1
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Hu J, Song L, Ning M, Niu X, Han M, Gao C, Feng X, Cai H, Li T, Li F, Li H, Gong D, Song W, Liu L, Pu J, Liu J, Smith J, Sun H, Huang Y. A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families. BMC Biol 2024; 22:31. [PMID: 38317190 PMCID: PMC10845735 DOI: 10.1186/s12915-024-01817-0] [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: 09/01/2022] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A virus (IAV), harbors almost all subtypes of IAVs and resists to many IAVs which cause extreme virulence in chicken and human. However, the response of duck's adaptive immune system to IAV infection is poorly characterized due to lack of a detailed gene map of the major histocompatibility complex (MHC). RESULTS We herein reported a chromosome-scale Beijing duck assembly by integrating Nanopore, Bionano, and Hi-C data. This new reference genome SKLA1.0 covers 40 chromosomes, improves the contig N50 of the previous duck assembly with highest contiguity (ZJU1.0) of more than a 5.79-fold, surpasses the chicken and zebra finch references in sequence contiguity and contains a complete genomic map of the MHC. Our 3D MHC genomic map demonstrated that gene family arrangement in this region was primordial; however, families such as AnplMHCI, AnplMHCIIβ, AnplDMB, NKRL (NK cell receptor-like genes) and BTN underwent gene expansion events making this area complex. These gene families are distributed in two TADs and genes sharing the same TAD may work in a co-regulated model. CONCLUSIONS These observations supported the hypothesis that duck's adaptive immunity had been optimized with expanded and diversified key immune genes which might help duck to combat influenza virus. This work provided a high-quality Beijing duck genome for biological research and shed light on new strategies for AIV control.
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Affiliation(s)
- Jiaxiang Hu
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Linfei Song
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Mengfei Ning
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Xinyu Niu
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Mengying Han
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Chuze Gao
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Xingwei Feng
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Han Cai
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Te Li
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Fangtao Li
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Huifang Li
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Daoqing Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Weitao Song
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Long Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Juan Pu
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Jinhua Liu
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Honglei Sun
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China.
| | - Yinhua Huang
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China.
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2
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Rautenschlein S, Schat KA. The Immunological Basis for Vaccination. Avian Dis 2024; 67:366-379. [PMID: 38300658 DOI: 10.1637/aviandiseases-d-23-99996] [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: 08/01/2023] [Accepted: 08/29/2023] [Indexed: 02/02/2024]
Abstract
Vaccination is crucial for health protection of poultry and therefore important to maintaining high production standards. Proper vaccination requires knowledge of the key players of the well-orchestrated immune system of birds, their interdependence and delicate regulation, and, subsequently, possible modes of stimulation through vaccine antigens and adjuvants. The knowledge about the innate and acquired immune systems of birds has increased significantly during the recent years but open questions remain and have to be elucidated further. Despite similarities between avian and mammalian species in their composition of immune cells and modes of activation, important differences exist, including differences in the innate, but also humoral and cell-mediated immunity with respect to, for example, signaling transduction pathways, antigen presentation, and cell repertoires. For a successful vaccination strategy in birds it always has to be considered that genotype and age of the birds at the time point of immunization as well as their microbiota composition may have an impact and may drive the immune reactions into different directions. Recent achievements in the understanding of the concept of trained immunity will contribute to the advancement of current vaccine types helping to improve protection beyond the specificity of an antigen-driven immune response. The fast developments in new omics technologies will provide insights into protective B- and T-cell epitopes involved in cross-protection, which subsequently will lead to the improvement of vaccine efficacy in poultry.
