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Kastner P, Aukenova A, Chan S. Evolution of the Ikaros family transcription factors: From a deuterostome ancestor to humans. Biochem Biophys Res Commun 2024; 694:149399. [PMID: 38134477 DOI: 10.1016/j.bbrc.2023.149399] [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: 12/08/2023] [Accepted: 12/17/2023] [Indexed: 12/24/2023]
Abstract
Ikaros family proteins (Ikaros, Helios, Aiolos, Eos) are zinc finger transcription factors essential for the development and function of the adaptive immune system. They also control developmental events in neurons and other cell types, suggesting that they possess crucial functions across disparate cell types. These functions are likely shared among the organisms in which these factors exist, and it is thus important to obtain a view of their distribution and conservation across organisms. How this family evolved remains poorly understood. Here we mined protein, mRNA and DNA databases to identify proteins with DNA-binding domains homologous to that of Ikaros. We show that Ikaros-related proteins exist in organisms from all four deuterostome phyla (chordates, echinoderms, hemichordates, xenacoelomorpha), but not in more distant groups. While most non-vertebrates have a single family member, this family grew to six members in the acoel worm Hofstenia miamia, three in jawless and four in jawed vertebrates. Most residues involved in DNA contact from zinc fingers 2 to 4 were identical across the Ikaros family, suggesting conserved mechanisms for target sequence recognition. Further, we identified a novel KRKxxxPxK/R motif that inhibits DNA binding in vitro which was conserved across the deuterostome phyla. We also identified a EψψxxxψM(D/E)QAIxxAIxYLGA(D/E)xL motif conserved among human Ikaros, Aiolos, Helios and subsets of chordate proteins, and motifs that are specific to subsets of vertebrate family members. Some of these motifs are targets of mutations in human patients. Finally we show that the atypical family member Pegasus emerged only in vertebrates, which is consistent with its function in bone. Our data provide a novel evolutionary perspective for Ikaros family proteins and suggest that they have conserved regulatory functions across deuterostomes.
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Affiliation(s)
- Philippe Kastner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), ILLKIRCH, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, ILLKIRCH, France; Centre National de la Recherche Scientifique (CNRS), UMR7104, ILLKIRCH, France; Université de Strasbourg, ILLKIRCH, France; Faculté de Médecine, Université de Strasbourg, Strasbourg, France.
| | - Adina Aukenova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), ILLKIRCH, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, ILLKIRCH, France; Centre National de la Recherche Scientifique (CNRS), UMR7104, ILLKIRCH, France; Université de Strasbourg, ILLKIRCH, France
| | - Susan Chan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), ILLKIRCH, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, ILLKIRCH, France; Centre National de la Recherche Scientifique (CNRS), UMR7104, ILLKIRCH, France; Université de Strasbourg, ILLKIRCH, France.
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2
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Arya P, Pradhan P, Paria A, Sharma R, Verma DK, Ravindra, Rathore G, Sood N. Ontogeny and tissue-specific expression of immune-relevant genes in Catla catla (Hamilton). Gene Expr Patterns 2019; 34:119071. [DOI: 10.1016/j.gep.2019.119071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/31/2019] [Accepted: 09/11/2019] [Indexed: 01/29/2023]
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3
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Abstract
Proteins and RNA molecules are deposited into the developing egg by the mother. These gene products will drive the first stages of development and are coded by maternal genes. Maternal genes are essential, yet, despite their importance, their evolutionary dynamics is largely unknown. Here I review the current knowledge of maternal gene evolution. The evolutionary origin of maternal genes tends to be more recent than that of zygotic genes. Some studies support the theoretical prediction that maternal genes evolve faster than zygotic genes. However, most studies were done on a limited set of species and genes. I also discuss the way forward to understand the evolution of maternal genes by combining high-throughput genomics and theoretical evolutionary approaches.
