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Melepat B, Li T, Vinkler M. Natural selection directing molecular evolution in vertebrate viral sensors. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 154:105147. [PMID: 38325501 DOI: 10.1016/j.dci.2024.105147] [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: 03/14/2023] [Revised: 12/30/2023] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
Diseases caused by pathogens contribute to molecular adaptations in host immunity. Variety of viral pathogens challenging animal immunity can drive positive selection diversifying receptors recognising the infections. However, whether distinct virus sensing systems differ across animals in their evolutionary modes remains unclear. Our review provides a comparative overview of natural selection shaping molecular evolution in vertebrate viral-binding pattern recognition receptors (PRRs). Despite prevailing negative selection arising from the functional constraints, multiple lines of evidence now suggest diversifying selection in the Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I-like receptors (RLRs) and oligoadenylate synthetases (OASs). In several cases, location of the positively selected sites in the ligand-binding regions suggests effects on viral detection although experimental support is lacking. Unfortunately, in most other PRR families including the AIM2-like receptor family, C-type lectin receptors (CLRs), and cyclic GMP-AMP synthetase studies characterising their molecular evolution are rare, preventing comparative insight. We indicate shared characteristics of the viral sensor evolution and highlight priorities for future research.
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Affiliation(s)
- Balraj Melepat
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic
| | - Tao Li
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic
| | - Michal Vinkler
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic.
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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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Pereira PDC, Diniz DG, da Costa ER, Magalhães NGDM, da Silva ADJF, Leite JGS, Almeida NIP, Cunha KDN, de Melo MAD, Vasconcelos PFDC, Diniz JAP, Brites D, Anthony DC, Diniz CWP, Guerreiro-Diniz C. Genes, inflammatory response, tolerance, and resistance to virus infections in migratory birds, bats, and rodents. Front Immunol 2023; 14:1239572. [PMID: 37711609 PMCID: PMC10497949 DOI: 10.3389/fimmu.2023.1239572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Abstract
Normally, the host immunological response to viral infection is coordinated to restore homeostasis and protect the individual from possible tissue damage. The two major approaches are adopted by the host to deal with the pathogen: resistance or tolerance. The nature of the responses often differs between species and between individuals of the same species. Resistance includes innate and adaptive immune responses to control virus replication. Disease tolerance relies on the immune response allowing the coexistence of infections in the host with minimal or no clinical signs, while maintaining sufficient viral replication for transmission. Here, we compared the virome of bats, rodents and migratory birds and the molecular mechanisms underlying symptomatic and asymptomatic disease progression. We also explore the influence of the host physiology and environmental influences on RNA virus expression and how it impacts on the whole brain transcriptome of seemingly healthy semipalmated sandpiper (Calidris pusilla) and spotted sandpiper (Actitis macularius). Three time points throughout the year were selected to understand the importance of longitudinal surveys in the characterization of the virome. We finally revisited evidence that upstream and downstream regulation of the inflammatory response is, respectively, associated with resistance and tolerance to viral infections.
