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Valek L, Tran BN, Tegeder I. Cold avoidance and heat pain hypersensitivity in neuronal nucleoredoxin knockout mice. Free Radic Biol Med 2022; 192:84-97. [PMID: 36126861 DOI: 10.1016/j.freeradbiomed.2022.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 08/15/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022]
Abstract
Nucleoredoxin is a thioredoxin-like oxidoreductase that mainly acts as oxidase and thereby regulates calcium calmodulin kinase Camk2a, an effector of nitric oxide mediated synaptic potentiation and nociceptive sensitization. We asked here if and how NXN affects thermal sensation and nociception in mice using pan-neuronal NXN deletion driven by Nestin-Cre, and sensory neuron specific deletion driven by Advillin-Cre. In a thermal gradient ring, where mice can freely choose the temperature of well-being, Nestin-NXN-/- mice avoided unpleasant cold temperatures. In neuropathic and inflammatory nociceptive models, Nestin-NXN-/- and Advillin-NXN-/- mice displayed subtle phenotypes of heightened heat nociception. Abnormal thermal in vivo responses were associated with heightened calcium influx upon stimulation of transient receptor channels, with heightened oxygen consumption upon disruption of the mitochondrial membrane potential and with higher density of neurite trees of primary sensory neurons of the dorsal root ganglia in cultures. The data suggest that loss of NXN's balancing redox functions leads to maladaptive changes in sensory neurons that manifest in vivo as polyneuropathy-like abnormal cold sensitivity and heat "pain".
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Affiliation(s)
- Lucie Valek
- Institute of Clinical Pharmacology, Goethe-University, Faculty of Medicine, Frankfurt, Germany
| | - Bao Ngoc Tran
- Institute of Clinical Pharmacology, Goethe-University, Faculty of Medicine, Frankfurt, Germany
| | - Irmgard Tegeder
- Institute of Clinical Pharmacology, Goethe-University, Faculty of Medicine, Frankfurt, Germany.
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2
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Microbiota and Transcriptomic Effects of an Essential Oil Blend and Its Delivery Route Compared to an Antibiotic Growth Promoter in Broiler Chickens. Microorganisms 2022; 10:microorganisms10050861. [PMID: 35630307 PMCID: PMC9147064 DOI: 10.3390/microorganisms10050861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022] Open
Abstract
This study evaluated the effect of the delivery of a commercial essential oil blend containing the phytonutrients star anise, cinnamon, rosemary, and thyme oil (via different routes) on broiler chickens’ ileal and ceca microbiota and liver transcriptome compared to an antibiotic growth promoter. Eggs were incubated and allocated into three groups: non-injected, in ovo saline, and in ovo essential oil. On day 18 of incubation, 0.2 mL of essential oil in saline (dilution ratio of 2:1) or saline alone was injected into the amnion. At hatch, chicks were assigned to post-hatch treatment combinations: (A) a negative control (corn-wheat-soybean diet), (B) in-feed antibiotics, (C) in-water essential oil (250 mL/1000 L of drinking water), (D) in ovo saline, (E) in ovo essential oil, and (F) in ovo essential oil plus in-water essential oil in eight replicate cages (six birds/cage) and raised for 28 days. On days 21 and 28, one and two birds per cage were slaughtered, respectively, to collect gut content and liver tissues for further analysis. Alpha and beta diversity differed significantly between ileal and ceca samples but not between treatment groups. In-feed antibiotic treatment significantly increased the proportion of specific bacteria in the family Lachnospiraceae while reducing the proportion of bacteria in the genus Christensenellaceae in the ceca, compared to other treatments. Sex-controlled differential expression of genes related to cell signaling and tight junctions were recorded. This study provides data that could guide the use of these feed additives and a foundation for further research.
