Many of the samples were of known relation to each other (sire, dam, and progeny sets), making it possible to characterize lineage-level haplotypes in these animals. We identified 52 Mafa-A and 74 Mafa-B haplotypes in this cohort, many of which were restricted to specific sample origins. We also characterized full-length MHC class I transcripts using Pacific Biosciences (PacBio) RS II single-molecule real-time (SMRT) sequencing. This technology allows for complete read-through of unfragmented MHC class I transcripts (~1100 bp in length), so no assembly is required to unambiguously resolve novel full-length sequences. Overall, we identified 311 total full-length transcripts in a subset of 72 cynomolgus macaques from these Chinese breeding facilities; 130 of these sequences were novel and an additional 115 extended existing short database sequences to span the complete open reading frame. This significantly expands the number of Mafa-A, Mafa-B, and Mafa-I full-length alleles in the official cynomolgus macaque MHC class I database. The PacBio technique described here represents a general method for full-length allele discovery and genotyping that can be extended to other complex immune loci such as MHC class II, killer immunoglobulin-like receptors, and Fc gamma receptors.
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Affiliation(s)
- Julie A Karl
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Michael E Graham
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Katelyn E Heimbruch
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Samantha M Gieger
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Gaby G M Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA.
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 585 Science Drive, Madison, WI, 53711, USA.
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41
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Gonzalez-Nieto L, Domingues A, Ricciardi M, Gutman MJ, Maxwell HS, Pedreño-Lopez N, Bailey V, Magnani DM, Martins MA. Analysis of Simian Immunodeficiency Virus-specific CD8+ T-cells in Rhesus Macaques by Peptide-MHC-I Tetramer Staining. J Vis Exp 2016. [PMID: 28060314 DOI: 10.3791/54881] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Peptide-major histocompatibility complex class I (pMHC-I) tetramers have been an invaluable tool to study CD8+ T-cell responses. Because these reagents directly bind to T-cell receptors on the surface of CD8+ T-lymphocytes, fluorochrome-labeled pMHC-I tetramers enable the accurate detection of antigen (Ag)-specific CD8+ T-cells without the need for in vitro re-stimulation. Moreover, when combined with multi-color flow cytometry, pMHC-I tetramer staining can reveal key aspects of Ag-specific CD8+ T-cells, including differentiation stage, memory phenotype, and activation status. These types of analyses have been especially useful in the field of HIV immunology where CD8+ T-cells can affect progression to AIDS. Experimental infection of rhesus macaques with simian immunodeficiency virus (SIV) provides an invaluable tool to study cellular immunity against the AIDS virus. As a result, considerable progress has been made in defining and characterizing T-cell responses in this animal model. Here we present an optimized protocol for enumerating SIV-specific CD8+ T-cells in rhesus macaques by pMHC-I tetramer staining. Our assay permits the simultaneous quantification and memory phenotyping of two pMHC-I tetramer+ CD8+ T-cell populations per test, which might be useful for tracking SIV-specific CD8+ T-cell responses generated by vaccination or SIV infection. Considering the relevance of nonhuman primates in biomedical research, this methodology is applicable for studying CD8+ T-cell responses in multiple disease settings.