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Affiliation(s)
- Silke Rautenschlein
- Clinic for Poultry, University of Veterinary Medicine Hannover, Clinic for Poultry, Hannover, Lower Saxony 30559, Germany,
| | - Karel A Schat
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
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3
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Fiddaman SR, Dimopoulos EA, Lebrasseur O, du Plessis L, Vrancken B, Charlton S, Haruda AF, Tabbada K, Flammer PG, Dascalu S, Marković N, Li H, Franklin G, Symmons R, Baron H, Daróczi-Szabó L, Shaymuratova DN, Askeyev IV, Putelat O, Sana M, Davoudi H, Fathi H, Mucheshi AS, Vahdati AA, Zhang L, Foster A, Sykes N, Baumberg GC, Bulatović J, Askeyev AO, Askeyev OV, Mashkour M, Pybus OG, Nair V, Larson G, Smith AL, Frantz LAF. Ancient chicken remains reveal the origins of virulence in Marek's disease virus. Science 2023; 382:1276-1281. [PMID: 38096384 DOI: 10.1126/science.adg2238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 10/25/2023] [Indexed: 12/18/2023]
Abstract
The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek's disease virus (MDV), which causes lymphoid tumors in chickens, has experienced a marked increase in virulence over the past century. Today, MDV infections kill >90% of unvaccinated birds, and controlling it costs more than US$1 billion annually. By sequencing MDV genomes derived from archeological chickens, we demonstrate that it has been circulating for at least 1000 years. We functionally tested the Meq oncogene, one of 49 viral genes positively selected in modern strains, demonstrating that ancient MDV was likely incapable of driving tumor formation. Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.
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Affiliation(s)
| | - Evangelos A Dimopoulos
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ophélie Lebrasseur
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS/Université Toulouse III Paul Sabatier, Toulouse, France
- Instituto Nacional de Antropología y Pensamiento Latinoamericano, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Louis du Plessis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Sophy Charlton
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Ashleigh F Haruda
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Kristina Tabbada
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | | | | | | | - Hannah Li
- Institute of Immunity and Transplantation, University College London, London, UK
| | | | | | | | | | - Dilyara N Shaymuratova
- Laboratory of Biomonitoring, The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, Kazan, Russia
| | - Igor V Askeyev
- Laboratory of Biomonitoring, The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, Kazan, Russia
| | | | - Maria Sana
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Hossein Davoudi
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
| | - Homa Fathi
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
| | - Amir Saed Mucheshi
- Department of Art and Architecture, Payame Noor University (PNU), Tehran, Iran
| | - Ali Akbar Vahdati
- Iranian Ministry of Cultural Heritage, Tourism, and Handicrafts, North Khorasan Office, Iran
| | - Liangren Zhang
- Department of Archaeology, School of History, Nanjing University, China
| | | | - Naomi Sykes
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Gabrielle Cass Baumberg
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Jelena Bulatović
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Arthur O Askeyev
- Laboratory of Biomonitoring, The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, Kazan, Russia
| | - Oleg V Askeyev
- Laboratory of Biomonitoring, The Institute of Problems in Ecology and Mineral Wealth, Tatarstan Academy of Sciences, Kazan, Russia
| | - Marjan Mashkour
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
- CNRS, National Museum Natural History Paris, Paris, France
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
| | - Venugopal Nair
- Department of Biology, University of Oxford, Oxford, UK
- Viral Oncogenesis Group, Pirbright Institute, Woking, UK
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | | | - Laurent A F Frantz
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universitat, Munich, Germany
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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4
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Bertzbach LD, Kohn M, You Y, Kossak L, Sabsabi MA, Kheimar A, Härtle S, Kaufer BB. In vitro infection of primary chicken lymphocytes with Marek's disease virus. STAR Protoc 2023; 4:102343. [PMID: 37270781 DOI: 10.1016/j.xpro.2023.102343] [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: 03/24/2023] [Revised: 04/25/2023] [Accepted: 05/10/2023] [Indexed: 06/06/2023] Open
Abstract
Marek's disease virus (MDV) is a highly oncogenic alphaherpesvirus that infects immune cells and causes a deadly lymphoproliferative disease in chickens. Cytokines and monoclonal antibodies promote the survival of chicken lymphocytes in vitro. Here, we describe protocols for the isolation, maintenance, and efficient MDV infection of primary chicken lymphocytes and lymphocyte cell lines. This facilitates the investigation of key aspects of the MDV life cycle in the primary target cells of viral replication, latency, genome integration, and reactivation. For complete details on the use and execution of this protocol, please refer to Schermuly et al.,1 Bertzbach et al. (2019),2 and You et al.3 For a comprehensive background on MDV, please see Osterrieder et al.4 and Bertzbach et al. (2020).5.