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Idelfonso-García OG, Alarcón-Sánchez BR, Vásquez-Garzón VR, Baltiérrez-Hoyos R, Villa-Treviño S, Muriel P, Serrano H, Pérez-Carreón JI, Arellanes-Robledo J. Is Nucleoredoxin a Master Regulator of Cellular Redox Homeostasis? Its Implication in Different Pathologies. Antioxidants (Basel) 2022; 11:antiox11040670. [PMID: 35453355 PMCID: PMC9030443 DOI: 10.3390/antiox11040670] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 01/27/2023] Open
Abstract
Nucleoredoxin (NXN), an oxidoreductase enzyme, contributes to cellular redox homeostasis by regulating different signaling pathways in a redox-dependent manner. By interacting with seven proteins so far, namely disheveled (DVL), protein phosphatase 2A (PP2A), phosphofructokinase-1 (PFK1), translocation protein SEC63 homolog (SEC63), myeloid differentiation primary response gene-88 (MYD88), flightless-I (FLII), and calcium/calmodulin-dependent protein kinase II type alpha (CAMK2A), NXN is involved in the regulation of several key cellular processes, including proliferation, organogenesis, cell cycle progression, glycolysis, innate immunity and inflammation, motility, contraction, protein transport into the endoplasmic reticulum, neuronal plasticity, among others; as a result, NXN has been implicated in different pathologies, such as cancer, alcoholic and polycystic liver disease, liver fibrogenesis, obesity, Robinow syndrome, diabetes mellitus, Alzheimer’s disease, and retinitis pigmentosa. Together, this evidence places NXN as a strong candidate to be a master redox regulator of cell physiology and as the hub of different redox-sensitive signaling pathways and associated pathologies. This review summarizes and discusses the current insights on NXN-dependent redox regulation and its implication in different pathologies.
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Affiliation(s)
- Osiris Germán Idelfonso-García
- Laboratory of Liver Diseases, National Institute of Genomic Medicine–INMEGEN, Mexico City 14610, Mexico; (O.G.I.-G.); (B.R.A.-S.); (J.I.P.-C.)
- Department of Health Sciences, Metropolitan Autonomous University-Iztapalapa Campus, Mexico City 09340, Mexico;
| | - Brisa Rodope Alarcón-Sánchez
- Laboratory of Liver Diseases, National Institute of Genomic Medicine–INMEGEN, Mexico City 14610, Mexico; (O.G.I.-G.); (B.R.A.-S.); (J.I.P.-C.)
- Department of Cell Biology, Center for Research and Advanced Studies of the National Polytechnic Institute–CINVESTAV-IPN, Mexico City 07360, Mexico;
| | - Verónica Rocío Vásquez-Garzón
- Laboratory of Fibrosis and Cancer, Faculty of Medicine and Surgery, ‘Benito Juárez’ Autonomous University of Oaxaca–UABJO, Oaxaca 68020, Mexico; (V.R.V.-G.); (R.B.-H.)
- Directorate of Cátedras, National Council of Science and Technology–CONACYT, Mexico City 03940, Mexico
| | - Rafael Baltiérrez-Hoyos
- Laboratory of Fibrosis and Cancer, Faculty of Medicine and Surgery, ‘Benito Juárez’ Autonomous University of Oaxaca–UABJO, Oaxaca 68020, Mexico; (V.R.V.-G.); (R.B.-H.)
- Directorate of Cátedras, National Council of Science and Technology–CONACYT, Mexico City 03940, Mexico
| | - Saúl Villa-Treviño
- Department of Cell Biology, Center for Research and Advanced Studies of the National Polytechnic Institute–CINVESTAV-IPN, Mexico City 07360, Mexico;
| | - Pablo Muriel
- Laboratory of Experimental Hepatology, Department of Pharmacology, Center for Research and Advanced Studies of the National Polytechnic Institute–CINVESTAV-IPN, Mexico City 07360, Mexico;
| | - Héctor Serrano
- Department of Health Sciences, Metropolitan Autonomous University-Iztapalapa Campus, Mexico City 09340, Mexico;
| | - Julio Isael Pérez-Carreón
- Laboratory of Liver Diseases, National Institute of Genomic Medicine–INMEGEN, Mexico City 14610, Mexico; (O.G.I.-G.); (B.R.A.-S.); (J.I.P.-C.)
| | - Jaime Arellanes-Robledo
- Laboratory of Liver Diseases, National Institute of Genomic Medicine–INMEGEN, Mexico City 14610, Mexico; (O.G.I.-G.); (B.R.A.-S.); (J.I.P.-C.)