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4
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Spirov AV, Myasnikova EM. Evolutionary Stability of Gene Regulatory Networks That Define the Temporal Identity of Neuroblasts. Mol Biol 2019. [DOI: 10.1134/s0026893319020158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Müller V, de Boer RJ, Bonhoeffer S, Szathmáry E. An evolutionary perspective on the systems of adaptive immunity. Biol Rev Camb Philos Soc 2017; 93:505-528. [PMID: 28745003 DOI: 10.1111/brv.12355] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 12/22/2022]
Abstract
We propose an evolutionary perspective to classify and characterize the diverse systems of adaptive immunity that have been discovered across all major domains of life. We put forward a new function-based classification according to the way information is acquired by the immune systems: Darwinian immunity (currently known from, but not necessarily limited to, vertebrates) relies on the Darwinian process of clonal selection to 'learn' by cumulative trial-and-error feedback; Lamarckian immunity uses templated targeting (guided adaptation) to internalize heritable information on potential threats; finally, shotgun immunity operates through somatic mechanisms of variable targeting without feedback. We argue that the origin of Darwinian (but not Lamarckian or shotgun) immunity represents a radical innovation in the evolution of individuality and complexity, and propose to add it to the list of major evolutionary transitions. While transitions to higher-level units entail the suppression of selection at lower levels, Darwinian immunity re-opens cell-level selection within the multicellular organism, under the control of mechanisms that direct, rather than suppress, cell-level evolution for the benefit of the individual. From a conceptual point of view, the origin of Darwinian immunity can be regarded as the most radical transition in the history of life, in which evolution by natural selection has literally re-invented itself. Furthermore, the combination of clonal selection and somatic receptor diversity enabled a transition from limited to practically unlimited capacity to store information about the antigenic environment. The origin of Darwinian immunity therefore comprises both a transition in individuality and the emergence of a new information system - the two hallmarks of major evolutionary transitions. Finally, we present an evolutionary scenario for the origin of Darwinian immunity in vertebrates. We propose a revival of the concept of the 'Big Bang' of vertebrate immunity, arguing that its origin involved a 'difficult' (i.e. low-probability) evolutionary transition that might have occurred only once, in a common ancestor of all vertebrates. In contrast to the original concept, we argue that the limiting innovation was not the generation of somatic diversity, but the regulatory circuitry needed for the safe operation of amplifiable immune responses with somatically acquired targeting. Regulatory complexity increased abruptly by genomic duplications at the root of the vertebrate lineage, creating a rare opportunity to establish such circuitry. We discuss the selection forces that might have acted at the origin of the transition, and in the subsequent stepwise evolution leading to the modern immune systems of extant vertebrates.
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Affiliation(s)
- Viktor Müller
- Parmenides Center for the Conceptual Foundations of Science, 82049 Pullach/Munich, Germany.,Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary.,Evolutionary Systems Research Group, MTA Centre for Ecological Research, 8237 Tihany, Hungary
| | - Rob J de Boer
- Theoretical Biology, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Sebastian Bonhoeffer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland
| | - Eörs Szathmáry
- Parmenides Center for the Conceptual Foundations of Science, 82049 Pullach/Munich, Germany.,Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary.,Evolutionary Systems Research Group, MTA Centre for Ecological Research, 8237 Tihany, Hungary
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6
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Mitchell JL, Seng A, Yankee TM. Expression and splicing of Ikaros family members in murine and human thymocytes. Mol Immunol 2017; 87:1-11. [PMID: 28376432 DOI: 10.1016/j.molimm.2017.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 03/08/2017] [Accepted: 03/17/2017] [Indexed: 11/18/2022]
Abstract
The Ikaros family of transcription factors includes five highly homologous members that can homodimerize or heterodimerize in any combination. Dimerization is essential for their ability to bind DNA and function as transcription factors. Previous studies showed that eliminating the function of the entire family blocks lymphocyte development while deletion of individual family members has relatively minor defects. These data indicate that multiple family members function during T cell development, so we examined the changes in expression of each family member as thymocytes progressed from the CD4-CD8- double negative (DN) to the CD4+CD8+ double positive (DP) developmental stage. Further, we compared the expression of each family member in murine and human thymocytes. In both species, Ikaros and Aiolos mRNA levels increased as thymocytes progressed through the DN to DP transition, but the corresponding increases in protein levels were only observed in mice. Further, Ikaros and Aiolos underwent extensive alternative splicing in mice, whereas only Ikaros was extensively spliced in humans. Helios mRNA and protein levels decreased during murine T cell development, but increased during human T cell development. These differences in the expression and splicing of Ikaros family members between human and murine thymocytes strongly suggest that the Ikaros family of transcription factors regulates murine and human T cell development differently, although the similarities across Ikaros family members may allow different proteins to fulfill similar functions.