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Affiliation(s)
- Patrick Douglas Corrêa Pereira
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Daniel Guerreiro Diniz
- Seção de Hepatologia, Laboratório de Microscopia Eletrônica, Instituto Evandro Chagas, Belém, Pará, Brazil
- Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Laboratório de Investigações em Neurodegeneração e Infecção, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Emanuel Ramos da Costa
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
- Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Laboratório de Investigações em Neurodegeneração e Infecção, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Nara Gyzely de Morais Magalhães
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Anderson de Jesus Falcão da Silva
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Jéssica Gizele Sousa Leite
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Natan Ibraim Pires Almeida
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Kelle de Nazaré Cunha
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Mauro André Damasceno de Melo
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Pedro Fernando da Costa Vasconcelos
- Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará, Belém, Pará, Brazil
- Seção de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
| | - José Antonio Picanço Diniz
- Seção de Hepatologia, Laboratório de Microscopia Eletrônica, Instituto Evandro Chagas, Belém, Pará, Brazil
| | - Dora Brites
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Daniel Clive Anthony
- Department of Pharmacology, Laboratory of Experimental Neuropathology, University of Oxford, Oxford, United Kingdom
| | - Cristovam Wanderley Picanço Diniz
- Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Laboratório de Investigações em Neurodegeneração e Infecção, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Cristovam Guerreiro-Diniz
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
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4
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Katayama M, Fukuda T, Kato N, Nagamine T, Nakaya Y, Nakajima N, Onuma M. Cultured fibroblasts of the Okinawa rail present delayed innate immune response compared to that of chicken. PLoS One 2023; 18:e0290436. [PMID: 37607189 PMCID: PMC10443837 DOI: 10.1371/journal.pone.0290436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 08/08/2023] [Indexed: 08/24/2023] Open
Abstract
The Okinawa rail is endemic to Okinawa Island and is categorized as an endangered animal. In this study, we focused on innate immunity because it is the first line of host defense. In particular, signals recognizing foreign RNA (e.g., viruses) are important for host defense because they activate the host immune system. The retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) families (RIG-I, MDA5, and LGP2) are sensors that activate innate immunity. Therefore, we analyzed these functions in the Okinawa rail using genomic and cellular analyses of fibroblasts. Fibroblasts can be obtained from dead individuals, allowing these cells to be obtained from dead individuals, which is particularly useful for endangered species. The MDA5 gene of Okinawa rail was sequenced using the Sanger method following PCR amplification and extraction of the amplified sequence from agarose gel. Additionally, mRNA expression analysis of cultured fibroblasts exposed to poly I:C was done. The MDA5 gene was found to be a mutated nonfunctional gene in the Okinawa rail. The mRNA expression rates of inflammatory cytokine genes type I IFN, and Mx1 were slower in Okinawa rail than in chicken cultured fibroblasts. Similar to the mRNA expression results, cell number and live cell ratio also slowly decreased in the Okinawa rail compared with chicken cultured fibroblasts, indicating that the innate immune reaction differs between chicken and the Okinawa rail. To the best of our knowledge, this is the first experimental evaluation of the loss of function of the Okinawa rail innate immune genes. In conclusion, our results provide a basis for conservation strategies for the endangered Okinawa rail.
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Affiliation(s)
- Masafumi Katayama
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Tomokazu Fukuda
- Graduate School of Science and Engineering, Iwate University, Morioka-city, Japan
| | - Noriko Kato
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | | | | | - Nobuyoshi Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Manabu Onuma
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
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5
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Bertram H, Wilhelmi S, Rajavel A, Boelhauve M, Wittmann M, Ramzan F, Schmitt AO, Gültas M. Comparative Investigation of Coincident Single Nucleotide Polymorphisms Underlying Avian Influenza Viruses in Chickens and Ducks. BIOLOGY 2023; 12:969. [PMID: 37508399 PMCID: PMC10375970 DOI: 10.3390/biology12070969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/26/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023]
Abstract
Avian influenza is a severe viral infection that has the potential to cause human pandemics. In particular, chickens are susceptible to many highly pathogenic strains of the virus, resulting in significant losses. In contrast, ducks have been reported to exhibit rapid and effective innate immune responses to most avian influenza virus (AIV) infections. To explore the distinct genetic programs that potentially distinguish the susceptibility/resistance of both species to AIV, the investigation of coincident SNPs (coSNPs) and their differing causal effects on gene functions in both species is important to gain novel insight into the varying immune-related responses of chickens and ducks. By conducting a pairwise genome alignment between these species, we identified coSNPs and their respective effect on AIV-related differentially expressed genes (DEGs) in this study. The examination of these genes (e.g., CD74, RUBCN, and SHTN1 for chickens and ABCA3, MAP2K6, and VIPR2 for ducks) reveals their high relevance to AIV. Further analysis of these genes provides promising effector molecules (such as IκBα, STAT1/STAT3, GSK-3β, or p53) and related key signaling pathways (such as NF-κB, JAK/STAT, or Wnt) to elucidate the complex mechanisms of immune responses to AIV infections in both chickens and ducks.