- Directorate of Cátedras, National Council of Science and Technology–CONACYT, Mexico City 03940, Mexico
- Correspondence: ; Tel.: +52-55-5350-1900 (ext. 1218)
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Tran BN, Valek L, Wilken-Schmitz A, Fuhrmann DC, Namgaladze D, Wittig I, Tegeder I. Reduced exploratory behavior in neuronal nucleoredoxin knockout mice. Redox Biol 2021; 45:102054. [PMID: 34198070 PMCID: PMC8254043 DOI: 10.1016/j.redox.2021.102054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 11/07/2022] Open
Abstract
Nucleoredoxin is a thioredoxin-like redoxin that has been recognized as redox modulator of WNT signaling. Using a Yeast-2-Hybrid screen, we identified calcium calmodulin kinase 2a, Camk2a, as a prominent prey in a brain library. Camk2a is crucial for nitric oxide dependent processes of neuronal plasticity of learning and memory. Therefore, the present study assessed functions of NXN in neuronal Nestin-NXN-/- deficient mice. The NXN-Camk2a interaction was confirmed by coimmunoprecipitation, and by colocalization in neuropil and dendritic spines. Functionally, Camk2a activity was reduced in NXN deficient neurons and restored with recombinant NXN. Proteomics revealed reduced oxidation in the hippocampus of Nestin-NXN-/- deficient mice, including Camk2a, further synaptic and mitochondrial proteins, and was associated with a reduction of mitochondrial respiration. Nestin-NXN-/- mice were healthy and behaved normally in behavioral tests of anxiety, activity and sociability. They had no cognitive deficits in touchscreen based learning & memory tasks, but omitted more trials showing a lower interest in the reward. They also engaged less in rewarding voluntary wheel running, and in exploratory behavior in IntelliCages. Accuracy was enhanced owing to the loss of exploration. The data suggested that NXN maintained the oxidative state of Camk2a and thereby its activity. In addition, it supported oxidation of other synaptic and mitochondrial proteins, and mitochondrial respiration. The loss of NXN-dependent pro-oxidative functions manifested in a loss of exploratory drive and reduced interest in reward in behaving mice.
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Affiliation(s)
- Bao Ngoc Tran
- Institute of Clinical Pharmacology, Goethe-University, Medical Faculty, Frankfurt, Germany
| | - Lucie Valek
- Institute of Clinical Pharmacology, Goethe-University, Medical Faculty, Frankfurt, Germany
| | - Annett Wilken-Schmitz
- Institute of Clinical Pharmacology, Goethe-University, Medical Faculty, Frankfurt, Germany
| | | | - Dimitry Namgaladze
- Institute of Biochemistry I, Goethe-University, Medical Faculty, Frankfurt, Germany
| | - Ilka Wittig
- Functional Proteomics Group, Institute of Cardiovascular Physiology, Goethe-University, Medical Faculty, Frankfurt, Germany
| | - Irmgard Tegeder
- Institute of Clinical Pharmacology, Goethe-University, Medical Faculty, Frankfurt, Germany.
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Valek L, Tegeder I. Nucleoredoxin Knockdown in SH-SY5Y Cells Promotes Cell Renewal. Antioxidants (Basel) 2021; 10:antiox10030449. [PMID: 33805811 PMCID: PMC7999887 DOI: 10.3390/antiox10030449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 01/13/2023] Open
Abstract
Nucleoredoxin (NXN) is a redox regulator of Disheveled and thereby of WNT signaling. Deficiency in mice leads to cranial dysmorphisms and defects of heart, brain, and bone, suggesting defects of cell fate determination. We used shRNA-mediated knockdown of NXN in SH-SY5Y neuroblastoma cells to study its impact on neuronal cells. We expected that shNXN cells would easily succumb to redox stress, but there were no differences in viability on stimulation with hydrogen peroxide. Instead, the proliferation of naïve shNXN cells was increased with a higher rate of mitotic cells in cell cycle analyses. In addition, basal respiratory rates were higher, whereas the relative change in oxygen consumption upon mitochondrial stressors was similar to control cells. shNXN cells had an increased expression of redox-sensitive heat shock proteins, Hsc70/HSPA8 and HSP90, and autophagy markers suggested an increase in autophagosome formation upon stimulation with bafilomycin and higher flux under low dose rapamycin. A high rate of self-renewal, autophagy, and upregulation of redox-sensitive chaperones appears to be an attractive anti-aging combination if it were to occur in neurons in vivo for which SH-SY5Y cells are a model.
