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Cashman S, Lampe K, Sheridan R, Hoebe K. An ENU mutagenesis approach to dissect "self"-induced immune responses: Unraveling the genetic footprint of immunosurveillance. Oncoimmunology 2021; 1:856-862. [PMID: 23162753 PMCID: PMC3489741 DOI: 10.4161/onci.20580] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The immune system exerts a critical function as it recognizes and eliminates transformed or neoplastic cells, a process also referred to as immunosurveillance. NK cells play a particularly important role in that they are able to recognize tumor cells via “missing-self”—i.e., the absence of major histocompatibility complex Class I on target cells. Moreover, recent studies suggest that NK cells also participate in the onset and regulation of adaptive immune responses. The exact molecular pathways by which this occurs, however, remain poorly understood. To obtain further insight into the genes that are required for self-induced immune responses via NK cell-mediated cell death, our laboratory initiated a forward genetic approach using N-ethyl-N-nitrosourea (ENU) as a mutagen. Specifically, we tested the ability of NK cells from G3 ENU germline mice to recognize missing-self target cells and induce CD8+ T-cell responses following immunization with irradiated tumor cells. Here we present two ENU germline mutants, designated Ace and Chip, that are defective in the recognition of β-2 microglobulin-deficient target cells, yet exhibit improved clearance of B16 melanoma cells in vivo. Coarse mapping and whole genome sequencing of the Chip mutation revealed a missense mutation causing a T’A amino acid substitution in the highly conserved third immuno-receptor tyrosine-based switch motif of CD244 (2B4). The forward genetic approach described here promises to reveal important insight into critical genes that are required for host responses involved in anticancer immunity.
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Affiliation(s)
- Siobhan Cashman
- Department of Molecular and Cellular Immunology; Cincinnati Children's Hospital Research Foundation; Cincinnati, OH USA
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Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice. Proc Natl Acad Sci U S A 2020; 117:12931-12942. [PMID: 32457148 DOI: 10.1073/pnas.1921224117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Retinal disease and loss of vision can result from any disruption of the complex pathways controlling retinal development and homeostasis. Forward genetics provides an excellent tool to find, in an unbiased manner, genes that are essential to these processes. Using N-ethyl-N-nitrosourea mutagenesis in mice in combination with a screening protocol using optical coherence tomography (OCT) and automated meiotic mapping, we identified 11 mutations presumably causative of retinal phenotypes in genes previously known to be essential for retinal integrity. In addition, we found multiple statistically significant gene-phenotype associations that have not been reported previously and decided to target one of these genes, Sfxn3 (encoding sideroflexin-3), using CRISPR/Cas9 technology. We demonstrate, using OCT, light microscopy, and electroretinography, that two Sfxn3 -/- mouse lines developed progressive and severe outer retinal degeneration. Electron microscopy showed thinning of the retinal pigment epithelium and disruption of the external limiting membrane. Using single-cell RNA sequencing of retinal cells isolated from C57BL/6J mice, we demonstrate that Sfxn3 is expressed in several bipolar cell subtypes, retinal ganglion cells, and some amacrine cell subtypes but not significantly in Müller cells or photoreceptors. In situ hybridization confirmed these findings. Furthermore, pathway analysis suggests that Sfxn3 may be associated with synaptic homeostasis. Importantly, electron microscopy analysis showed disruption of synapses and synaptic ribbons in the outer plexiform layer of Sfxn3 -/- mice. Our work describes a previously unknown requirement for Sfxn3 in retinal function.
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FUNATO H. Forward genetic approach for behavioral neuroscience using animal models. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2020; 96:10-31. [PMID: 31932526 PMCID: PMC6974404 DOI: 10.2183/pjab.96.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Forward genetics is a powerful approach to understand the molecular basis of animal behaviors. Fruit flies were the first animal to which this genetic approach was applied systematically and have provided major discoveries on behaviors including sexual, learning, circadian, and sleep-like behaviors. The development of different classes of model organism such as nematodes, zebrafish, and mice has enabled genetic research to be conducted using more-suitable organisms. The unprecedented success of forward genetic approaches was the identification of the transcription-translation negative feedback loop composed of clock genes as a fundamental and conserved mechanism of circadian rhythm. This approach has now expanded to sleep/wakefulness in mice. A conventional strategy such as dominant and recessive screenings can be modified with advances in DNA sequencing and genome editing technologies.
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Affiliation(s)
- Hiromasa FUNATO
- Department of Anatomy, Faculty of Medicine, Toho University, Tokyo, Japan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Ibaraki, Japan
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Methodology and theoretical basis of forward genetic screening for sleep/wakefulness in mice. Proc Natl Acad Sci U S A 2019; 116:16062-16067. [PMID: 31337678 DOI: 10.1073/pnas.1906774116] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The regulatory network of genes and molecules in sleep/wakefulness remains to be elucidated. Here we describe the methodology and workflow of the dominant screening of randomly mutagenized mice and discuss theoretical basis of forward genetics research for sleep in mice. Our high-throughput screening employs electroencephalogram (EEG) and electromyogram (EMG) to stage vigilance states into a wake, rapid eye movement sleep (REMS) and non-REM sleep (NREMS). Based on their near-identical sleep/wake behavior, C57BL/6J (B6J) and C57BL/6N (B6N) are chosen as mutagenized and counter strains, respectively. The total time spent in the wake and NREMS, as well as the REMS episode duration, shows sufficient reproducibility with small coefficients of variance, indicating that these parameters are most suitable for quantitative phenotype-driven screening. Coarse linkage analysis of the quantitative trait, combined with whole-exome sequencing, can identify the gene mutation associated with sleep abnormality. Our simulations calculate the achievable LOD score as a function of the phenotype strength and the numbers of mice examined. A pedigree showing a mild decrease in total wake time resulting from a heterozygous point mutation in the Cacna1a gene is described as an example.
