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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: 8] [Impact Index Per Article: 8.0] [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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Islam MA, Rony SA, Rahman MB, Cinar MU, Villena J, Uddin MJ, Kitazawa H. Improvement of Disease Resistance in Livestock: Application of Immunogenomics and CRISPR/Cas9 Technology. Animals (Basel) 2020; 10:E2236. [PMID: 33260762 PMCID: PMC7761152 DOI: 10.3390/ani10122236] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/18/2020] [Accepted: 11/26/2020] [Indexed: 01/09/2023] Open
Abstract
Disease occurrence adversely affects livestock production and animal welfare, and have an impact on both human health and public perception of food-animals production. Combined efforts from farmers, animal scientists, and veterinarians have been continuing to explore the effective disease control approaches for the production of safe animal-originated food. Implementing the immunogenomics, along with genome editing technology, has been considering as the key approach for safe food-animal production through the improvement of the host genetic resistance. Next-generation sequencing, as a cutting-edge technique, enables the production of high throughput transcriptomic and genomic profiles resulted from host-pathogen interactions. Immunogenomics combine the transcriptomic and genomic data that links to host resistance to disease, and predict the potential candidate genes and their genomic locations. Genome editing, which involves insertion, deletion, or modification of one or more genes in the DNA sequence, is advancing rapidly and may be poised to become a commercial reality faster than it has thought. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) [CRISPR/Cas9] system has recently emerged as a powerful tool for genome editing in agricultural food production including livestock disease management. CRISPR/Cas9 mediated insertion of NRAMP1 gene for producing tuberculosis resistant cattle, and deletion of CD163 gene for producing porcine reproductive and respiratory syndrome (PRRS) resistant pigs are two groundbreaking applications of genome editing in livestock. In this review, we have highlighted the technological advances of livestock immunogenomics and the principles and scopes of application of CRISPR/Cas9-mediated targeted genome editing in animal breeding for disease resistance.
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Affiliation(s)
- Md. Aminul Islam
- Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh;
- Food and Feed Immunology Group, Graduate School of Agricultural University Science, Tohoku University, Sendai 980-8572, Japan;
- Livestock Immunology Unit, International Research and Education Centre for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
| | - Sharmin Aqter Rony
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh;
| | - Mohammad Bozlur Rahman
- Department of Livestock Services, Krishi Khamar Sarak, Farmgate, Dhaka 1215, Bangladesh;
| | - Mehmet Ulas Cinar
- Department of Animal Science, Faculty of Agriculture, Erciyes University, 38039 Kayseri, Turkey;
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Julio Villena
- Food and Feed Immunology Group, Graduate School of Agricultural University Science, Tohoku University, Sendai 980-8572, Japan;
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli, (CERELA), Tucuman 4000, Argentina
| | - Muhammad Jasim Uddin
- Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh;
- School of Veterinary Science, Gatton Campus, The University of Queensland, Brisbane 4072, Australia
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Graduate School of Agricultural University Science, Tohoku University, Sendai 980-8572, Japan;
- Livestock Immunology Unit, International Research and Education Centre for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
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Mueller RC, Mallig N, Smith J, Eöery L, Kuo RI, Kraus RHS. Avian Immunome DB: an example of a user-friendly interface for extracting genetic information. BMC Bioinformatics 2020; 21:502. [PMID: 33176685 PMCID: PMC7661159 DOI: 10.1186/s12859-020-03764-3] [Citation(s) in RCA: 5] [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: 05/15/2020] [Accepted: 09/17/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Genomic and genetic studies often require a target list of genes before conducting any hypothesis testing or experimental verification. With the ever-growing number of sequenced genomes and a variety of different annotation strategies, comes the potential for ambiguous gene symbols, making it cumbersome to capture the "correct" set of genes. In this article, we present and describe the Avian Immunome DB (AVIMM) for easy gene property extraction as exemplified by avian immune genes. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes. It is a vital trait to study particularly in birds considering that they are a significant driver in spreading zoonotic diseases. With the completion of phase II of the B10K ("Bird 10,000 Genomes") consortium's whole-genome sequencing effort, we have included 363 annotated bird genomes in addition to other publicly available bird genome data which serve as a valuable foundation for AVIMM. CONSTRUCTION AND CONTENT A relational database with avian immune gene evidence from Gene Ontology, Ensembl, UniProt and the B10K consortium has been designed and set up. The foundation stone or the "seed" for the initial set of avian immune genes is based on the well-studied model organism chicken (Gallus gallus). Gene annotations, different transcript isoforms, nucleotide sequences and protein information, including amino acid sequences, are included. Ambiguous gene names (symbols) are resolved within the database and linked to their canonical gene symbol. AVIMM is supplemented by a command-line interface and a web front-end to query the database. UTILITY AND DISCUSSION The internal mapping of unique gene symbol identifiers to canonical gene symbols allows for an ambiguous gene property search. The database is organised within core and feature tables, which makes it straightforward to extend for future purposes. The database design is ready to be applied to other taxa or biological processes. Currently, the database contains 1170 distinct avian immune genes with canonical gene symbols and 612 synonyms across 363 bird species. While the command-line interface readily integrates into bioinformatics pipelines, the intuitive web front-end with download functionality offers sophisticated search functionalities and tracks the origin for each record. AVIMM is publicly accessible at https://avimm.ab.mpg.de .