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Affiliation(s)
- Julie L Mitchell
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, United States
| | - Amara Seng
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, United States
| | - Thomas M Yankee
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, United States.
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7
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Martín-Ibáñez R, Pardo M, Giralt A, Miguez A, Guardia I, Marion-Poll L, Herranz C, Esgleas M, Garcia-Díaz Barriga G, Edel MJ, Vicario-Abejón C, Alberch J, Girault JA, Chan S, Kastner P, Canals JM. Helios expression coordinates the development of a subset of striatopallidal medium spiny neurons. Development 2017; 144:1566-1577. [PMID: 28289129 PMCID: PMC5399659 DOI: 10.1242/dev.138248] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 03/03/2017] [Indexed: 12/25/2022]
Abstract
Here, we unravel the mechanism of action of the Ikaros family zinc finger protein Helios (He) during the development of striatal medium spiny neurons (MSNs). He regulates the second wave of striatal neurogenesis involved in the generation of striatopallidal neurons, which express dopamine 2 receptor and enkephalin. To exert this effect, He is expressed in neural progenitor cells (NPCs) keeping them in the G1/G0 phase of the cell cycle. Thus, a lack of He results in an increase of S-phase entry and S-phase length of NPCs, which in turn impairs striatal neurogenesis and produces an accumulation of the number of cycling NPCs in the germinal zone (GZ), which end up dying at postnatal stages. Therefore, He−/− mice show a reduction in the number of dorso-medial striatal MSNs in the adult that produces deficits in motor skills acquisition. In addition, overexpression of He in NPCs induces misexpression of DARPP-32 when transplanted in mouse striatum. These findings demonstrate that He is involved in the correct development of a subset of striatopallidal MSNs and reveal new cellular mechanisms for neuronal development. Summary: The transcription factor Helios regulates G1-S transition to promote neuronal differentiation of a striatopallidal neuronal subpopulation involved in motor skill acquisition.
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Affiliation(s)
- Raquel Martín-Ibáñez
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain.,Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain.,Research and Development Unit, Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Mónica Pardo
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain.,Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain
| | - Albert Giralt
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain.,Pathophysiology of Neurodegenerative Diseases Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Andrés Miguez
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain.,Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain
| | - Inés Guardia
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain.,Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain
| | - Lucile Marion-Poll
- Inserm UMR-S839; Université Pierre et Marie Curie (UPMC, Paris 6), Sorbonne Universités; Institut du Fer à Moulin, 75005 Paris, France
| | - Cristina Herranz
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain.,Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain.,Research and Development Unit, Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Miriam Esgleas
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain
| | - Gerardo Garcia-Díaz Barriga
- Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain.,Pathophysiology of Neurodegenerative Diseases Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Michael J Edel
- Control of Pluripotency Laboratory, Department of Biomedical Sciences, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain.,Victor Chang Cardiac Research Institute, Sydney, New South Wales, 2010 Australia.,School of Medicine and Pharmacology, Anatomy, Physiology and Human Biology, CCTRM, University of Western Australia, Western Australia, 6009 Australia
| | - Carlos Vicario-Abejón
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain.,Departamento de Neurobiología Molecular, Celular y del Desarrollo, Instituto Cajal, Consejo Superior de Investigaciones Científicas (CSIC), 28002 Madrid, Spain
| | - Jordi Alberch
- Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain
| | - Jean-Antoine Girault
- Inserm UMR-S839; Université Pierre et Marie Curie (UPMC, Paris 6), Sorbonne Universités; Institut du Fer à Moulin, 75005 Paris, France
| | - Susan Chan
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain.,Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain
| | - Philippe Kastner