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Affiliation(s)
- Luca D Bertzbach
- Freie Universität Berlin, Institute of Virology, 14163 Berlin, Germany; Leibniz Institute of Virology (LIV), Department of Viral Transformation, 20251 Hamburg, Germany
| | - Marina Kohn
- Ludwig-Maximilians-Universität, Department for Veterinary Sciences, 82152 Planegg/Martinsried, Germany
| | - Yu You
- Freie Universität Berlin, Institute of Virology, 14163 Berlin, Germany
| | - Lisa Kossak
- Freie Universität Berlin, Institute of Virology, 14163 Berlin, Germany
| | | | - Ahmed Kheimar
- Freie Universität Berlin, Institute of Virology, 14163 Berlin, Germany; Sohag University, Faculty of Veterinary Medicine, Department of Poultry Diseases, 82524 Sohag, Egypt
| | - Sonja Härtle
- Ludwig-Maximilians-Universität, Department for Veterinary Sciences, 82152 Planegg/Martinsried, Germany.
| | - Benedikt B Kaufer
- Freie Universität Berlin, Institute of Virology, 14163 Berlin, Germany; Freie Universität Berlin, Veterinary Centre for Resistance Research (TZR), 14163 Berlin, Germany.
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5
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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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6
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Herrera-Ong LR. Strategic construction of mRNA vaccine derived from conserved and experimentally validated epitopes of avian influenza type A virus: a reverse vaccinology approach. Clin Exp Vaccine Res 2023; 12:156-171. [PMID: 37214143 PMCID: PMC10193103 DOI: 10.7774/cevr.2023.12.2.156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 03/31/2023] [Indexed: 05/24/2023] Open
Abstract
Purpose The development of vaccines that confer protection against multiple avian influenza A (AIA) virus strains is necessary to prevent the emergence of highly infectious strains that may result in more severe outbreaks. Thus, this study applied reverse vaccinology approach in strategically constructing messenger RNA (mRNA) vaccine construct against avian influenza A (mVAIA) to induce cross-protection while targeting diverse AIA virulence factors. Materials and Methods Immunoinformatics tools and databases were utilized to identify conserved experimentally validated AIA epitopes. CD8+ epitopes were docked with dominant chicken major histocompatibility complexes (MHCs) to evaluate complex formation. Conserved epitopes were adjoined in the optimized mVAIA sequence for efficient expression in Gallus gallus. Signal sequence for targeted secretory expression was included. Physicochemical properties, antigenicity, toxicity, and potential cross-reactivity were assessed. The tertiary structure of its protein sequence was modeled and validated in silico to investigate the accessibility of adjoined B-cell epitope. Potential immune responses were also simulated in C-ImmSim. Results Eighteen experimentally validated epitopes were found conserved (Shannon index <2.0) in the study. These include one B-cell (SLLTEVETPIRNEWGCR) and 17 CD8+ epitopes, adjoined in a single mRNA construct. The CD8+ epitopes docked favorably with MHC peptide-binding groove, which were further supported by the acceptable ΔGbind (-28.45 to -40.59 kJ/mol) and Kd (<1.00) values. The incorporated Sec/SPI (secretory/signal peptidase I) cleavage site was also recognized with a high probability (0.964814). Adjoined B-cell epitope was found within the disordered and accessible regions of the vaccine. Immune simulation results projected cytokine production, lymphocyte activation, and memory cell generation after the 1st dose of mVAIA. Conclusion Results suggest that mVAIA possesses stability, safety, and immunogenicity. In vitro and in vivo confirmation in subsequent studies are anticipated.