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Sardar S, Kerr A, Vaartjes D, Moltved ER, Karosiene E, Gupta R, Andersson Å. The oncoprotein TBX3 is controlling severity in experimental arthritis. Arthritis Res Ther 2019; 21:16. [PMID: 30630509 PMCID: PMC6329118 DOI: 10.1186/s13075-018-1797-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/14/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Development of autoimmune diseases is the result of a complex interplay between hereditary and environmental factors, with multiple genes contributing to the pathogenesis in human disease and in experimental models for disease. The T-box protein 3 is a transcriptional repressor essential during early embryonic development, in the formation of bone and additional organ systems, and in tumorigenesis. METHODS With the aim to find novel genes important for autoimmune inflammation, we have performed genetic studies of collagen-induced arthritis (CIA), a mouse experimental model for rheumatoid arthritis. RESULTS We showed that a small genetic fragment on mouse chromosome 5, including Tbx3 and three additional protein-coding genes, is linked to severe arthritis and high titers of anti-collagen antibodies. Gene expression studies have revealed differential expression of Tbx3 in B cells, where low expression was accompanied by a higher B cell response upon B cell receptor stimulation in vitro. Furthermore, we showed that serum TBX3 levels rise concomitantly with increasing severity of CIA. CONCLUSIONS From these results, we suggest that TBX3 is a novel factor important for the regulation of gene transcription in the immune system and that genetic polymorphisms, resulting in lower expression of Tbx3, are contributing to a more severe form of CIA and high titers of autoantibodies. We also propose TBX3 as a putative diagnostic biomarker for rheumatoid arthritis.
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Affiliation(s)
- Samra Sardar
- Section for Molecular and Cellular Pharmacology, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Present address: Nordic Bioscience A/S, Copenhagen, Denmark
| | - Alish Kerr
- Section for Molecular and Cellular Pharmacology, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Present address: Nuritas, Dublin, Ireland
| | - Daniëlle Vaartjes
- Section for Molecular and Cellular Pharmacology, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Present address: Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Emilie Riis Moltved
- Section for Molecular and Cellular Pharmacology, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Present address: IQVIA, Copenhagen, Denmark Denmark
| | - Edita Karosiene
- Department of Bio and Health Informatics, Kemitorvet 208, Technical University of Denmark, Lyngby, Denmark
- Present address: Novo Nordisk A/S, Copenhagen, Denmark
| | - Ramneek Gupta
- Department of Bio and Health Informatics, Kemitorvet 208, Technical University of Denmark, Lyngby, Denmark
| | - Åsa Andersson
- Section for Molecular and Cellular Pharmacology, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Rydberg Laboratory of Applied Sciences, ETN, Halmstad University, Halmstad, Sweden
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Morin MD, Wang Y, Jones BT, Mifune Y, Su L, Shi H, Moresco EMY, Zhang H, Beutler B, Boger DL. Diprovocims: A New and Exceptionally Potent Class of Toll-like Receptor Agonists. J Am Chem Soc 2018; 140:14440-14454. [PMID: 30272974 DOI: 10.1021/jacs.8b09223] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A screen conducted with nearly 100000 compounds and a surrogate functional assay for stimulation of an immune response that measured the release of TNF-α from treated human THP-1 myeloid cells differentiated along the macrophage line led to the discovery of the diprovocims. Unique to these efforts and of special interest, the screening leads for this new class of activators of an immune response came from a compound library designed to promote cell-surface receptor dimerization. Subsequent comprehensive structure-activity relationship studies improved the potency 800-fold over that of the screening leads, providing diprovocim-1 and diprovocim-2. The diprovocims act by inducing cell-surface toll-like receptor (TLR)-2 dimerization and activation with TLR1 (TLR1/TLR2 agonist), bear no structural similarity to any known natural or synthetic TLR agonist, and are easy to prepare and synthetically modify, and selected members are active in both human and murine systems. The most potent diprovocim (3, diprovocim-1) elicits full agonist activity at extraordinarily low concentrations (EC50 = 110 pM) in human THP-1 cells, being more potent than the naturally derived TLR1/TLR2 agonist Pam3CSK4 or any other known small molecule TLR agonist.
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Affiliation(s)
- Matthew D Morin
- Department of Chemistry and the Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 United States
| | - Ying Wang
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Brian T Jones
- Department of Chemistry and the Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 United States
| | - Yuto Mifune
- Department of Chemistry and the Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 United States
| | - Lijing Su
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Hexin Shi
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Hong Zhang
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Bruce Beutler
- Center for the Genetics of Host Defense , University of Texas Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - Dale L Boger
- Department of Chemistry and the Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 United States
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Lohman BK, Steinel NC, Weber JN, Bolnick DI. Gene Expression Contributes to the Recent Evolution of Host Resistance in a Model Host Parasite System. Front Immunol 2017; 8:1071. [PMID: 28955327 PMCID: PMC5600903 DOI: 10.3389/fimmu.2017.01071] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/16/2017] [Indexed: 12/31/2022] Open
Abstract
Heritable population differences in immune gene expression following infection can reveal mechanisms of host immune evolution. We compared gene expression in infected and uninfected threespine stickleback (Gasterosteus aculeatus) from two natural populations that differ in resistance to a native cestode parasite, Schistocephalus solidus. Genes in both the innate and adaptive immune system were differentially expressed as a function of host population, infection status, and their interaction. These genes were enriched for loci controlling immune functions known to differ between host populations or in response to infection. Coexpression network analysis identified two distinct processes contributing to resistance: parasite survival and suppression of growth. Comparing networks between populations showed resistant fish have a dynamic expression profile while susceptible fish are static. In summary, recent evolutionary divergence between two vertebrate populations has generated population-specific gene expression responses to parasite infection, affecting parasite establishment and growth.