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Inserm U964, Centre National de la Recherche Scientifique (CNRS) UMR 7104, 67400 Illkirch-Graffenstaden, France.,Faculté de Médecine, Université de Strasbourg, 67081 Strasbourg, France
| | - Josep M Canals
- Stem Cells and Regenerative Medicine Laboratory, Production and Validation Center of Advanced Therapies (Creatio), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain .,Neuroscience Institute, University of Barcelona, 08036 Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain.,Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), Spain.,Research and Development Unit, Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
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8
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Lipkin E, Strillacci MG, Eitam H, Yishay M, Schiavini F, Soller M, Bagnato A, Shabtay A. The Use of Kosher Phenotyping for Mapping QTL Affecting Susceptibility to Bovine Respiratory Disease. PLoS One 2016; 11:e0153423. [PMID: 27077383 PMCID: PMC4831767 DOI: 10.1371/journal.pone.0153423] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 03/29/2016] [Indexed: 02/06/2023] Open
Abstract
Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in feedlot cattle, caused by multiple pathogens that become more virulent in response to stress. As clinical signs often go undetected and various preventive strategies failed, identification of genes affecting BRD is essential for selection for resistance. Selective DNA pooling (SDP) was applied in a genome wide association study (GWAS) to map BRD QTLs in Israeli Holstein male calves. Kosher scoring of lung adhesions was used to allocate 122 and 62 animals to High (Glatt Kosher) and Low (Non-Kosher) resistant groups, respectively. Genotyping was performed using the Illumina BovineHD BeadChip according to the Infinium protocol. Moving average of -logP was used to map QTLs and Log drop was used to define their boundaries (QTLRs). The combined procedure was efficient for high resolution mapping. Nineteen QTLRs distributed over 13 autosomes were found, some overlapping previous studies. The QTLRs contain polymorphic functional and expression candidate genes to affect kosher status, with putative immunological and wound healing activities. Kosher phenotyping was shown to be a reliable means to map QTLs affecting BRD morbidity.
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Affiliation(s)
- Ehud Lipkin
- Department of Genetics, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Harel Eitam
- Department of Ruminant Sciences, Agricultural Research Organization (ARO), Bet-Dagan, Israel
| | - Moran Yishay
- Department of Ruminant Sciences, Agricultural Research Organization (ARO), Bet-Dagan, Israel
| | | | - Morris Soller
- Department of Genetics, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Ariel Shabtay
- Department of Ruminant Sciences, Agricultural Research Organization (ARO), Bet-Dagan, Israel
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9
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Rieder SA, Metidji A, Glass DD, Thornton AM, Ikeda T, Morgan BA, Shevach EM. Eos Is Redundant for Regulatory T Cell Function but Plays an Important Role in IL-2 and Th17 Production by CD4+ Conventional T Cells. THE JOURNAL OF IMMUNOLOGY 2015; 195:553-63. [PMID: 26062998 DOI: 10.4049/jimmunol.1500627] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/18/2015] [Indexed: 11/19/2022]
Abstract
Eos belongs to the Ikaros family of transcription factors. It was reported to be a regulatory T cell (Treg) signature gene, to play a critical role in Treg suppressor functions, and to maintain Treg stability. We used mice with a global deficiency in Eos to re-examine the role of Eos expression in both Tregs and conventional T cells (Tconvs). Tregs from Eos-deficient (Eos(-/-)) mice developed normally, displayed a normal Treg phenotype, and exhibited normal suppressor function in vitro. Eos(-/-) Tregs were as effective as Tregs from wild-type (WT) mice in suppressing inflammation in a model of inflammatory bowel disease. Bone marrow (BM) from Eos(-/-) mice was as effective as that from WT mice in controlling T cell activation when used to reconstitute immunodeficient mice in the presence of scurfy fetal liver cells. Surprisingly, Eos was expressed in activated Tconvs and was required for IL-2 production, CD25 expression, and proliferation in vitro by CD4(+) Tconvs. Eos(-/-) mice developed more severe experimental autoimmune encephalomyelitis than WT mice, displayed increased numbers of effector T cells in the periphery and CNS, and amplified IL-17 production. In conclusion, our studies are not consistent with a role for Eos in Treg development and function but demonstrate that Eos plays an important role in the activation and differentiation of Tconvs.