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Huybrechts Y, Mortier G, Boudin E, Van Hul W. WNT Signaling and Bone: Lessons From Skeletal Dysplasias and Disorders. Front Endocrinol (Lausanne) 2020; 11:165. [PMID: 32328030 PMCID: PMC7160326 DOI: 10.3389/fendo.2020.00165] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/09/2020] [Indexed: 12/15/2022] Open
Abstract
Skeletal dysplasias are a diverse group of heritable diseases affecting bone and cartilage growth. Throughout the years, the molecular defect underlying many of the diseases has been identified. These identifications led to novel insights in the mechanisms regulating bone and cartilage growth and homeostasis. One of the pathways that is clearly important during skeletal development and bone homeostasis is the Wingless and int-1 (WNT) signaling pathway. So far, three different WNT signaling pathways have been described, which are all activated by binding of the WNT ligands to the Frizzled (FZD) receptors. In this review, we discuss the skeletal disorders that are included in the latest nosology of skeletal disorders and that are caused by genetic defects involving the WNT signaling pathway. The number of skeletal disorders caused by defects in WNT signaling genes and the clinical phenotype associated with these disorders illustrate the importance of the WNT signaling pathway during skeletal development as well as later on in life to maintain bone mass. The knowledge gained through the identification of the genes underlying these monogenic conditions is used for the identification of novel therapeutic targets. For example, the genes underlying disorders with altered bone mass are all involved in the canonical WNT signaling pathway. Consequently, targeting this pathway is one of the major strategies to increase bone mass in patients with osteoporosis. In addition to increasing the insights in the pathways regulating skeletal development and bone homeostasis, knowledge of rare skeletal dysplasias can also be used to predict possible adverse effects of these novel drug targets. Therefore, this review gives an overview of the skeletal and extra-skeletal phenotype of the different skeletal disorders linked to the WNT signaling pathway.
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Yoda S, Lin JJ, Lawrence MS, Burke BJ, Friboulet L, Langenbucher A, Dardaei L, Prutisto-Chang K, Dagogo-Jack I, Timofeevski S, Hubbeling H, Gainor JF, Ferris LA, Riley AK, Kattermann KE, Timonina D, Heist RS, Iafrate AJ, Benes CH, Lennerz JK, Mino-Kenudson M, Engelman JA, Johnson TW, Hata AN, Shaw AT. Sequential ALK Inhibitors Can Select for Lorlatinib-Resistant Compound ALK Mutations in ALK-Positive Lung Cancer. Cancer Discov 2018; 8:714-729. [PMID: 29650534 PMCID: PMC5984716 DOI: 10.1158/2159-8290.cd-17-1256] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/28/2018] [Accepted: 04/06/2018] [Indexed: 01/16/2023]
Abstract
The cornerstone of treatment for advanced ALK-positive lung cancer is sequential therapy with increasingly potent and selective ALK inhibitors. The third-generation ALK inhibitor lorlatinib has demonstrated clinical activity in patients who failed previous ALK inhibitors. To define the spectrum of ALK mutations that confer lorlatinib resistance, we performed accelerated mutagenesis screening of Ba/F3 cells expressing EML4-ALK. Under comparable conditions, N-ethyl-N-nitrosourea (ENU) mutagenesis generated numerous crizotinib-resistant but no lorlatinib-resistant clones harboring single ALK mutations. In similar screens with EML4-ALK containing single ALK resistance mutations, numerous lorlatinib-resistant clones emerged harboring compound ALK mutations. To determine the clinical relevance of these mutations, we analyzed repeat biopsies from lorlatinib-resistant patients. Seven of 20 samples (35%) harbored compound ALK mutations, including two identified in the ENU screen. Whole-exome sequencing in three cases confirmed the stepwise accumulation of ALK mutations during sequential treatment. These results suggest that sequential ALK inhibitors can foster the emergence of compound ALK mutations, identification of which is critical to informing drug design and developing effective therapeutic strategies.Significance: Treatment with sequential first-, second-, and third-generation ALK inhibitors can select for compound ALK mutations that confer high-level resistance to ALK-targeted therapies. A more efficacious long-term strategy may be up-front treatment with a third-generation ALK inhibitor to prevent the emergence of on-target resistance. Cancer Discov; 8(6); 714-29. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 663.