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Affiliation(s)
- Brian K Lohman
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - Natalie C Steinel
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States.,Department of Medical Education, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Jesse N Weber
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States.,Division of Biological Sciences, The University of Montana, Missoula, MT, United States
| | - Daniel I Bolnick
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
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Affiliation(s)
- Casey W. Dunn
- Department of Ecology and Evolutionary Biology Brown University 80 Waterman St Providence RIUSA
| | - Catriona Munro
- Department of Ecology and Evolutionary Biology Brown University 80 Waterman St Providence RIUSA
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9
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Gallego-Llamas J, Timms AE, Pitstick R, Peters J, Carlson GA, Beier DR. Improvement of ENU Mutagenesis Efficiency Using Serial Injection and Mismatch Repair Deficiency Mice. PLoS One 2016; 11:e0159377. [PMID: 27441645 PMCID: PMC4956170 DOI: 10.1371/journal.pone.0159377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/03/2016] [Indexed: 12/05/2022] Open
Abstract
ENU mutagenesis is a powerful method for generating novel lines of mice that are informative with respect to both fundamental biological processes and human disease. Rapid developments in genomic technology have made the task of identifying causal mutations by positional cloning remarkably efficient. One limitation of this approach remains the mutation frequency achievable using standard treatment protocols, which currently generate approximately 1–2 sequence changes per megabase when optimized. In this study we used two strategies to attempt to increase the number of mutations induced by ENU treatment. One approach employed mice carrying a mutation in the DNA repair enzyme Msh6. The second strategy involved injection of ENU to successive generations of mice. To evaluate the number of ENU-induced mutations, single mice or pooled samples were analyzed using whole exome sequencing. The results showed that there is considerable variability in the induced mutation frequency using these approaches, but an overall increase in ENU-induced variants from one generation to another was observed. The analysis of the mice deficient for Msh6 also showed an increase in the ENU-induced variants compared to the wild-type ENU-treated mice. However, in both cases the increase in ENU-induced mutation frequency was modest.
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Affiliation(s)
- Jabier Gallego-Llamas
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA, United States of America
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Andrew E. Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA, United States of America
| | - Rose Pitstick
- McLaughlin Research Institute, Great Falls, MT, United States of America
| | - Janet Peters
- McLaughlin Research Institute, Great Falls, MT, United States of America
| | - George A. Carlson
- McLaughlin Research Institute, Great Falls, MT, United States of America
| | - David R. Beier
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA, United States of America
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States of America
- * E-mail:
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10
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Morin MD, Wang Y, Jones BT, Su L, Surakattula MMRP, Berger M, Huang H, Beutler EK, Zhang H, Beutler B, Boger DL. Discovery and Structure-Activity Relationships of the Neoseptins: A New Class of Toll-like Receptor-4 (TLR4) Agonists. J Med Chem 2016; 59:4812-30. [PMID: 27050713 DOI: 10.1021/acs.jmedchem.6b00177] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Herein, we report studies leading to the discovery of the neoseptins and a comprehensive examination of the structure-activity relationships (SARs) of this new class of small-molecule mouse Toll-like receptor 4 (mTLR4) agonists. The compounds in this class, which emerged from screening an α-helix mimetic library, stimulate the immune response, act by a well-defined mechanism (mouse TLR4 agonist), are easy to produce and structurally manipulate, exhibit exquisite SARs, are nontoxic, and elicit improved and qualitatively different responses compared to lipopolysaccharide, even though they share the same receptor.
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Affiliation(s)
- Matthew D Morin
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ying Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Brian T Jones
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lijing Su
- Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Murali M R P Surakattula
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael Berger
- Department of Genetics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hua Huang
- Department of Genetics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Elliot K Beutler
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hong Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Dale L Boger
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Nmf9 Encodes a Highly Conserved Protein Important to Neurological Function in Mice and Flies. PLoS Genet 2015; 11:e1005344. [PMID: 26131556 PMCID: PMC4488434 DOI: 10.1371/journal.pgen.1005344] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/09/2015] [Indexed: 01/15/2023] Open
Abstract
Many protein-coding genes identified by genome sequencing remain without functional annotation or biological context. Here we define a novel protein-coding gene, Nmf9, based on a forward genetic screen for neurological function. ENU-induced and genome-edited null mutations in mice produce deficits in vestibular function, fear learning and circadian behavior, which correlated with Nmf9 expression in inner ear, amygdala, and suprachiasmatic nuclei. Homologous genes from unicellular organisms and invertebrate animals predict interactions with small GTPases, but the corresponding domains are absent in mammalian Nmf9. Intriguingly, homozygotes for null mutations in the Drosophila homolog, CG45058, show profound locomotor defects and premature death, while heterozygotes show striking effects on sleep and activity phenotypes. These results link a novel gene orthology group to discrete neurological functions, and show conserved requirement across wide phylogenetic distance and domain level structural changes. Genome sequencing projects have identified large numbers of genes that encode proteins of unknown function. Many of these genes show strong evolutionary conservation, predicting important and well-conserved functions. A fraction of these show strong conservation of core domains but dynamic changes in other domains, predicting both conserved and lineage-dependent functions. Here we identify neurological functions associated with one such gene identified by a forward genetic screen in mice. We use recently developed genome editing tools both to confirm the mouse studies and to test comparative functions in a model insect, the fruit fly Drosophila melanogaster. Each of these species has a single homolog of this gene family, but differ by inclusion of a ras-association (RA) domain present in most invertebrate species but missing in mammals. Null mutations in both mice and flies produce neurological phenotypes, but while the mouse phenotypes are comparatively mild (vestibular deficits, mild tremor, hyperactivity, mild circadian phenotypes and abnormal fear learning–but normal viability and breeding), null flies rarely survive to adulthood and surviving flies have severe locomotor deficits. Interestingly, heterozygous flies have significant sleep-related phenotypes. Together, our results provide a detailed first look at comparative function for a gene lineage with an unusual evolutionary history.
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Moresco EMY, Li X, Beutler B. Going forward with genetics: recent technological advances and forward genetics in mice. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 182:1462-73. [PMID: 23608223 DOI: 10.1016/j.ajpath.2013.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/05/2013] [Indexed: 12/24/2022]
Abstract
Forward genetic analysis is an unbiased approach for identifying genes essential to defined biological phenomena. When applied to mice, it is one of the most powerful methods to facilitate understanding of the genetic basis of human biology and disease. The speed at which disease-causing mutations can be identified in mutagenized mice has been markedly increased by recent advances in DNA sequencing technology. Creating and analyzing mutant phenotypes may therefore become rate-limiting in forward genetic experimentation. We review the forward genetic approach and its future in the context of recent technological advances, in particular massively parallel DNA sequencing, induced pluripotent stem cells, and haploid embryonic stem cells.