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Affiliation(s)
- Hendrik Bertram
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
| | - Selina Wilhelmi
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Abirami Rajavel
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Marc Boelhauve
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
| | - Margareta Wittmann
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
| | - Faisal Ramzan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Mehmet Gültas
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
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6
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Włodarczyk R, Těšický M, Vinkler M, Novotný M, Remisiewicz M, Janiszewski T, Minias P. Divergent evolution drives high diversity of toll-like receptors (TLRs) in passerine birds: Buntings and finches. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 144:104704. [PMID: 37019350 DOI: 10.1016/j.dci.2023.104704] [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: 12/21/2022] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 06/05/2023]
Abstract
Toll-like receptors (TLRs) form a key component of animal innate immunity, being responsible for recognition of conserved microbial structures. As such, TLRs may be subject to diversifying and balancing selection, which maintains allelic variation both within and between populations. However, most research on TLRs in non-model avian species is focused on bottlenecked populations with depleted genetic variation. Here, we assessed variation at the extracellular domains of three TLR genes (TLR1LA, TLR3, TLR4) across eleven species from two passerine families of buntings (Emberizidae) and finches (Fringillidae), all having large breeding population sizes (millions of individuals). We found extraordinary TLR polymorphism in our study taxa, with >100 alleles detected at TLR1LA and TLR4 across species and high haplotype diversity (>0.75) in several species. Despite recent species divergence, no nucleotide allelic variants were shared between species, suggesting rapid TLR evolution. Higher variation at TLR1LA and TLR4 than TLR3 was associated with a stronger signal of diversifying selection, as measured with nucleotide substitutions rates and the number of positively selected sites (PSS). Structural protein modelling of TLRs showed that some PSS detected within TLR1LA and TLR4 were previously recognized as functionally important sites or were located in their proximity, possibly affecting ligand recognition. Furthermore, we identified PSS responsible for major surface electrostatic charge clustering, which may indicate their adaptive importance. Our study provides compelling evidence for the divergent evolution of TLR genes in buntings and finches and indicates that high TLR variation may be adaptively maintained via diversifying selection acting on functional ligand binding sites.
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Affiliation(s)
- Radosław Włodarczyk
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Martin Těšický
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic
| | - Michal Vinkler
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, Czech Republic
| | - Marian Novotný
- Charles University, Faculty of Science, Department of Cell Biology, Viničná 7, 128 43, Prague, Czech Republic
| | - Magdalena Remisiewicz
- Bird Migration Research Station, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland
| | - Tomasz Janiszewski
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
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7
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Gao L, Liu R, Luo D, Li K, Qi X, Liu C, Zhang Y, Cui H, Wang S, Gao Y, Wang X. Avian Reovirus σA Protein Inhibits Type I Interferon Production by Abrogating Interferon Regulatory Factor 7 Activation. J Virol 2023; 97:e0178522. [PMID: 36511697 PMCID: PMC9888210 DOI: 10.1128/jvi.01785-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 11/20/2022] [Indexed: 12/15/2022] Open
Abstract
Type I interferon (IFN) response is the first line of host-based innate immune defense against viral infections. However, viruses have developed multiple strategies to counter host IFN responses, so they may continue infecting hosts via effective replication. Avian reovirus (ARV), an RNA virus, causes viral arthritis or tenosynovitis in chickens. Previous studies have shown that ARV is highly resistant to the antiviral effects of IFN. However, the underlying mechanisms that enable ARV to block the IFN pathway remain unclear. In this study, we found that ectopic expression of ARV protein, σA, significantly inhibited the production of IFN-β induced by melanoma-differentiation-associated gene 5 (MDA5) and poly(I·C). Knockdown of σA during ARV infection enhances the IFN-β response and suppresses viral replication. ARV σA inhibited the MDA5-mediated IFN-β activation by targeting interferon regulatory factor 7 (IRF7). Further studies demonstrated that σA interacts with IRF7, thereby blocking IRF7 dimerization and nuclear translocation, finally leading to the inhibition of IFN-β production. These findings reveal a novel mechanism that allows ARV to evade host antiviral immunity. IMPORTANCE ARV, the causative agent of viral arthritis or tenosynovitis in chickens, has a significant economic impact as it results in poor weight gain and increased feed conversion ratios. The MDA5-mediated IFN-β signal pathway plays an important role in host antiviral defense. Therefore, RNA viruses have developed mechanisms to counter this signaling pathway and successfully establish infection. However, the strategies adopted by ARV to block MDA5-IRF7 signaling remain unclear. In the current study, we demonstrated that ARV σA inhibits this pathway by binding to IRF7, which blocked IRF7 dimerization and nuclear translocation. Our findings may provide insights into how avian reovirus counteracts the innate antiviral immunity of the host to ensure viral replication.