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Affiliation(s)
- Satoshi Yoda
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jessica J Lin
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Luc Friboulet
- Gustave Roussy Cancer Campus, Université Paris Saclay, INSERM U981, Paris, France
| | - Adam Langenbucher
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Leila Dardaei
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Ibiayi Dagogo-Jack
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Harper Hubbeling
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Lorin A Ferris
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Amanda K Riley
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts
| | | | - Daria Timonina
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts
| | - Rebecca S Heist
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - A John Iafrate
- Cancer Center and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jochen K Lennerz
- Cancer Center and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Mari Mino-Kenudson
- Cancer Center and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Ted W Johnson
- Pfizer Worldwide Research and Development, La Jolla, California
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts.
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Alice T Shaw
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts.
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
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White JJ, Mazzeu JF, Coban-Akdemir Z, Bayram Y, Bahrambeigi V, Hoischen A, van Bon BWM, Gezdirici A, Gulec EY, Ramond F, Touraine R, Thevenon J, Shinawi M, Beaver E, Heeley J, Hoover-Fong J, Durmaz CD, Karabulut HG, Marzioglu-Ozdemir E, Cayir A, Duz MB, Seven M, Price S, Ferreira BM, Vianna-Morgante AM, Ellard S, Parrish A, Stals K, Flores-Daboub J, Jhangiani SN, Gibbs RA, Brunner HG, Sutton VR, Lupski JR, Carvalho CMB. WNT Signaling Perturbations Underlie the Genetic Heterogeneity of Robinow Syndrome. Am J Hum Genet 2018; 102:27-43. [PMID: 29276006 DOI: 10.1016/j.ajhg.2017.10.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/06/2017] [Indexed: 12/12/2022] Open
Abstract
Locus heterogeneity characterizes a variety of skeletal dysplasias often due to interacting or overlapping signaling pathways. Robinow syndrome is a skeletal disorder historically refractory to molecular diagnosis, potentially stemming from substantial genetic heterogeneity. All current known pathogenic variants reside in genes within the noncanonical Wnt signaling pathway including ROR2, WNT5A, and more recently, DVL1 and DVL3. However, ∼70% of autosomal-dominant Robinow syndrome cases remain molecularly unsolved. To investigate this missing heritability, we recruited 21 families with at least one family member clinically diagnosed with Robinow or Robinow-like phenotypes and performed genetic and genomic studies. In total, four families with variants in FZD2 were identified as well as three individuals from two families with biallelic variants in NXN that co-segregate with the phenotype. Importantly, both FZD2 and NXN are relevant protein partners in the WNT5A interactome, supporting their role in skeletal development. In addition to confirming that clustered -1 frameshifting variants in DVL1 and DVL3 are the main contributors to dominant Robinow syndrome, we also found likely pathogenic variants in candidate genes GPC4 and RAC3, both linked to the Wnt signaling pathway. These data support an initial hypothesis that Robinow syndrome results from perturbation of the Wnt/PCP pathway, suggest specific relevant domains of the proteins involved, and reveal key contributors in this signaling cascade during human embryonic development. Contrary to the view that non-allelic genetic heterogeneity hampers gene discovery, this study demonstrates the utility of rare disease genomic studies to parse gene function in human developmental pathways.