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Affiliation(s)
- Leana Rich Herrera-Ong
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Metro Manila, Philippines
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7
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Racle J, Guillaume P, Schmidt J, Michaux J, Larabi A, Lau K, Perez MAS, Croce G, Genolet R, Coukos G, Zoete V, Pojer F, Bassani-Sternberg M, Harari A, Gfeller D. Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes. Immunity 2023:S1074-7613(23)00129-2. [PMID: 37023751 DOI: 10.1016/j.immuni.2023.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 11/09/2022] [Accepted: 03/15/2023] [Indexed: 04/08/2023]
Abstract
CD4+ T cells orchestrate the adaptive immune response against pathogens and cancer by recognizing epitopes presented on class II major histocompatibility complex (MHC-II) molecules. The high polymorphism of MHC-II genes represents an important hurdle toward accurate prediction and identification of CD4+ T cell epitopes. Here we collected and curated a dataset of 627,013 unique MHC-II ligands identified by mass spectrometry. This enabled us to precisely determine the binding motifs of 88 MHC-II alleles across humans, mice, cattle, and chickens. Analysis of these binding specificities combined with X-ray crystallography refined our understanding of the molecular determinants of MHC-II motifs and revealed a widespread reverse-binding mode in HLA-DP ligands. We then developed a machine-learning framework to accurately predict binding specificities and ligands of any MHC-II allele. This tool improves and expands predictions of CD4+ T cell epitopes and enables us to discover viral and bacterial epitopes following the aforementioned reverse-binding mode.
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Affiliation(s)
- Julien Racle
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland; Agora Cancer Research Centre, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.
| | - Philippe Guillaume
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland; Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Julien Schmidt
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland; Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Justine Michaux
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland; Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Amédé Larabi
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kelvin Lau
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marta A S Perez
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Giancarlo Croce
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland; Agora Cancer Research Centre, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Raphaël Genolet
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland; Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - George Coukos
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland; Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - Vincent Zoete
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Florence Pojer
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland; Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Alexandre Harari
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Agora Cancer Research Centre, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland; Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland; Agora Cancer Research Centre, Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.
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8
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Contemplating immunopeptidomes to better predict them. Semin Immunol 2023; 66:101708. [PMID: 36621290 DOI: 10.1016/j.smim.2022.101708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023]
Abstract
The identification of T-cell epitopes is key for a complete molecular understanding of immune recognition mechanisms in infectious diseases, autoimmunity and cancer. T-cell epitopes further provide targets for personalized vaccines and T-cell therapy, with several therapeutic applications in cancer immunotherapy and elsewhere. T-cell epitopes consist of short peptides displayed on Major Histocompatibility Complex (MHC) molecules. The recent advances in mass spectrometry (MS) based technologies to profile the ensemble of peptides displayed on MHC molecules - the so-called immunopeptidome - had a major impact on our understanding of antigen presentation and MHC ligands. On the one hand, these techniques enabled researchers to directly identify hundreds of thousands of peptides presented on MHC molecules, including some that elicited T-cell recognition. On the other hand, the data collected in these experiments revealed fundamental properties of antigen presentation pathways and significantly improved our ability to predict naturally presented MHC ligands and T-cell epitopes across the wide spectrum of MHC alleles found in human and other organisms. Here we review recent computational developments to analyze experimentally determined immunopeptidomes and harness these data to improve our understanding of antigen presentation and MHC binding specificities, as well as our ability to predict MHC ligands. We further discuss the strengths and limitations of the latest approaches to move beyond predictions of antigen presentation and tackle the challenges of predicting TCR recognition and immunogenicity.