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Schwensow N, Mazzoni CJ, Marmesat E, Fickel J, Peacock D, Kovaliski J, Sinclair R, Cassey P, Cooke B, Sommer S. High adaptive variability and virus-driven selection on major histocompatibility complex (MHC) genes in invasive wild rabbits in Australia. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1329-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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43
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Burwitz BJ, Malouli D, Bimber BN, Reed JS, Ventura AB, Hancock MH, Uebelhoer LS, Bhusari A, Hammond KB, Espinosa Trethewy RG, Klug A, Legasse AW, Axthelm MK, Nelson JA, Park BS, Streblow DN, Hansen SG, Picker LJ, Früh K, Sacha JB. Cross-Species Rhesus Cytomegalovirus Infection of Cynomolgus Macaques. PLoS Pathog 2016; 12:e1006014. [PMID: 27829026 PMCID: PMC5102353 DOI: 10.1371/journal.ppat.1006014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/20/2016] [Indexed: 12/14/2022] Open
Abstract
Cytomegaloviruses (CMV) are highly species-specific due to millennia of co-evolution and adaptation to their host, with no successful experimental cross-species infection in primates reported to date. Accordingly, full genome phylogenetic analysis of multiple new CMV field isolates derived from two closely related nonhuman primate species, Indian-origin rhesus macaques (RM) and Mauritian-origin cynomolgus macaques (MCM), revealed distinct and tight lineage clustering according to the species of origin, with MCM CMV isolates mirroring the limited genetic diversity of their primate host that underwent a population bottleneck 400 years ago. Despite the ability of Rhesus CMV (RhCMV) laboratory strain 68-1 to replicate efficiently in MCM fibroblasts and potently inhibit antigen presentation to MCM T cells in vitro, RhCMV 68-1 failed to productively infect MCM in vivo, even in the absence of host CD8+ T and NK cells. In contrast, RhCMV clone 68-1.2, genetically repaired to express the homologues of the HCMV anti-apoptosis gene UL36 and epithelial cell tropism genes UL128 and UL130 absent in 68-1, efficiently infected MCM as evidenced by the induction of transgene-specific T cells and virus shedding. Recombinant variants of RhCMV 68-1 and 68-1.2 revealed that expression of either UL36 or UL128 together with UL130 enabled productive MCM infection, indicating that multiple layers of cross-species restriction operate even between closely related hosts. Cumulatively, these results implicate cell tropism and evasion of apoptosis as critical determinants of CMV transmission across primate species barriers, and extend the macaque model of human CMV infection and immunology to MCM, a nonhuman primate species with uniquely simplified host immunogenetics.
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Affiliation(s)
- Benjamin J. Burwitz
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Daniel Malouli
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Benjamin N. Bimber
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Jason S. Reed
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Abigail B. Ventura
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Meaghan H. Hancock
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Luke S. Uebelhoer
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Amruta Bhusari
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Katherine B. Hammond
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Renee G. Espinosa Trethewy
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Alex Klug
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Alfred W. Legasse
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Michael K. Axthelm
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Jay A. Nelson
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Byung S. Park
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Daniel N. Streblow
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Scott G. Hansen
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Louis J. Picker
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Klaus Früh
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Jonah B. Sacha
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon, United States of America
- * E-mail:
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44
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Maness NJ. The Importance of Understanding MHC-I Diversity in Nonhuman Primate Models of Human Infectious Diseases. Toxicol Pathol 2016; 45:157-160. [PMID: 27729588 DOI: 10.1177/0192623316672072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Decades of research, including the 1996 Nobel Prize in Medicine, confirm the evolutionary and immunological importance of CD8 T lymphocytes (TCD8+) that target peptides bound by the highly variable major histocompatibility complex class I (MHC-I) proteins. However, their perceived importance has varied dramatically over the past decade. Regardless, there remains myriad reasons to consider the diversity of MHC-I alleles and the TCD8+ that target them as enormously important in infectious disease research. Thus, understanding these molecules in the best animal models of human disease could be a necessity for optimizing the translational potential of these models. Knowledge of macaque MHC has substantially improved their utility for modeling HIV and could aid in modeling other viruses as well, both in the context of distribution of alleles across treatment groups in vaccine trials and in deciphering mechanisms of immune control of pathogens for which specific MHC alleles demonstrate differential impacts on disease.
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Affiliation(s)
- Nicholas J Maness
- 1 Tulane University School of Medicine, Tulane National Primate Research Center, Covington, Louisiana, USA
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45
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Song X, Zhang P, Huang K, Chen D, Guo S, Qi X, He G, Pan R, Li B. The influence of positive selection and trans-species evolution on DPB diversity in the golden snub-nosed monkeys (Rhinopithecus roxellana). Primates 2016; 57:489-99. [PMID: 27209173 DOI: 10.1007/s10329-016-0544-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/28/2016] [Indexed: 10/21/2022]
Abstract
Genetic variation plays a significant role in the adaptive potential of the endangered species. The variation at major histocompatibility complex (MHC) genes can offer valuable information on selective pressure related to natural selection and environmental adaptation, particularly the ability of a host to continuously resist evolving parasites. Thus, the genetic polymorphism on exon 2 of the MHC DPB1 gene in the golden snub-nosed monkeys (Rhinopithecus roxellana) was specifically analyzed. The results show that the 6 Rhro-DPB1 alleles identified from 87 individuals exhibit positive selection and trans-species polymorphism. The results also imply that although the populations of the species have experienced dramatic reduction and severe habitat fragmentation in recent Chinese history, balancing selection still maintains relatively consistent, with moderate DPB1 polymorphism. Thus, the study provides valuable information and evidence in developing effective strategies and tactics for genetic health and population size expansion of the species. It also offers strong genetic background for further studies on other primate species, particularly those in Rhinopithecus-a further endeavor that would result in fully understanding the MHC genetic information of the Asian colobines.