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Affiliation(s)
- Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA
| | - Juliana F Mazzeu
- University of Brasilia, Brasilia 70910, Brazil; Robinow Syndrome Foundation, Anoka, MN 55303, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA
| | - Vahid Bahrambeigi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA; Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Bregje W M van Bon
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Francis Ramond
- Service de Génétique, CHU-Hôpital Nord, 42000 Saint-Etienne, France
| | - Renaud Touraine
- Service de Génétique, CHU-Hôpital Nord, 42000 Saint-Etienne, France
| | - Julien Thevenon
- Inserm UMR 1231 GAD team, Genetics of Developmental Anomalies, Université de Bourgogne-Franche Comté, 21000 Dijon, France; FHU-TRANSLAD, Université de Bourgogne, 21000 CHU Dijon, France; Centre de génétique, Hôpital Couple-Enfant, CHU de Grenoble-Alpes, 38700 La Tronche, France
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erin Beaver
- Mercy Clinic-Kids Genetics, Mercy Children's Hospital St. Louis, St. Louis, MO 63141, USA
| | - Jennifer Heeley
- Mercy Clinic-Kids Genetics, Mercy Children's Hospital St. Louis, St. Louis, MO 63141, USA
| | - Julie Hoover-Fong
- Greenberg Center for Skeletal Dysplasias, McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Ceren D Durmaz
- Department of Medical Genetics, Ankara University School of Medicine, 06100 Ankara, Turkey
| | - Halil Gurhan Karabulut
- Department of Medical Genetics, Ankara University School of Medicine, 06100 Ankara, Turkey
| | - Ebru Marzioglu-Ozdemir
- Department of Medical Genetics, Erzurum Regional and Training Hospital, 25070 Erzurum, Turkey
| | - Atilla Cayir
- Erzurum Training and Research Hospital, Department of Pediatric Endocrinology, 25070 Erzurum, Turkey
| | - Mehmet B Duz
- Department of Medical Genetics, Cerrahpasa Medical School, Istanbul University, 34452 Istanbul, Turkey
| | - Mehmet Seven
- Department of Medical Genetics, Cerrahpasa Medical School, Istanbul University, 34452 Istanbul, Turkey
| | - Susan Price
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford OX3 7LD, UK
| | | | - Angela M Vianna-Morgante
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Sao Paulo - SP 05508-090, Brazil
| | - Sian Ellard
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK; Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX1 2LU, UK
| | - Andrew Parrish
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Karen Stals
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Josue Flores-Daboub
- Department of Pediatric Genetics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Han G Brunner
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department of Clinical Genetics, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, 6202 AZ Maastricht, the Netherlands
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA.
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Ye Z, Sun L, Li R, Han M, Zhuang Y, Wu X, Xu T. Generation of a Mouse Full-length Balancer with Versatile Cassette-shuttling Selection Strategy. Int J Biol Sci 2016; 12:911-6. [PMID: 27489495 PMCID: PMC4971730 DOI: 10.7150/ijbs.15172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/20/2016] [Indexed: 11/22/2022] Open
Abstract
Balancer chromosomes are important tools for a variety of genetic manipulations in lower model organisms, owing to their ability to suppress recombination. In mouse, however, such effort has not been accomplished, mostly due to the size of the chromosomes and the complexity of multiple step chromosomal engineering. We developed an effective and versatile cassette-shuttling selection (CASS) strategy involving only two selection markers to achieve the sequential production of multiple large inversions along the chromosome. Using this strategy, we successfully generated the first full-length balancer in mice and showed that Balancer 17M-GFP can efficiently suppress recombination. Our study has not only generated a useful genetic resource, but also provided a strategy for constructing mammalian balancer chromosomes.
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Affiliation(s)
- Zhisheng Ye
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Collaborative Innovation Center for Genetics and Development, Fudan-Yale Biomedical Research Center, Institute of Developmental Biology and Molecular Medicine, Fudan University, Shanghai 200433, China
| | - Lei Sun
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Collaborative Innovation Center for Genetics and Development, Fudan-Yale Biomedical Research Center, Institute of Developmental Biology and Molecular Medicine, Fudan University, Shanghai 200433, China
| | - Rongbo Li
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Collaborative Innovation Center for Genetics and Development, Fudan-Yale Biomedical Research Center, Institute of Developmental Biology and Molecular Medicine, Fudan University, Shanghai 200433, China
| | - Min Han
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Collaborative Innovation Center for Genetics and Development, Fudan-Yale Biomedical Research Center, Institute of Developmental Biology and Molecular Medicine, Fudan University, Shanghai 200433, China.; 2. Howard Hughes Medical Institute, Department of Molecular, Cellular, Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Yuan Zhuang
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Collaborative Innovation Center for Genetics and Development, Fudan-Yale Biomedical Research Center, Institute of Developmental Biology and Molecular Medicine, Fudan University, Shanghai 200433, China.; 3. Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiaohui Wu
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Collaborative Innovation Center for Genetics and Development, Fudan-Yale Biomedical Research Center, Institute of Developmental Biology and Molecular Medicine, Fudan University, Shanghai 200433, China
| | - Tian Xu
- 1. State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Collaborative Innovation Center for Genetics and Development, Fudan-Yale Biomedical Research Center, Institute of Developmental Biology and Molecular Medicine, Fudan University, Shanghai 200433, China.; 4. Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, New Haven, CT 06536, USA
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10