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Affiliation(s)
- Sadiye Amcaoglu Rieder
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892; and
| | - Amina Metidji
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892; and
| | - Deborah Dacek Glass
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892; and
| | - Angela M Thornton
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892; and
| | - Tohru Ikeda
- Cutaneous Biology Research Center, Department of Dermatology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02129
| | - Bruce A Morgan
- Cutaneous Biology Research Center, Department of Dermatology, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02129
| | - Ethan M Shevach
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892; and
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10
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John LB, Trengove MC, Fraser FW, Yoong SH, Ward AC. Pegasus, the 'atypical' Ikaros family member, influences left-right asymmetry and regulates pitx2 expression. Dev Biol 2013; 377:46-54. [PMID: 23499657 DOI: 10.1016/j.ydbio.2013.02.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 02/21/2013] [Accepted: 02/21/2013] [Indexed: 12/12/2022]
Abstract
Members of the Ikaros family of zinc-finger transcription factors have been shown to be critical for immune and blood cell development. However, the role of the most divergent family member, Pegasus, has remained elusive, although it shows conservation to invertebrate Hunchback proteins that influence embryonic patterning through regulation of homeodomain genes. Zebrafish was employed as a relevant model to investigate the function of Pegasus since it possesses a single pegasus orthologue with high homology to its mammalian counterparts. During zebrafish embryogenesis pegasus transcripts were initially maternally-derived and later replaced by zygotic expression in the diencephalon, tectum, hindbrain, thymus, eye, and ultimately the exocrine pancreas and intestine. Morpholino-mediated knockdown of the zebrafish pegasus gene resulted in disrupted left-right asymmetry of the gut and pancreas. Molecular analysis indicated that zebrafish Pegasus localised to the nucleus in discrete non-nucleolar structures and bound the 'atypical' DNA sequence GN3GN2G, confirming its presumed role as a transcriptional regulator. In vivo transcriptome analysis identified candidate target genes, several of which encoded homeodomain transcription factors. One of these, pitx2, implicated in left-right asymmetry, possessed appropriate 'atypical' Pegasus binding sites in its promoter. Knockdown of Pegasus affected both the level and asymmetry of pitx2 expression, as well as disrupting the asymmetry of the lefty2 and spaw genes, explaining the perturbed left-right patterning in pegasus morphants. Collectively these results provide the first definitive insights into the in vivo role of Pegasus, supporting the notion that it acts as a broader regulator of development, with potential parallels to the related invertebrate Hunchback proteins.
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Affiliation(s)
- Liza B John
- School of Medicine and Molecular & Medical Research Strategic Research Centre, Deakin University, Waurn Ponds, Victoria, Australia
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11
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Paradzik M, Novak S, Mokrovic G, Bordukalo Niksic T, Heckel D, Stipic J, Pavicic Baldani D, Cicin-Sain L, Antica M. Ikaros family transcription factors expression in rat thymus: detection of impaired development. Int J Immunopathol Pharmacol 2013; 25:893-900. [PMID: 23298480 DOI: 10.1177/039463201202500407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The expression of Ikaros family transcription factors and consequently their signalling pathway is limiting for hematopoietic and lymphocyte development in mice and human. Due to their importance, these transcription factors are highly homologous between species. As an initial approach to examining the possible involvement of Ikaros transcription factors in pathogenesis of rat lymphoid development, we analyzed the expression of all known Ikaros family members, Ikaros, Aiolos, Helios, Eos and Pegasus in the rat thymus. We established a semi-quantitative RT-PCR to detect mRNA of each transcription factor. For the first time we give evidence of the expression of Ikaros family transcription factors in the rat thymus. Further, we evaluated whether their mRNA expression was succumbed to changes when the rats were exposed to ethanol, as a known debilitating agent during development. Therefore we analyzed the thymus of adult rats whose mothers were forced to drink ethanol during gestation, to detect possible changes in thymus mRNA expression levels of Ikaros, Aiolos, Helios, Eos and Pegasus. We found that rats prenatally exposed to ethanol show a slightly higher expression of Ikaros family transcription factors in the adult thymus when compared to control rats, but these differences were not statistically significant. We further studied the distribution of the major lymphocyte subpopulations in the rat thymus according to CD3, CD4 and CD8 expression by four color flow cytometry. We found a higher incidence of CD3 positive cells in the double positive, CD4+CD8+ thymic subpopulation of rats prenatally exposed to ethanol when compared to non-exposed animals. Our findings indicate that ethanol exposure of pregnant rats might influence the development of CD3 positive cells in the thymus of the offspring but this result should be further tackled at the level of transcription factor expression.