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Affiliation(s)
- Xiaoyue Song
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Pei Zhang
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Dan Chen
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Songtao Guo
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xiaoguang Qi
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Gang He
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Ruliang Pan
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China.,The School of Anatomy, Physiology and Human Biology, University of Western Australia, Perth, Australia
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, and College of Life Sciences, Northwest University, Xi'an, 710069, China. .,Xi'an Branch of Chinese Academy of Sciences, Xi'an, China.
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46
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de Groot NG, Blokhuis JH, Otting N, Doxiadis GGM, Bontrop RE. Co-evolution of the MHC class I and KIR gene families in rhesus macaques: ancestry and plasticity. Immunol Rev 2016; 267:228-45. [PMID: 26284481 PMCID: PMC4544828 DOI: 10.1111/imr.12313] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Researchers dealing with the human leukocyte antigen (HLA) class I and killer immunoglobulin receptor (KIR) multi‐gene families in humans are often wary of the complex and seemingly different situation that is encountered regarding these gene families in Old World monkeys. For the sake of comparison, the well‐defined and thoroughly studied situation in humans has been taken as a reference. In macaques, both the major histocompatibility complex class I and KIR gene families are plastic entities that have experienced various rounds of expansion, contraction, and subsequent recombination processes. As a consequence, haplotypes in macaques display substantial diversity with regard to gene copy number variation. Additionally, for both multi‐gene families, differential levels of polymorphism (allelic variation), and expression are observed as well. A comparative genetic approach has allowed us to answer questions related to ancestry, to shed light on unique adaptations of the species’ immune system, and to provide insights into the genetic events and selective pressures that have shaped the range of these gene families.
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Affiliation(s)
- Natasja G de Groot
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands
| | - Jeroen H Blokhuis
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands
| | - Nel Otting
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands
| | - Gaby G M Doxiadis
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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47
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Demasius W, Weikard R, Hadlich F, Buitkamp J, Kühn C. A novel RNAseq-assisted method for MHC class I genotyping in a non-model species applied to a lethal vaccination-induced alloimmune disease. BMC Genomics 2016; 17:365. [PMID: 27188848 PMCID: PMC4869273 DOI: 10.1186/s12864-016-2688-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/30/2016] [Indexed: 12/02/2022] Open
Abstract
Background MHC class I genotyping is essential for a wide range of biomedical, immunological and biodiversity applications. Whereas in human a comprehensive MHC class I allele catalogue is available, respective data in non-model species is scarce in spite of decades of research. Results Taking advantage of the new high-throughput RNA sequencing technology (RNAseq), we developed a novel RNAseq-assisted method (RAMHCIT) for MHC class I typing at nucleotide level. RAMHCIT is performed on white blood cells, which highly express MHC class I molecules enabling reliable discovery of new alleles and discrimination of closely related alleles due to the high coverage of alleles with reads. RAMHCIT is more comprehensive than previous methods, because no targeted PCR pre-amplification of MHC loci is necessary, which avoids preselection of alleles as usually encountered, when amplification with MHC class I primers is performed prior to sequencing. In addition to allele identification, RAMHCIT also enables quantification of MHC class I expression at allele level, which was remarkably consistent across individuals. Conclusions Successful application of RAMHCIT is demonstrated on a data set from cattle with different phenotype regarding a lethal, vaccination-induced alloimmune disease (bovine neonatal pancytopenia), for which MHC class I alleles had been postulated as causal agents. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2688-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wiebke Demasius
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Rosemarie Weikard
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Frieder Hadlich
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Johannes Buitkamp
- Institute of Animal Breeding, Bavarian State Research Center for Agriculture, 85586, Grub, Germany
| | - Christa Kühn
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany. .,Faculty of Agricultural and Environmental Sciences, University Rostock, 18059, Rostock, Germany.