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Affiliation(s)
- Eva Marie Y Moresco
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75235-8505, USA
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Abstract
All multicellular organisms protect themselves against pathogens using sophisticated immune defenses. Functionally interconnected humoral and cellular facilities maintain immune homeostasis in the absence of overt infection and regulate the initiation and termination of immune responses directed against pathogens. Immune responses of invertebrates, such as flies, are innate and usually stereotyped; those of vertebrates, encompassing species as diverse as jawless fish and humans, are additionally adaptive, enabling more rapid and efficient immune reactivity upon repeated encounters with a pathogen. Many of the attributes historically defining innate and adaptive immunity are in fact common to both, blurring their functional distinction and emphasizing shared ancestry and co-evolution. These findings provide indications of the evolutionary forces underlying the origin of somatic diversification of antigen receptors and contribute to our understanding of the complex phenotypes of human immune disorders. Moreover, informed by phylogenetic considerations and inspired by improved knowledge of functional networks, new avenues emerge for innovative therapeutic strategies.
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Abstract
The last decades have seen numerous approaches being used to decipher biological phenomena, notably the strategies we employ to defend ourselves against pathogenic attacks. From microarrays to genetics to computing technologies, all have supported a better but not yet comprehensive understanding of the pathways regulating our immune system. Limitations are notably exemplified by cases of immune deficiencies in humans that often result in high susceptibility to infections or even death, without the genetic cause being evident. To provide further insight into the mechanisms by which pathogen detection and eradication occur, several in vivo strategies can be used. The current review focuses on one of them, namely germline mutagenesis in the mouse. After describing the main technical aspects of this forward genetic approach, we will discuss particular germline mutants that have all been instrumental in deciphering innate or adaptive immune responses. Mutations in previously uncharacterized genes in the mouse, like Unc93B or Themis, have demonstrated the impartiality of forward genetics and led to the identification of new crucial immunity actors. Some mutants, like PanR1, have informed us on particular protein domains and their specific functions. Finally, certain mutations identified by this non-hypothesis-driven method have revealed previously unknown gene functions, as recently illustrated by memi, which links a particular nucleoside salvage enzyme to cell proliferation and apoptosis.
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Affiliation(s)
- Onjee Choi
- National Heart and Lung Institute, Imperial College London, London, UK
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15
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Arnold CN, Barnes MJ, Berger M, Blasius AL, Brandl K, Croker B, Crozat K, Du X, Eidenschenk C, Georgel P, Hoebe K, Huang H, Jiang Z, Krebs P, La Vine D, Li X, Lyon S, Moresco EMY, Murray AR, Popkin DL, Rutschmann S, Siggs OM, Smart NG, Sun L, Tabeta K, Webster V, Tomisato W, Won S, Xia Y, Xiao N, Beutler B. ENU-induced phenovariance in mice: inferences from 587 mutations. BMC Res Notes 2012; 5:577. [PMID: 23095377 PMCID: PMC3532239 DOI: 10.1186/1756-0500-5-577] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 09/03/2012] [Indexed: 11/22/2022] Open
Abstract
Background We present a compendium of N-ethyl-N-nitrosourea (ENU)-induced mouse mutations, identified in our laboratory over a period of 10 years either on the basis of phenotype or whole genome and/or whole exome sequencing, and archived in the Mutagenetix database. Our purpose is threefold: 1) to formally describe many point mutations, including those that were not previously disclosed in peer-reviewed publications; 2) to assess the characteristics of these mutations; and 3) to estimate the likelihood that a missense mutation induced by ENU will create a detectable phenotype. Findings In the context of an ENU mutagenesis program for C57BL/6J mice, a total of 185 phenotypes were tracked to mutations in 129 genes. In addition, 402 incidental mutations were identified and predicted to affect 390 genes. As previously reported, ENU shows strand asymmetry in its induction of mutations, particularly favoring T to A rather than A to T in the sense strand of coding regions and splice junctions. Some amino acid substitutions are far more likely to be damaging than others, and some are far more likely to be observed. Indeed, from among a total of 494 non-synonymous coding mutations, ENU was observed to create only 114 of the 182 possible amino acid substitutions that single base changes can achieve. Based on differences in overt null allele frequencies observed in phenotypic vs. non-phenotypic mutation sets, we infer that ENU-induced missense mutations create detectable phenotype only about 1 in 4.7 times. While the remaining mutations may not be functionally neutral, they are, on average, beneath the limits of detection of the phenotypic assays we applied. Conclusions Collectively, these mutations add to our understanding of the chemical specificity of ENU, the types of amino acid substitutions it creates, and its efficiency in causing phenovariance. Our data support the validity of computational algorithms for the prediction of damage caused by amino acid substitutions, and may lead to refined predictions as to whether specific amino acid changes are responsible for observed phenotypes. These data form the basis for closer in silico estimations of the number of genes mutated to a state of phenovariance by ENU within a population of G3 mice.
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Affiliation(s)
- Carrie N Arnold
- Department of Genetics, The Scripps Research Institute, La Jolla, CA 92037, USA
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Ermann J, Glimcher LH. After GWAS: mice to the rescue? Curr Opin Immunol 2012; 24:564-70. [PMID: 23031443 DOI: 10.1016/j.coi.2012.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/04/2012] [Accepted: 09/05/2012] [Indexed: 12/12/2022]
Abstract
The genetic basis of human autoimmune diseases remains incompletely understood, despite significant progress from genome-wide association studies (GWAS). In this review we outline how studies in mice may help filling these knowledge gaps. Forward genetic approaches including mutagenesis screens and quantitative trait locus (QTL) mapping studies can identify candidate genes for in depth analysis in human patient populations. Reverse genetic approaches utilize genetically engineered mice to analyze the function of disease-associated genes and their variants. Inbred strains are a distinctive feature of mouse genetics and we discuss their history, advantages and disadvantages. Three factors need to be considered when comparing experimental results from studies in mice and humans: In addition to species-specific differences, phenotypes are affected by the genetic background of the mouse strain being analyzed, and by microbial factors. Despite of these complexities, mice are essential discovery tools in the post GWAS era.