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Lan Y, Zhang N, Liu H, Xu J, Jiang R. Golgb1 regulates protein glycosylation and is crucial for mammalian palate development. Development 2016; 143:2344-55. [PMID: 27226319 DOI: 10.1242/dev.134577] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/09/2016] [Indexed: 12/14/2022]
Abstract
Cleft palate is a common major birth defect for which currently known causes account for less than 30% of pathology in humans. In this study, we carried out mutagenesis screening in mice to identify new regulators of palatogenesis. Through genetic linkage mapping and whole-exome sequencing, we identified a loss-of-function mutation in the Golgb1 gene that co-segregated with cleft palate in a new mutant mouse line. Golgb1 is a ubiquitously expressed large coiled-coil protein, also known as giantin, that is localized at the Golgi membrane. Using CRISPR/Cas9-mediated genome editing, we generated and analyzed developmental defects in mice carrying additional Golgb1 loss-of-function mutations, which supported a crucial requirement for Golgb1 in palate development. Through maxillary explant culture assays, we demonstrate that the Golgb1 mutant embryos have intrinsic defects in palatal shelf elevation. Just prior to the developmental stage of palatal shelf elevation in wild-type littermates, Golgb1 mutant embryos exhibit increased cell density, reduced hyaluronan accumulation and impaired protein glycosylation in the palatal mesenchyme. Together, these results demonstrate that, although it is a ubiquitously expressed Golgi-associated protein, Golgb1 has specific functions in protein glycosylation and tissue morphogenesis.
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Affiliation(s)
- Yu Lan
- Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Nian Zhang
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Han Liu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jingyue Xu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Rulang Jiang
- Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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11
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Simon MM, Moresco EMY, Bull KR, Kumar S, Mallon AM, Beutler B, Potter PK. Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing. Mamm Genome 2015; 26:486-500. [PMID: 26449678 PMCID: PMC4602060 DOI: 10.1007/s00335-015-9603-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/01/2015] [Indexed: 02/07/2023]
Abstract
Mutagenesis-based screens in mice are a powerful discovery platform to identify novel genes or gene functions associated with disease phenotypes. An N-ethyl-N-nitrosourea (ENU) mutagenesis screen induces single nucleotide variants randomly in the mouse genome. Subsequent phenotyping of mutant and wildtype mice enables the identification of mutated pathways resulting in phenotypes associated with a particular ENU lesion. This unbiased approach to gene discovery conducts the phenotyping with no prior knowledge of the functional mutations. Before the advent of affordable next generation sequencing (NGS), ENU variant identification was a limiting step in gene characterization, akin to ‘finding a needle in a haystack’. The emergence of a reliable reference genome alongside advances in NGS has propelled ENU mutation discovery from an arduous, time-consuming exercise to an effective and rapid form of mutation discovery. This has permitted large mouse facilities worldwide to use ENU for novel mutation discovery in a high-throughput manner, helping to accelerate basic science at the mechanistic level. Here, we describe three different strategies used to identify ENU variants from NGS data and some of the subsequent steps for mutation characterisation.
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Affiliation(s)
- Michelle M Simon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK.
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Katherine R Bull
- Nuffield Department of Medicine and Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK.,MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Saumya Kumar
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Paul K Potter
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
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12
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Tenin G, Clowes C, Wolton K, Krejci E, Wright JA, Lovell SC, Sedmera D, Hentges KE. Erbb2 is required for cardiac atrial electrical activity during development. PLoS One 2014; 9:e107041. [PMID: 25269082 PMCID: PMC4182046 DOI: 10.1371/journal.pone.0107041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 08/13/2014] [Indexed: 01/16/2023] Open
Abstract
The heart is the first organ required to function during embryonic development and is absolutely necessary for embryo survival. Cardiac activity is dependent on both the sinoatrial node (SAN), which is the pacemaker of heart's electrical activity, and the cardiac conduction system which transduces the electrical signal though the heart tissue, leading to heart muscle contractions. Defects in the development of cardiac electrical function may lead to severe heart disorders. The Erbb2 (Epidermal Growth Factor Receptor 2) gene encodes a member of the EGF receptor family of receptor tyrosine kinases. The Erbb2 receptor lacks ligand-binding activity but forms heterodimers with other EGF receptors, stabilising their ligand binding and enhancing kinase-mediated activation of downstream signalling pathways. Erbb2 is absolutely necessary in normal embryonic development and homozygous mouse knock-out Erbb2 embryos die at embryonic day (E)10.5 due to severe cardiac defects. We have isolated a mouse line, l11Jus8, from a random chemical mutagenesis screen, which carries a hypomorphic missense mutation in the Erbb2 gene. Homozygous mutant embryos exhibit embryonic lethality by E12.5-13. The l11Jus8 mutants display cardiac haemorrhage and a failure of atrial function due to defects in atrial electrical signal propagation, leading to an atrial-specific conduction block, which does not affect ventricular conduction. The l11Jus8 mutant phenotype is distinct from those reported for Erbb2 knockout mouse mutants. Thus, the l11Jus8 mouse reveals a novel function of Erbb2 during atrial conduction system development, which when disrupted causes death at mid-gestation.