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Bevaart L, Aalbers CJ, Vierboom MPM, Broekstra N, Kondova I, Breedveld E, Hauck B, Wright JF, Tak PP, Vervoordeldonk MJ. Safety, Biodistribution, and Efficacy of an AAV-5 Vector Encoding Human Interferon-Beta (ART-I02) Delivered via Intra-Articular Injection in Rhesus Monkeys with Collagen-Induced Arthritis. HUM GENE THER CL DEV 2016; 26:103-12. [PMID: 26086763 DOI: 10.1089/humc.2015.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Preclinical studies to assess biodistribution, safety, and initial efficacy of ART-I02, an adeno-associated type 5 (rAAV5) vector expressing human interferon β (hIFN-β), were performed in a total of 24 rhesus monkeys with collagen-induced arthritis. All monkeys were naïve or showed limited neutralizing antibody (Nab) titers to AAV5 at the start of the study. Animals were injected with a single intra-articular dose of ART-I02 or placebo, consisting of 3.2×10(13) vg (Dose A=maximum feasible dose), 4.58×10(12) vg (Dose B), or placebo in the first affected finger joint, the ipsilateral knee, and ankle joint at the same time point. Animals were monitored for clinical parameters and well-being with a maximum of 4 weeks, with the option that the severity of arthritis could necessitate an earlier time point of sacrifice. No adverse events were noted after injection of ART-I02. No abnormalities were observed after histological evaluation of all organs. At both dose levels, immunohistochemical staining indicated expression of hIFN-β. In animals injected with Dose A, we observed stabilization or a reduction in swelling in the finger joint in which vector was administered. The highest copy numbers of vector DNA were detected in synovial tissue of the injected joint and the draining lymph node of the injected knee. High titers of Nab to rAAV5 were observed at the end of the study. Five monkeys developed an rAAV5-specific T-cell response. Two monkeys developed Nab to hIFN-β. In conclusion, intra-articular injection of ART-I02 was well-tolerated and did not induce adverse events. After administration of Dose A of ART-I02, we observed a beneficial effect on joint swelling, substantiated by decreased histological inflammation and bone erosion scores. A GMP vector for clinical application has been manufactured and is currently being tested in GLP rodent studies, with the aim to move forward to a clinical trial.
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Affiliation(s)
| | - Caroline J Aalbers
- 1 Arthrogen B.V., Amsterdam 1105 BA, The Netherlands .,2 Division of Clinical Immunology and Rheumatology, Academic Medical Center/University of Amsterdam , 1105 AZ, The Netherlands
| | - Michel P M Vierboom
- 3 Department of Immunobiology, Biomedical Primate Research Centre , Rijswijk 2288 GH, The Netherlands
| | | | - Ivanela Kondova
- 3 Department of Immunobiology, Biomedical Primate Research Centre , Rijswijk 2288 GH, The Netherlands
| | - Elia Breedveld
- 3 Department of Immunobiology, Biomedical Primate Research Centre , Rijswijk 2288 GH, The Netherlands
| | - Bernd Hauck
- 4 Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia , Philadelphia, PA 19104
| | - J Fraser Wright
- 4 Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia , Philadelphia, PA 19104
| | - Paul Peter Tak
- 1 Arthrogen B.V., Amsterdam 1105 BA, The Netherlands .,2 Division of Clinical Immunology and Rheumatology, Academic Medical Center/University of Amsterdam , 1105 AZ, The Netherlands
| | - Margriet J Vervoordeldonk
- 1 Arthrogen B.V., Amsterdam 1105 BA, The Netherlands .,2 Division of Clinical Immunology and Rheumatology, Academic Medical Center/University of Amsterdam , 1105 AZ, The Netherlands
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Minias P, Bateson ZW, Whittingham LA, Johnson JA, Oyler-McCance S, Dunn PO. Contrasting evolutionary histories of MHC class I and class II loci in grouse--effects of selection and gene conversion. Heredity (Edinb) 2016; 116:466-76. [PMID: 26860199 DOI: 10.1038/hdy.2016.6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/18/2015] [Indexed: 11/09/2022] Open
Abstract
Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens.
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Affiliation(s)
- P Minias
- Department of Teacher Training and Biodiversity Studies, University of Łódź, Łódź, Poland.,Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Z W Bateson
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - L A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - J A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, TX, USA
| | - S Oyler-McCance
- Fort Collins Science Center, US Geological Survey, Fort Collins, CO, USA
| | - P O Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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50
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Adaptive and neutral genetic differentiation among Scottish and endangered Irish red grouse (Lagopus lagopus scotica). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0810-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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