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Affiliation(s)
- M Paradzik
- Division of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia
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12
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Martín-Ibáñez R, Crespo E, Esgleas M, Urban N, Wang B, Waclaw R, Georgopoulos K, Martínez S, Campbell K, Vicario-Abejón C, Alberch J, Chan S, Kastner P, Rubenstein JL, Canals JM. Helios transcription factor expression depends on Gsx2 and Dlx1&2 function in developing striatal matrix neurons. Stem Cells Dev 2012; 21:2239-51. [PMID: 22142223 DOI: 10.1089/scd.2011.0607] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Development of the nervous system is finely regulated by consecutive expression of cell-specific transcription factors. Here we show that Helios, a member of the Ikaros transcription factor family, is expressed in ectodermal and neuroectodermal-derived tissues. During embryonic development, Helios is expressed by several brain structures including the lateral ganglionic eminence (LGE, the striatal anlage); the cingulated, insular and retrosplenial cortex; the hippocampus; and the accessory olfactory bulb. Moreover, Helios is also expressed by Purkinje neurons during postnatal cerebellar development. Within the LGE, Helios expression follows a dynamic spatio-temporal pattern starting at embryonic stages (E14.5), peaking at E18.5, and completely disappearing during postnatal development. Helios is expressed by a small population of nestin-positive neural progenitor cells located in the subventricular zone as well as by a larger population of immature neurons distributed throughout the mantle zone. In the later, Helios is preferentially expressed in the matrix compartment, where it colocalizes with Bcl11b and Foxp1, well-known markers of striatal projection neurons. In addition, we observed that Helios expression is not detected in Dlx1/2 and Gsx2 null mutants, while its expression is maintained in Ascl1 mutants. These findings allow us to introduce a new transcription factor in the cascade of events that take part of striatal development postulating the existence of at least 4 different neural progenitors in the LGE. An Ascl1-independent but Gsx2- & Dlx1/2-dependent precursor will express Helios defining a new lineage for a subset of matrix striatal neurons.
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Affiliation(s)
- Raquel Martín-Ibáñez
- Department of Cell Biology, Immunology and Neuroscience, and Cell Therapy Program, Faculty of Medicine, Institut d'Investigacions Biomèdiques August Pi i Sunyer-IDIBAPS, University of Barcelona, Barcelona, Spain
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Laing KJ, Hansen JD. Fish T cells: recent advances through genomics. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2011; 35:1282-1295. [PMID: 21414347 DOI: 10.1016/j.dci.2011.03.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Revised: 01/14/2011] [Accepted: 03/06/2011] [Indexed: 05/30/2023]
Abstract
This brief review is intended to provide a concise overview of the current literature concerning T cells, advances in identifying distinct T cell functional subsets, and in distinguishing effector cells from memory cells. We compare and contrast a wealth of recent progress made in T cell immunology of teleost, elasmobranch, and agnathan fish, to knowledge derived from mammalian T cell studies. From genome studies, fish clearly have most components associated with T cell function and we can speculate on the presence of putative T cell subsets, and the ability to detect their differentiation to form memory cells. Some recombinant proteins for T cell associated cytokines and antibodies for T cell surface receptors have been generated that will facilitate studying the functional roles of teleost T cells during immune responses. Although there is still a long way to go, major advances have occurred in recent years for investigating T cell responses, thus phenotypic and functional characterization is on the near horizon.