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Affiliation(s)
- Joerg Ermann
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Robert Brigham Arthritis Center, Boston, MA 02215, USA.
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17
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Mutation of the gastric hydrogen-potassium ATPase alpha subunit causes iron-deficiency anemia in mice. Blood 2011; 118:6418-25. [PMID: 21976678 DOI: 10.1182/blood-2011-04-350082] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Iron is an essential component of heme and hemoglobin, and therefore restriction of iron availability directly limits erythropoiesis. In the present study, we report a defect in iron absorption that results in iron-deficiency anemia, as revealed by an N-ethyl-N-nitrosourea-induced mouse phenotype called sublytic. Homozygous sublytic mice develop hypochromic microcytic anemia with reduced osmotic fragility of RBCs. The sublytic phenotype stems from impaired gastrointestinal iron absorption caused by a point mutation of the gastric hydrogen-potassium ATPase α subunit encoded by Atp4a, which results in achlorhydria. The anemia of sublytic homozygotes can be corrected by feeding with a high-iron diet or by parenteral injection of iron dextran; rescue can also be achieved by providing acidified drinking water to sublytic homozygotes. These findings establish the necessity of the gastric proton pump for iron absorption and effective erythropoiesis.
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18
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Sheridan R, Lampe K, Shanmukhappa SK, Putnam P, Keddache M, Divanovic S, Bezerra J, Hoebe K. Lampe1: an ENU-germline mutation causing spontaneous hepatosteatosis identified through targeted exon-enrichment and next-generation sequencing. PLoS One 2011; 6:e21979. [PMID: 21760938 PMCID: PMC3131302 DOI: 10.1371/journal.pone.0021979] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 06/14/2011] [Indexed: 01/22/2023] Open
Abstract
Using a small scale ENU mutagenesis approach we identified a recessive germline mutant, designated Lampe1 that exhibited growth retardation and spontaneous hepatosteatosis. Low resolution mapping based on 20 intercrossed Lampe1 mice revealed linkage to a ∼14 Mb interval on the distal site of chromosome 11 containing a total of 285 genes. Exons and 50 bp flanking sequences within the critical region were enriched with sequence capture microarrays and subsequently analyzed by next-generation sequencing. Using this approach 98.1 percent of the targeted DNA was covered with a depth of 10 or more reads per nucleotide and 3 homozygote mutations were identified. Two mutations represented intronic nucleotide changes whereas one mutation affected a splice donor site in intron 11–12 of Palmitoyl Acetyl-coenzyme A oxygenase-1 (Acox1), causing skipping of exon 12. Phenotyping of Acox1Lampe1 mutants revealed a progression from hepatosteatosis to steatohepatitis, and ultimately hepatocellular carcinoma. The current approach provides a highly efficient and affordable method to identify causative mutations induced by ENU mutagenesis and animal models relevant to human pathology.
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Affiliation(s)
- Rachel Sheridan
- Department of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Kristin Lampe
- Department of Molecular Immunology, Cincinnati Children's Hospital Research Foundation, Cincinnati, Ohio, United States of America
| | - Shiva Kumar Shanmukhappa
- Division of Comparative Medicine and Pathology, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America
| | - Patrick Putnam
- Department of Human Genetics, Cincinnati Children's Hospital Research Foundation, Cincinnati, Ohio, United States of America
| | - Mehdi Keddache
- Department of Human Genetics, Cincinnati Children's Hospital Research Foundation, Cincinnati, Ohio, United States of America
| | - Senad Divanovic
- Department of Molecular Immunology, Cincinnati Children's Hospital Research Foundation, Cincinnati, Ohio, United States of America
| | - Jorge Bezerra
- Department of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Research Foundation, Cincinnati, Ohio, United States of America
| | - Kasper Hoebe
- Department of Molecular Immunology, Cincinnati Children's Hospital Research Foundation, Cincinnati, Ohio, United States of America
- * E-mail:
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19
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Abstract
Large-scale projects are providing rapid global access to a wealth of mouse genetic resources to help discover disease genes and to manipulate their function.
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Affiliation(s)
| | | | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Darren W Logan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
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20
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Justice MJ, Siracusa LD, Stewart AF. Technical approaches for mouse models of human disease. Dis Model Mech 2011; 4:305-10. [PMID: 21558063 PMCID: PMC3097452 DOI: 10.1242/dmm.000901] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The mouse is the leading organism for disease research. A rich resource of genetic variation occurs naturally in inbred and special strains owing to spontaneous mutations. However, one can also obtain desired gene mutations by using the following processes: targeted mutations that eliminate function in the whole organism or in a specific tissue; forward genetic screens using chemicals or transposons; or the introduction of exogenous transgenes as DNAs, bacterial artificial chromosomes (BACs) or reporter constructs. The mouse is the only mammal that provides such a rich resource of genetic diversity coupled with the potential for extensive genome manipulation, and is therefore a powerful application for modeling human disease. This poster review outlines the major genome manipulations available in the mouse that are used to understand human disease: natural variation, reverse genetics, forward genetics, transgenics and transposons. Each of these applications will be essential for understanding the diversity that is being discovered within the human population.
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Affiliation(s)
- Monica J Justice
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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21
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Severity of innate immune-mediated colitis is controlled by the cytokine deficiency-induced colitis susceptibility-1 (Cdcs1) locus. Proc Natl Acad Sci U S A 2011; 108:7137-41. [PMID: 21482794 DOI: 10.1073/pnas.1104234108] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Genetic modifier loci influence the phenotypic expression of many Mendelian traits; insight into disease pathogenesis gained from their identification in animal disease models may impact the treatment of human multigenic disorders. We previously described an innate immune-driven model of spontaneous ulcerative colitis in T-bet(-/-).Rag2(-/-) double-deficient mice that resembles human ulcerative colitis. On a BALB/c background, this disease is highly penetrant and results in the development of colorectal cancer. However, we observed that colitis in T-bet(-/-).Rag2(-/-) mice on a C57BL/6 background was significantly less severe. Quantitative trait locus analysis using an N2 backcross strategy revealed a single major quantitative trait locus on chromosome 3 that mapped to the Cdcs1 (cytokine deficiency-induced colitis susceptibility-1) locus previously identified in the Il10(-/-) and Gnai2(-/-) colitis models. Congenic introduction of the susceptible Cdcs1 interval from C3H/He into the C57BL/6 background restored colitis severity. Bone marrow reconstitution experiments further mapped the effect of host genetics on disease severity to the hematopoietic compartment. There were distinct differences in the expression of several Cdcs1 genes in bone marrow-derived dendritic cells from Cdcs1 congenic mice. We conclude that the Cdcs1 locus controls colitis severity in T-bet(-/-).Rag2(-/-) mice through innate immune cells.