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Halabi S, Kaufman J. New vistas unfold: Chicken MHC molecules reveal unexpected ways to present peptides to the immune system. Front Immunol 2022; 13:886672. [PMID: 35967451 PMCID: PMC9372762 DOI: 10.3389/fimmu.2022.886672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/07/2022] [Indexed: 11/27/2022] Open
Abstract
The functions of a wide variety of molecules with structures similar to the classical class I and class II molecules encoded by the major histocompatibility complex (MHC) have been studied by biochemical and structural studies over decades, with many aspects for humans and mice now enshrined in textbooks as dogma. However, there is much variation of the MHC and MHC molecules among the other jawed vertebrates, understood in the most detail for the domestic chicken. Among the many unexpected features in chickens is the co-evolution between polymorphic TAP and tapasin genes with a dominantly-expressed class I gene based on a different genomic arrangement compared to typical mammals. Another important discovery was the hierarchy of class I alleles for a suite of properties including size of peptide repertoire, stability and cell surface expression level, which is also found in humans although not as extreme, and which led to the concept of generalists and specialists in response to infectious pathogens. Structural studies of chicken class I molecules have provided molecular explanations for the differences in peptide binding compared to typical mammals. These unexpected phenomena include the stringent binding with three anchor residues and acidic residues at the peptide C-terminus for fastidious alleles, and the remodelling binding sites, relaxed binding of anchor residues in broad hydrophobic pockets and extension at the peptide C-terminus for promiscuous alleles. The first few studies for chicken class II molecules have already uncovered unanticipated structural features, including an allele that binds peptides by a decamer core. It seems likely that the understanding of how MHC molecules bind and present peptides to lymphocytes will broaden considerably with further unexpected discoveries through biochemical and structural studies for chickens and other non-mammalian vertebrates.
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Affiliation(s)
- Samer Halabi
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jim Kaufman
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Jim Kaufman,
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Bertzbach LD, Tregaskes CA, Martin RJ, Deumer US, Huynh L, Kheimar AM, Conradie AM, Trimpert J, Kaufman J, Kaufer BB. The Diverse Major Histocompatibility Complex Haplotypes of a Common Commercial Chicken Line and Their Effect on Marek's Disease Virus Pathogenesis and Tumorigenesis. Front Immunol 2022; 13:908305. [PMID: 35693787 PMCID: PMC9186122 DOI: 10.3389/fimmu.2022.908305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/29/2022] [Indexed: 02/05/2023] Open
Abstract
The major histocompatibility complex (MHC) is crucial for appropriate immune responses against invading pathogens. Chickens possess a single predominantly-expressed class I molecule with strong associations between disease resistance and MHC haplotype. For Marek's disease virus (MDV) infections of chickens, the MHC haplotype is one of the major determinants of genetic resistance and susceptibility. VALO specific pathogen free (SPF) chickens are widely used in biomedical research and vaccine production. While valuable findings originate from MDV infections of VALO SPF chickens, their MHC haplotypes and associated disease resistance remained elusive. In this study, we used several typing systems to show that VALO SPF chickens possess MHC haplotypes that include B9, B9:02, B15, B19 and B21 at various frequencies. Moreover, we associate the MHC haplotypes to MDV-induced disease and lymphoma formation and found that B15 homozygotes had the lowest tumor incidence while B21 homozygotes had the lowest number of organs with tumors. Finally, we found transmission at variable levels to all contact birds except B15/B21 heterozygotes. These data have immediate implications for the use of VALO SPF chickens and eggs in the life sciences and add another piece to the puzzle of the chicken MHC complex and its role in infections with this oncogenic herpesvirus.