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Affiliation(s)
- Kerry J Laing
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer, Research Center, Seattle, WA 98109, USA
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Daza DO, Sundström G, Bergqvist CA, Duan C, Larhammar D. Evolution of the insulin-like growth factor binding protein (IGFBP) family. Endocrinology 2011; 152:2278-89. [PMID: 21505050 DOI: 10.1210/en.2011-0047] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The evolution of the IGF binding protein (IGFBP) gene family has been difficult to resolve. Both chromosomal and serial duplications have been suggested as mechanisms for the expansion of this gene family. We have identified and annotated IGFBP sequences from a wide selection of vertebrate species as well as Branchiostoma floridae and Ciona intestinalis. By combining detailed sequence analysis with sequence-based phylogenies and chromosome information, we arrive at the following scenario: the ancestral chordate IGFBP gene underwent a local gene duplication, resulting in a gene pair adjacent to a HOX cluster. Subsequently, the gene family expanded in the two basal vertebrate tetraploidization (2R) resulting in the six IGFBP types that are presently found in placental mammals. The teleost fish ancestor underwent a third tetraploidization (3R) that further expanded the IGFBP repertoire. The five sequenced teleost fish genomes retain 9-11 of IGFBP genes. This scenario is supported by the phylogenies of three adjacent gene families in the HOX gene regions, namely the epidermal growth factor receptors (EGFR) and the Ikaros and distal-less (DLX) transcription factors. Our sequence comparisons show that several important structural components in the IGFBPs are ancestral vertebrate features that have been maintained in all orthologs, for instance the integrin interaction motif Arg-Gly-Asp in IGFBP-2. In contrast, the Arg-Gly-Asp motif in IGFBP-1 has arisen independently in mammals. The large degree of retention of IGFBP genes after the ancient expansion of the gene family strongly suggests that each gene evolved distinct and important functions early in vertebrate evolution.
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John LB, Ward AC. The Ikaros gene family: transcriptional regulators of hematopoiesis and immunity. Mol Immunol 2011; 48:1272-8. [PMID: 21477865 DOI: 10.1016/j.molimm.2011.03.006] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 03/07/2011] [Accepted: 03/08/2011] [Indexed: 01/10/2023]
Abstract
The Ikaros family of proteins - comprising Ikaros, Aiolos, Helios, Eos and Pegasus - are zinc finger transcription factors. These proteins participate in a complex network of interactions with gene regulatory elements, other family members and a raft of other transcriptional regulators to control gene expression including via chromatin remodelling. In this way, Ikaros family members regulate important cell-fate decisions during hematopoiesis, particularly in the development of the adaptive immune system. Mutation of several family members results in hematological malignancies,especially those of a lymphoid nature. This review describes the key roles of Ikaros proteins in development and disease, their mechanisms of action and gene targets, as well as explaining their evolutionary origins and role in the emergence of adaptive immunity.
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Affiliation(s)
- Liza B John
- School of Medicine, Deakin University, Waurn Ponds, Victoria 3217, Australia
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Ikaros expression in tongue sole macrophages: a marker for lipopolysaccharide- and lipoteichoic acid-induced inflammatory responses. Mol Biol Rep 2010; 38:2273-9. [PMID: 21069465 DOI: 10.1007/s11033-010-0358-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 10/21/2010] [Indexed: 12/30/2022]
Abstract
Ikaros, an important transcription factor plays a role in the development of hemato-lymphoid system, yet its functional importance in fish macrophages remains unknown. In this study, an Ikaros cDNA was cloned from the half-smooth tongue sole Cynoglossus semilaevis. The cDNA contained an open reading frame of 1,290 nucleotides that encoded a 430 amino acid protein. The deduced protein is structurally similar to dul from other species, for example human, axolotl, and possesses 3-zinc finger and 2-zinc finger domains at its N- and C-termini, respectively. Phylogenetic analysis revealed C. semilaevis Ikaros to be grouped with all the fish Ikaros, but branching from other Ikaros family members. Both semi-quantitative PCR and quantitative real-time PCR indicated Ikaros to be predominantly expressed in the immune-relevant tissues such as kidney, thymus, spleen and liver. In the macrophages cultured from C. semilaevis head kidney and challenged with lipopolysaccharide and lipoteichoic acid not only induced expression of the proinflammatory cytokines tumor necrosis factor-alpha and interleukin 1-beta but also caused up-regulation of Ikaros in a dose- and time-dependent fashions. All these data suggest that Ikaros might be a useful marker for inflammatory responses in C. semilaevis.