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22
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Lu P, Hankel IL, Knisz J, Marquardt A, Chiang MY, Grosse J, Constien R, Meyer T, Schroeder A, Zeitlmann L, Al-Alem U, Friedman AD, Elliott EI, Meyerholz DK, Waldschmidt TJ, Rothman PB, Colgan JD. The Justy mutation identifies Gon4-like as a gene that is essential for B lymphopoiesis. ACTA ACUST UNITED AC 2010; 207:1359-67. [PMID: 20530203 PMCID: PMC2901076 DOI: 10.1084/jem.20100147] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A recessive mutation named Justy was found that abolishes B lymphopoiesis but does not impair other major aspects of hematopoiesis. Transplantation experiments showed that homozygosity for Justy prevented hematopoietic progenitors from generating B cells but did not affect the ability of bone marrow stroma to support B lymphopoiesis. In bone marrow from mutant mice, common lymphoid progenitors and pre-pro–B cells appeared normal, but cells at subsequent stages of B lymphopoiesis were dramatically reduced in number. Under culture conditions that promoted B lymphopoiesis, mutant pre-pro–B cells remained alive and began expressing the B cell marker CD19 but failed to proliferate. In contrast, these cells were able to generate myeloid or T/NK precursors. Genetic and molecular analysis demonstrated that Justy is a point mutation within the Gon4-like (Gon4l) gene, which encodes a protein with homology to transcriptional regulators. This mutation was found to disrupt Gon4l pre-mRNA splicing and dramatically reduce expression of wild-type Gon4l RNA and protein. Consistent with a role for Gon4l in transcriptional regulation, the levels of RNA encoding C/EBPα and PU.1 were abnormally high in mutant B cell progenitors. Our findings indicate that the Gon4l protein is required for B lymphopoiesis and may function to regulate gene expression during this process.
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Affiliation(s)
- Ping Lu
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
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23
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L'Hôte D, Laissue P, Serres C, Montagutelli X, Veitia RA, Vaiman D. Interspecific resources: a major tool for quantitative trait locus cloning and speciation research. Bioessays 2010; 32:132-42. [PMID: 20091755 DOI: 10.1002/bies.200900027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Positional cloning of the quantitative trait locus (QTL) still encounters numerous difficulties, which explains why thousands of QTL have been mapped, while only a few have been identified at the molecular level. Here, we focus on a specific mapping tool that exists in plant and animal model species: interspecific recombinant congenic strains (IRCSs) or interspecific nearly isogenic lines (NILs). Such panels exhibit a much higher sequence diversity than intraspecific sets, thus enhancing the contrasts between phenotypes. In animals, it allows statistical significance to be reached even when using a limited number of individuals. Therefore, we argue that interspecific resources may constitute a major genetic tool for positional cloning and for understanding some bases of speciation mechanisms.
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24
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Barnes MJ, Aksoylar H, Krebs P, Bourdeau T, Arnold CN, Xia Y, Khovananth K, Engel I, Sovath S, Lampe K, Laws E, Saunders A, Butcher GW, Kronenberg M, Steinbrecher K, Hildeman D, Grimes HL, Beutler B, Hoebe K. Loss of T cell and B cell quiescence precedes the onset of microbial flora-dependent wasting disease and intestinal inflammation in Gimap5-deficient mice. THE JOURNAL OF IMMUNOLOGY 2010; 184:3743-54. [PMID: 20190135 DOI: 10.4049/jimmunol.0903164] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Homeostatic control of the immune system involves mechanisms that ensure the self-tolerance, survival and quiescence of hematopoietic-derived cells. In this study, we demonstrate that the GTPase of immunity associated protein (Gimap)5 regulates these processes in lymphocytes and hematopoietic progenitor cells. As a consequence of a recessive N-ethyl-N-nitrosourea-induced germline mutation in the P-loop of Gimap5, lymphopenia, hepatic extramedullary hematopoiesis, weight loss, and intestinal inflammation occur in homozygous mutant mice. Irradiated fetal liver chimeric mice reconstituted with Gimap5-deficient cells lose weight and become lymphopenic, demonstrating a hematopoietic cell-intrinsic function for Gimap5. Although Gimap5-deficient CD4(+) T cells and B cells appear to undergo normal development, they fail to proliferate upon Ag-receptor stimulation although NF-kappaB, MAP kinase and Akt activation occur normally. In addition, in Gimap5-deficient mice, CD4(+) T cells adopt a CD44(high)CD62L(low)CD69(low) phenotype and show reduced IL-7ralpha expression, and T-dependent and T-independent B cell responses are abrogated. Thus, Gimap5-deficiency affects a noncanonical signaling pathway required for Ag-receptor-induced proliferation and lymphocyte quiescence. Antibiotic-treatment or the adoptive transfer of Rag-sufficient splenocytes ameliorates intestinal inflammation and weight loss, suggesting that immune responses triggered by microbial flora causes the morbidity in Gimap5-deficient mice. These data establish Gimap5 as a key regulator of hematopoietic integrity and lymphocyte homeostasis.