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Affiliation(s)
| | - Clive A. Tregaskes
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Rebecca J. Martin
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Lan Huynh
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ahmed M. Kheimar
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Sohag University, Sohag, Egypt
| | | | - Jakob Trimpert
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Jim Kaufman
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Benedikt B. Kaufer
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
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Marek's disease virus prolongs survival of primary chicken B-cells by inducing a senescence-like phenotype. PLoS Pathog 2021; 17:e1010006. [PMID: 34673841 PMCID: PMC8562793 DOI: 10.1371/journal.ppat.1010006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 11/02/2021] [Accepted: 10/04/2021] [Indexed: 12/17/2022] Open
Abstract
Marek’s disease virus (MDV) is an alphaherpesvirus that causes immunosuppression and deadly lymphoma in chickens. Lymphoid organs play a central role in MDV infection in animals. B-cells in the bursa of Fabricius facilitate high levels of MDV replication and contribute to dissemination at early stages of infection. Several studies investigated host responses in bursal tissue of MDV-infected chickens; however, the cellular responses specifically in bursal B-cells has never been investigated. We took advantage of our recently established in vitro infection system to decipher the cellular responses of bursal B-cells to infection with a very virulent MDV strain. Here, we demonstrate that MDV infection extends the survival of bursal B-cells in culture. Microarray analyses revealed that most cytokine/cytokine-receptor-, cell cycle- and apoptosis-associated genes are significantly down-regulated in these cells. Further functional assays validated these strong effects of MDV infections on cell cycle progression and thus, B-cell proliferation. In addition, we confirmed that MDV infections protect B-cells from apoptosis and trigger an accumulation of the autophagy marker Lc3-II. Taken together, our data indicate that MDV-infected bursal B-cells show hallmarks of a senescence-like phenotype, leading to a prolonged B-cell survival. This study provides an in-depth analysis of bursal B-cell responses to MDV infection and important insights into how the virus extends the survival of these cells. Upon MDV entry via the respiratory tract, B-cells are among the first cells to be infected in the lung and allow an efficient amplification of the virus. B-cells ensure the transmission of the virus to activated T-cells in which it replicates and ultimately transforms CD4-positive T-cells. Although playing a pivotal role in the MDV life cycle, the response of B-cells to MDV is currently not fully understood. Here, by using an in vitro infection model of primary bursal B-cells, we show that MDV infection leads to a prolonged B-cell survival resulting from decreased cell proliferation, protection from apoptosis and activation of autophagy. Our study provides new insights into the B-cell response to MDV infection, demonstrating that MDV triggers a senescence-like phenotype in B-cells that could potentiate their role in MDV pathogenesis.
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The Marek's Disease Virus Unique Gene MDV082 Is Dispensable for Virus Replication but Contributes to a Rapid Disease Onset. J Virol 2021; 95:e0013121. [PMID: 34011541 DOI: 10.1128/jvi.00131-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Marek's disease virus (MDV) is a highly oncogenic alphaherpesvirus of chickens that causes lymphomas in various organs. Most MDV genes are conserved among herpesviruses, while others are unique to MDV and may contribute to pathogenesis and/or tumor formation. High transcript levels of the MDV-specific genes MDV082, RLORF11, and SORF6 were recently detected in lytically infected cells; however, it remained elusive if the respective proteins are expressed and if they play a role in MDV pathogenesis. In this study, we first addressed if these proteins are expressed by inserting FLAG tags at their N or C termini. We could demonstrate that among the three genes tested, MDV082 is the only gene that encodes a protein and is expressed very late in MDV plaques in vitro. To investigate the role of this novel MDV082 protein in MDV pathogenesis, we generated a recombinant virus that lacks expression of the MDV082 protein. Our data revealed that the MDV082 protein contributes to the rapid onset of Marek's disease but is not essential for virus replication, spread, and tumor formation. Taken together, this study sheds light on the expression of MDV-specific genes and unravels the role of the late protein MDV082 in MDV pathogenesis. IMPORTANCE MDV is a highly oncogenic alphaherpesvirus that causes Marek's disease in chickens. The virus causes immense economic losses in the poultry industry due to the high morbidity and mortality, but also the cost of the vaccination. MDV encodes over 100 genes that are involved in various processes of the viral life cycle. Functional characterization of MDV genes is an essential step toward understanding the complex virus life cycle and MDV pathogenesis. Here, we have identified a novel protein encoded by MDV082 and two potential noncoding RNAs (RLORF11 and SORF6). The novel MDV082 protein is not needed for efficient MDV replication and tumor formation. However, our data demonstrate that the MDV082 protein is involved in the rapid onset of Marek's disease.
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