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Affiliation(s)
- Ralf C. Mueller
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg, 78315 Radolfzell, Germany
- Department of Biology, University of Konstanz, Universitaetsstrasse 10, 78464 Konstanz, Germany
| | - Nicolai Mallig
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg, 78315 Radolfzell, Germany
- Department of Biology, University of Konstanz, Universitaetsstrasse 10, 78464 Konstanz, Germany
- HTWG Konstanz - University of Applied Sciences, Alfred-Wachtel-Str. 8, 78462 Konstanz, Germany
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Roslin, EH25 9RG UK
| | - Lél Eöery
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Roslin, EH25 9RG UK
| | - Richard I. Kuo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Roslin, EH25 9RG UK
| | - Robert H. S. Kraus
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg, 78315 Radolfzell, Germany
- Department of Biology, University of Konstanz, Universitaetsstrasse 10, 78464 Konstanz, Germany
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Dhanik A, R. Kirshner J, MacDonald D, Thurston G, C. Lin H, J. Murphy A, Zhang W. In-silico discovery of cancer-specific peptide-HLA complexes for targeted therapy. BMC Bioinformatics 2016; 17:286. [PMID: 27439771 PMCID: PMC4955262 DOI: 10.1186/s12859-016-1150-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/13/2016] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Major Histocompatibility Complex (MHC) or Human Leukocyte Antigen (HLA) Class I molecules bind to peptide fragments of proteins degraded inside the cell and display them on the cell surface. We are interested in peptide-HLA complexes involving peptides that are derived from proteins specifically expressed in cancer cells. Such complexes have been shown to provide an effective means of precisely targeting cancer cells by engineered T-cells and antibodies, which would be an improvement over current chemotherapeutic agents that indiscriminately kill proliferating cells. An important concern with the targeting of peptide-HLA complexes is off-target toxicity that could occur due to the presence of complexes similar to the target complex in cells from essential, normal tissues. RESULTS We developed a novel computational strategy for identifying potential peptide-HLA cancer targets and evaluating the likelihood of off-target toxicity associated with these targets. Our strategy combines sequence-based and structure-based approaches in a unique way to predict potential off-targets. The focus of our work is on the complexes involving the most frequent HLA class I allele HLA-A*02:01. Using our strategy, we predicted the off-target toxicity observed in past clinical trials. We employed it to perform a first-ever comprehensive exploration of the human peptidome to identify cancer-specific targets utilizing gene expression data from TCGA (The Cancer Genome Atlas) and GTEx (Gene Tissue Expression), and structural data from PDB (Protein Data Bank). We have thus identified a list of 627 peptide-HLA complexes across various TCGA cancer types. CONCLUSION Peptide-HLA complexes identified using our novel strategy could enable discovery of cancer-specific targets for engineered T-cells or antibody based therapy with minimal off-target toxicity.
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Affiliation(s)
- Ankur Dhanik
- Regeneron Pharmaceuticals Inc, Old Saw Mill River Road, Tarrytown, NY USA
| | | | - Douglas MacDonald
- Regeneron Pharmaceuticals Inc, Old Saw Mill River Road, Tarrytown, NY USA
| | - Gavin Thurston
- Regeneron Pharmaceuticals Inc, Old Saw Mill River Road, Tarrytown, NY USA
| | - Hsin C. Lin
- Regeneron Pharmaceuticals Inc, Old Saw Mill River Road, Tarrytown, NY USA
| | - Andrew J. Murphy
- Regeneron Pharmaceuticals Inc, Old Saw Mill River Road, Tarrytown, NY USA
| | - Wen Zhang
- Regeneron Pharmaceuticals Inc, Old Saw Mill River Road, Tarrytown, NY USA
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