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Affiliation(s)
- Michael J Barnes
- Department of Genetics, Scripps Research Institute, La Jolla, CA, USA
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25
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Using in vivo zebrafish models to understand the biochemical basis of neutrophilic respiratory disease. Biochem Soc Trans 2009; 37:830-7. [PMID: 19614603 DOI: 10.1042/bst0370830] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Neutrophilic inflammation in the lung protects against infectious disease, and usually resolves spontaneously after removal of the inflammatory stimulus. However, much lung disease is caused by a failure of resolution of neutrophilic inflammation. Our laboratory is seeking an understanding of the biochemical basis of inflammation resolution, using the zebrafish model system. Zebrafish larvae are transparent, allowing visualization of GFP (green fluorescent protein)-labelled leucocytes during inflammation in vivo, and they can be readily manipulated by a range of forward and reverse genetic techniques. This combination of advantages makes zebrafish a powerful tool for the study of in vivo inflammatory processes. Using this model, we have visualized the process of inflammation resolution in vivo, and identified a role for apoptosis in this process. In addition, we have performed a forward genetic screen for mutants with defective resolution of inflammation, and reverse genetic experiments examining the influence of candidate genes on inflammation resolution. We have established a platform for screening for compounds with anti-inflammatory activity, which has yielded a number of interesting leads. Looking forward to succeed in the future, we are working at combining mutants, transgenes and pharmacological agents to dissect the biochemical basis of inflammation resolution, and to identify compounds that might be used to treat patients with respiratory disease.
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26
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Abstract
Most inherited hemostatic disorders exhibit incomplete penetrance and variable expressivity, which can be because of genetic or environmental interactions. This wide phenotypic variability for a given disease can be partly explained by modifier gene interactions. Modifier gene interactions have been described for VWD, TTP and venous thrombosis associated with the factor V Leiden mutation. We have exploited advances in mouse genetics in an effort to identify novel genetic loci that may serve as candidate genetic modifiers for bleeding and thrombosis in humans. We have identified several loci affecting plasma VWF levels and have identified and characterized mouse models of ADAMTS13 deficiency and Factor V Leiden that could be useful for identifying novel genes contributing to thrombosis risk in humans.
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Affiliation(s)
- R J Westrick
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
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27
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Nguyen D, Xu T. The expanding role of mouse genetics for understanding human biology and disease. Dis Model Mech 2009; 1:56-66. [PMID: 19048054 DOI: 10.1242/dmm.000232] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
It has taken about 100 years since the mouse first captured our imagination as an intriguing animal for it to become the premier genetic model organism. An expanding repertoire of genetic technology, together with sequencing of the genome and biological conservation, place the mouse at the foremost position as a model to decipher mechanisms underlying biological and disease processes. The combined approaches of embryonic stem cell-based technologies, chemical and insertional mutagenesis have enabled the systematic interrogation of the mouse genome with the aim of creating, for the first time, a library of mutants in which every gene is disrupted. The hope is that phenotyping the mutants will reveal novel and interesting phenotypes that correlate with genes, to define the first functional map of a mammalian genome. This new milestone will have a great impact on our understanding of mammalian biology, and could significantly change the future of medical diagnosis and therapeutic development, where databases can be queried in silico for potential drug targets or underlying genetic causes of illnesses. Emerging innovative genetic strategies, such as somatic genetics, modifier screens and humanized mice, in combination with whole-genome mutagenesis will dramatically broaden the utility of the mouse. More significantly, allowing genome-wide genetic interrogations in the laboratory, will liberate the creativity of individual investigators and transform the mouse as a model for making original discoveries and establishing novel paradigms for understanding human biology and disease.
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Affiliation(s)
- Duc Nguyen
- Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
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28
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Blasius AL, Brandl K, Crozat K, Xia Y, Khovananth K, Krebs P, Smart NG, Zampolli A, Ruggeri ZM, Beutler BA. Mice with mutations of Dock7 have generalized hypopigmentation and white-spotting but show normal neurological function. Proc Natl Acad Sci U S A 2009; 106:2706-11. [PMID: 19202056 PMCID: PMC2650330 DOI: 10.1073/pnas.0813208106] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2008] [Indexed: 12/30/2022] Open
Abstract
The classical recessive coat color mutation misty (m) arose spontaneously on the DBA/J background and causes generalized hypopigmentation and localized white-spotting in mice, with a lack of pigment on the belly, tail tip, and paws. Here we describe moonlight (mnlt), a second hypopigmentation and white-spotting mutation identified on the C57BL/6J background, which yields a phenotypic copy of m/m coat color traits. We demonstrate that the 2 mutations are allelic. m/m and mnlt/mnlt phenotypes both result from mutations that truncate the dedicator of cytokinesis 7 protein (DOCK7), a widely expressed Rho family guanine nucleotide exchange factor. Although Dock7 is transcribed at high levels in the developing brain and has been implicated in both axon development and myelination by in vitro studies, we find no requirement for DOCK7 in neurobehavioral function in vivo. However, DOCK7 has non-redundant role(s) related to the distribution and function of dermal and follicular melanocytes.
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Affiliation(s)
| | | | | | - Yu Xia
- Departments of Genetics and
| | | | | | | | - Antonella Zampolli
- Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Zaverio M. Ruggeri
- Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
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29
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Sordino P, Andreakis N, Brown ER, Leccia NI, Squarzoni P, Tarallo R, Alfano C, Caputi L, D'Ambrosio P, Daniele P, D'Aniello E, D'Aniello S, Maiella S, Miraglia V, Russo MT, Sorrenti G, Branno M, Cariello L, Cirino P, Locascio A, Spagnuolo A, Zanetti L, Ristoratore F. Natural variation of model mutant phenotypes in Ciona intestinalis. PLoS One 2008; 3:e2344. [PMID: 18523552 PMCID: PMC2391289 DOI: 10.1371/journal.pone.0002344] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Accepted: 04/17/2008] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The study of ascidians (Chordata, Tunicata) has made a considerable contribution to our understanding of the origin and evolution of basal chordates. To provide further information to support forward genetics in Ciona intestinalis, we used a combination of natural variation and neutral population genetics as an approach for the systematic identification of new mutations. In addition to the significance of developmental variation for phenotype-driven studies, this approach can encompass important implications in evolutionary and population biology. METHODOLOGY/PRINCIPAL FINDINGS Here, we report a preliminary survey for naturally occurring mutations in three geographically interconnected populations of C. intestinalis. The influence of historical, geographical and environmental factors on the distribution of abnormal phenotypes was assessed by means of 12 microsatellites. We identified 37 possible mutant loci with stereotyped defects in embryonic development that segregate in a way typical of recessive alleles. Local populations were found to differ in genetic organization and frequency distribution of phenotypic classes. CONCLUSIONS/SIGNIFICANCE Natural genetic polymorphism of C. intestinalis constitutes a valuable source of phenotypes for studying embryonic development in ascidians. Correlating genetic structure and the occurrence of abnormal phenotypes is a crucial focus for understanding the selective forces that shape natural finite populations, and may provide insights of great importance into the evolutionary mechanisms that generate animal diversity.