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Affiliation(s)
- Li Gao
- Division of Avian Immunosuppressive Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Rui Liu
- Division of Avian Immunosuppressive Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Dan Luo
- Division of Avian Immunosuppressive Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Kai Li
- Division of Avian Immunosuppressive Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Xiaole Qi
- Division of Avian Immunosuppressive Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Changjun Liu
- Division of Avian Immunosuppressive Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Yanping Zhang
- Division of Avian Immunosuppressive Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Hongyu Cui
- Division of Avian Immunosuppressive Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Suyan Wang
- Division of Avian Immunosuppressive Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Yulong Gao
- Division of Avian Immunosuppressive Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Xiaomei Wang
- Division of Avian Immunosuppressive Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
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8
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Katayama M, Onuma M, Kato N, Nakajima N, Fukuda T. Organoids containing neural-like cells derived from chicken iPSCs respond to poly:IC through the RLR family. PLoS One 2023; 18:e0285356. [PMID: 37141289 PMCID: PMC10159107 DOI: 10.1371/journal.pone.0285356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/20/2023] [Indexed: 05/05/2023] Open
Abstract
There is still much room for development in pluripotent stem cell research on avian species compared to human stem cell studies. Neural cells are useful for the evaluation of risk assessment of infectious diseases since several avian species die of encephalitis derived from infectious diseases. In this study, we attempted to develop induced pluripotent stem cells (iPSCs) technology for avian species by forming organoids containing neural-like cells. In our previous study, we established two types iPSCs from chicken somatic cells, the first is iPSCs with PB-R6F reprogramming vector and the second is iPSCs with PB-TAD-7F reprogramming vector. In this study, we first compared the nature of these two cell types using RNA-seq analysis. The total gene expression of iPSCs with PB-TAD-7F was closer to that of chicken ESCs than that of iPSCs with PB-R6F; therefore, we used iPSCs with PB-TAD-7F to form organoids containing neural-like cells. We successfully established organoids containing neural-like cells from iPSCs using PB-TAD-7F. Furthermore, our organoids responded to poly:IC through the RIG-I-like receptor (RLR) family. In this study, we developed iPSCs technology for avian species via organoid formation. In the future, organoids containing neural-like cells from avian iPSCs can develop as a new evaluation tool for infectious disease risk in avian species, including endangered avian species.