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Systemically dispersed innate IL-13-expressing cells in type 2 immunity. Proc Natl Acad Sci U S A 2010; 107:11489-94. [PMID: 20534524 DOI: 10.1073/pnas.1003988107] [Citation(s) in RCA: 893] [Impact Index Per Article: 63.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Type 2 immunity is a stereotyped host response to allergens and parasitic helminths that is sustained in large part by the cytokines IL-4 and IL-13. Recent advances have called attention to the contributions by innate cells in initiating adaptive immunity, including a novel lineage-negative population of cells that secretes IL-13 and IL-5 in response to the epithelial cytokines IL-25 and IL-33. Here, we use IL-4 and IL-13 reporter mice to track lineage-negative innate cells that arise during type 2 immunity or in response to IL-25 and IL-33 in vivo. Unexpectedly, lineage-negative IL-25 (and IL-33) responsive cells are widely distributed in tissues of the mouse and are particularly prevalent in mesenteric lymph nodes, spleen, and liver. These cells expand robustly in response to exogenous IL-25 or IL-33 and after infection with the helminth Nippostrongylus brasiliensis, and they are the major innate IL-13-expressing cells under these conditions. Activation of these cells using IL-25 is sufficient for worm clearance, even in the absence of adaptive immunity. Widely dispersed innate type 2 helper cells, which we designate Ih2 cells, play an integral role in type 2 immune responses.
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Kasahara M. Genome duplication and T cell immunity. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2010; 92:7-36. [PMID: 20800811 DOI: 10.1016/s1877-1173(10)92002-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The adaptive immune system (AIS) mediated by T cells and B cells arose ~450 million years ago in a common ancestor of jawed vertebrates. This system was so successful that, once established, it has been maintained in all classes of jawed vertebrates with only minor modifications. One event thought to have contributed to the emergence of this form of AIS is two rounds of whole-genome duplication. This event enabled jawed vertebrate ancestors to acquire many paralogous genes, known as ohnologs, with essential roles in T cell and B cell immunity. Ohnologs encode the key components of the antigen presentation machinery and signal transduction pathway for lymphocyte activation as well as numerous transcription factors important for lymphocyte development. Recently, it has been discovered that jawless vertebrates have developed an AIS employing antigen receptors unrelated to T/B cell receptors, but with marked overall similarities to the AIS of jawed vertebrates. Emerging evidence suggests that a common ancestor of all vertebrates was equipped with T-lymphoid and B-lymphoid lineages.
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Affiliation(s)
- Masanori Kasahara
- Department of Pathology, Hokkaido, University Graduate School of Medicine, Sapporo, Japan
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Large EE, Mathies LD. hunchback and Ikaros-like zinc finger genes control reproductive system development in Caenorhabditis elegans. Dev Biol 2009; 339:51-64. [PMID: 20026024 DOI: 10.1016/j.ydbio.2009.12.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 11/30/2009] [Accepted: 12/09/2009] [Indexed: 01/29/2023]
Abstract
Here we provide evidence for a C2H2 zinc finger gene family with similarity to Ikaros and hunchback. The founding member of this family is Caenorhabditis elegans ehn-3, which has important and poorly understood functions in somatic gonad development. We examined the expression and function of four additional hunchback/Ikaros-like (HIL) genes in C. elegans reproductive system development. Two genes, ehn-3 and R08E3.4, are expressed in somatic gonadal precursors (SGPs) and have overlapping functions in their development. In ehn-3; R08E3.4 double mutants, we find defects in the generation of distal tip cells, anchor cells, and spermatheca; three of the five tissues derived from the SGPs. We provide in vivo evidence that C. elegans HIL proteins have functionally distinct zinc finger domains, with specificity residing in the N-terminal set of four zinc fingers and a likely protein-protein interaction domain provided by the C-terminal pair of zinc fingers. In addition, we find that a chimeric human Ikaros protein containing the N-terminal zinc fingers of EHN-3 functions in C. elegans. Together, these results lend support to the idea that the C. elegans HIL genes and Ikaros have similar functional domains. We propose that hunchback, Ikaros, and the HIL genes arose from a common ancestor that was present prior to the divergence of protostomes and deuterostomes.
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Affiliation(s)
- Edward E Large
- Department of Genetics, North Carolina State University, 3510 Thomas Hall, Raleigh, NC 27695-7614, USA
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