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Affiliation(s)
- Paolo Sordino
- Laboratory of Biochemistry and Molecular Biology, Stazione Zoologica Anton Dohrn, Naples, Italy.
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30
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Huang YH, Hoebe K, Sauer K. New therapeutic targets in immune disorders: ItpkB, Orai1 and UNC93B. Expert Opin Ther Targets 2008; 12:391-413. [PMID: 18348677 DOI: 10.1517/14728222.12.4.391] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Sequencing of the murine and human genomes has enabled large-scale functional genomics approaches to target identification. This holds the promise of drastically accelerating target discovery. Moreover, by providing an initial validation coincident with target identification, cell based cDNA or small interfering RNA (siRNA) screens and in particular genome-wide in vivo approaches, including forward or reverse genetics and analyses of natural gene polymorphisms, can move the relatively late step of target validation to the beginning of the process, reducing the risk of pursuing targets with little in vivo relevance. OBJECTIVE We critically discuss the value of combining functional genomics with traditional approaches for accelerating target identification and validation. METHODS We evaluate the potentials of inositol (1,4,5)trisphosphate 3-kinase B (ItpkB), Orai1 and UNC93B, three particularly interesting proteins that were recently identified through functional genomics, as targets in immune disorders. RESULTS/CONCLUSION Combining functional genomics with traditional approaches can accelerate target discovery and validation, but requires a follow-up platform that integrates and analyzes all relevant data for assessment of the clinical potential of the growing number of novel targets.
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Affiliation(s)
- Yina H Huang
- The Scripps Research Institute, Department of Immunology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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31
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Immunology in natura: clinical, epidemiological and evolutionary genetics of infectious diseases. Nat Immunol 2008; 8:1165-71. [PMID: 17952041 DOI: 10.1038/ni1535] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The field of human genetics of infectious diseases defines the genes and alleles rendering individuals (clinical genetics) and populations (epidemiological genetics) vulnerable to infection, and studies those selected by previous infections (evolutionary genetics). These disciplines--clinical, epidemiological and evolutionary genetics-delineate the redundant and nonredundant functions of host defense genes for past and present survival in natura--in natural ecosystems governed by natural selection. These disciplines, in other words, assess the ecologically relevant and evolutionarily selected roles of human genes and alleles in protective immunity to diverse and evolving microorganisms. The genetic dissection of human immunity to infection in natura provides unique immunological insight, making it an indispensable complement to experimental immunology in vitro and in vivo in plants and animals.
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32
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Abstract
The innate arm of our immune system is the first line of defence against infections. In addition, it is believed to drive adaptive immune responses, which help fight pathogens and provide long-term memory. As such, the innate immune system is instrumental for protection against pathogens that would otherwise destroy their host. Although our understanding of the innate immune components involved in pathogen sensing and fighting is improving, it is still limited. This is particularly exemplified by increased documentation of innate immune deficiencies in humans that often result in high and recurrent susceptibility to infections or even death, without the genetic cause being evident. To provide further insight into the mechanisms by which pathogen sensing and eradication occur, several strategies can be used. The current review focuses on the forward genetic approaches that have been used to dissect innate immunity in the fruit fly and the mouse. For both animal models, forward genetics has been instrumental in the deciphering of innate immunity and has greatly improved our understanding of how we respond to invading pathogens.
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33
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Beutler B. Neo-ligands for innate immune receptors and the etiology of sterile inflammatory disease. Immunol Rev 2008; 220:113-28. [PMID: 17979843 DOI: 10.1111/j.1600-065x.2007.00577.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microbe recognition based on a small collection of germline-encoded receptors carries a hidden liability: the possibility that mutational changes in the proteome will lead to self-recognition. The risk of self-recognition is enhanced, because innate immune receptors display low specificity, as they are driven to accommodate heterogeneous signature molecules found in the microbial world. The proteome structure is globally constrained by the innate immune sensing apparatus to satisfy a proscription against self-reactivity. But accidents happen, and here it is proposed that mutations creating neo-ligands for innate immune receptors are the proximal cause of sterile inflammatory diseases, which in turn embody the selective pressure that constrains the proteome. Such mutations are predictably dominant and may occur in the germline and also in somatic cells (e.g. in lymphocytes), causing inflammatory effects upon clonal expansion. They may also account for the inflammatory character of selected neoplastic diseases. The neo-ligand hypothesis accounts for the heritability, ambiguous linkage characteristics, phenotypic heterogeneity, and natural history of diverse forms of sterile inflammation. It explains sterile inflammatory diseases as conditions in which aberrant immune signaling is caused by proteome encroachment upon the ligand-recognition space over which the innate immune system stands guard.
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34
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Kuijl C, Tuin AW, Overkleeft H, Neefjes J. Reciprocal chemical genetics for swift lead and target identification. MOLECULAR BIOSYSTEMS 2008; 4:1001-8. [DOI: 10.1039/b803265n] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Abstract
Recognition of the microbial world is mediated chiefly by a small group of immune receptors that activate a characteristic host inflammatory response, the innate immune response. Known as the Toll-like receptors (TLRs), these molecules are represented among most metazoans. In mammals, forward genetic analysis of the lipopolysaccharide (LPS) response led to the identification of TLR4 as the LPS receptor. Through a combination of forward and reverse genetic studies, a relatively detailed understanding of the functions of mammalian TLRs has now been achieved. As discussed here, mutagenesis has revealed proteins that participate in TLR signaling pathways, and informed our understanding of the subtleties of these molecules' structure and function.
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