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Affiliation(s)
- Masafumi Katayama
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
| | - Manabu Onuma
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
| | - Noriko Kato
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
| | - Nobuyoshi Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
| | - Tomokazu Fukuda
- Graduate School of Science and Engineering, Iwate University, Ueda, Morioka-city, Japan
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9
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Krchlíková V, Hron T, Těšický M, Li T, Ungrová L, Hejnar J, Vinkler M, Elleder D. Dynamic Evolution of Avian RNA Virus Sensors: Repeated Loss of RIG-I and RIPLET. Viruses 2022; 15:3. [PMID: 36680044 PMCID: PMC9861763 DOI: 10.3390/v15010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA5) are key RNA virus sensors belonging to the RIG-I-like receptor (RLR) family. The activation of the RLR inflammasome leads to the establishment of antiviral state, mainly through interferon-mediated signaling. The evolutionary dynamics of RLRs has been studied mainly in mammals, where rare cases of RLR gene losses were described. By in silico screening of avian genomes, we previously described two independent disruptions of MDA5 in two bird orders. Here, we extend this analysis to approximately 150 avian genomes and report 16 independent evolutionary events of RIG-I inactivation. Interestingly, in almost all cases, these inactivations are coupled with genetic disruptions of RIPLET/RNF135, an ubiquitin ligase RIG-I regulator. Complete absence of any detectable RIG-I sequences is unique to several galliform species, including the domestic chicken (Gallus gallus). We further aimed to determine compensatory evolution of MDA5 in RIG-I-deficient species. While we were unable to show any specific global pattern of adaptive evolution in RIG-I-deficient species, in galliforms, the analyses of positive selection and surface charge distribution support the hypothesis of some compensatory evolution in MDA5 after RIG-I loss. This work highlights the dynamic nature of evolution in bird RNA virus sensors.
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Affiliation(s)
- Veronika Krchlíková
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Tomáš Hron
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Tao Li
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Lenka Ungrová
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Jiří Hejnar
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Daniel Elleder
- Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
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10
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Jax E, Franchini P, Sekar V, Ottenburghs J, Monné Parera D, Kellenberger RT, Magor KE, Müller I, Wikelski M, Kraus RHS. Comparative genomics of the waterfowl innate immune system. Mol Biol Evol 2022; 39:6649919. [PMID: 35880574 PMCID: PMC9356732 DOI: 10.1093/molbev/msac160] [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] [Indexed: 11/13/2022] Open
Abstract
Animal species differ considerably in their ability to fight off infections. Finding the genetic basis of these differences is not easy, as the immune response is comprised of a complex network of proteins that interact with one another to defend the body against infection. Here, we used population- and comparative genomics to study the evolutionary forces acting on the innate immune system in natural hosts of the avian influenza virus (AIV). For this purpose, we used a combination of hybrid capture, next- generation sequencing and published genomes to examine genetic diversity, divergence, and signatures of selection in 127 innate immune genes at a micro- and macroevolutionary time scale in 26 species of waterfowl. We show across multiple immune pathways (AIV-, toll-like-, and RIG-I -like receptors signalling pathways) that genes involved genes in pathogen detection (i.e., toll-like receptors) and direct pathogen inhibition (i.e., antimicrobial peptides and interferon-stimulated genes), as well as host proteins targeted by viral antagonist proteins (i.e., mitochondrial antiviral-signaling protein, [MAVS]) are more likely to be polymorphic, genetically divergent, and under positive selection than other innate immune genes. Our results demonstrate that selective forces vary across innate immune signaling signalling pathways in waterfowl, and we present candidate genes that may contribute to differences in susceptibility and resistance to infectious diseases in wild birds, and that may be manipulated by viruses. Our findings improve our understanding of the interplay between host genetics and pathogens, and offer the opportunity for new insights into pathogenesis and potential drug targets.
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Affiliation(s)
- Elinor Jax
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Biology and Biotechnologies "Charles Darwin", Sapienza University, Rome, Italy
| | - Vaishnovi Sekar
- Department of Biology, Lund University, Lund, Sweden.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Jente Ottenburghs
- Wildlife Ecology and Conservation Group, Wageningen University, Wageningen, The Netherlands.,Forest Ecology and Forest Management Group, Wageningen University, Wageningen, The Netherlands
| | | | - Roman T Kellenberger
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Katharine E Magor
- Department of Biological Sciences and Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Inge Müller
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
| | - Robert H S Kraus
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
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Buckley KM, Yoder JA. The evolution of innate immune receptors: investigating the diversity, distribution, and phylogeny of immune recognition across eukaryotes. Immunogenetics 2021; 74:1-4. [PMID: 34910229 PMCID: PMC8671053 DOI: 10.1007/s00251-021-01243-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, Comparative Medicine Institute, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
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