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Affiliation(s)
- Gennadiy Tenin
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Christopher Clowes
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Kathryn Wolton
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Eliska Krejci
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, and Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | | | - Simon C. Lovell
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - David Sedmera
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, and Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Kathryn E. Hentges
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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13
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Marchal C, Delorme-Hinoux V, Bariat L, Siala W, Belin C, Saez-Vasquez J, Riondet C, Reichheld JP. NTR/NRX define a new thioredoxin system in the nucleus of Arabidopsis thaliana cells. MOLECULAR PLANT 2014; 7:30-44. [PMID: 24253198 DOI: 10.1093/mp/sst162] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Thioredoxins (TRX) are key components of cellular redox balance, regulating many target proteins through thiol/disulfide exchange reactions. In higher plants, TRX constitute a complex multigenic family whose members have been found in almost all cellular compartments. Although chloroplastic and cytosolic TRX systems have been largely studied, the presence of a nuclear TRX system has been elusive for a long time. Nucleoredoxins (NRX) are potential nuclear TRX found in most eukaryotic organisms. In contrast to mammals, which harbor a unique NRX, angiosperms generally possess multiple NRX organized in three subfamilies. Here, we show that Arabidopsis thaliana has two NRX genes (AtNRX1 and AtNRX2), respectively, belonging to subgroups I and III. While NRX1 harbors typical TRX active sites (WCG/PPC), NRX2 has atypical active sites (WCRPC and WCPPF). Nevertheless, both NRX1 and NRX2 have disulfide reduction capacities, although NRX1 alone can be reduced by the thioredoxin reductase NTRA. We also show that both NRX1 and NRX2 have a dual nuclear/cytosolic localization. Interestingly, we found that NTRA, previously identified as a cytosolic protein, is also partially localized in the nucleus, suggesting that a complete TRX system is functional in the nucleus. We show that NRX1 is mainly found as a dimer in vivo. nrx1 and nrx2 knockout mutant plants exhibit no phenotypic perturbations under standard growth conditions. However, the nrx1 mutant shows a reduced pollen fertility phenotype, suggesting a specific role of NRX1 at the haploid phase.
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Affiliation(s)
- Corinne Marchal
- Université Perpignan Via Domitia, CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 58 Avenue Paul Alduy-Bat T, F-66860, Perpignan, France
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14
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Andrews TD, Whittle B, Field MA, Balakishnan B, Zhang Y, Shao Y, Cho V, Kirk M, Singh M, Xia Y, Hager J, Winslade S, Sjollema G, Beutler B, Enders A, Goodnow CC. Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models. Open Biol 2013; 2:120061. [PMID: 22724066 PMCID: PMC3376740 DOI: 10.1098/rsob.120061] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 04/16/2012] [Indexed: 01/17/2023] Open
Abstract
Accurate identification of sparse heterozygous single-nucleotide variants (SNVs) is a critical challenge for identifying the causative mutations in mouse genetic screens, human genetic diseases and cancer. When seeking to identify causal DNA variants that occur at such low rates, they are overwhelmed by false-positive calls that arise from a range of technical and biological sources. We describe a strategy using whole-exome capture, massively parallel DNA sequencing and computational analysis, which identifies with a low false-positive rate the majority of heterozygous and homozygous SNVs arising de novo with a frequency of one nucleotide substitution per megabase in progeny of N-ethyl-N-nitrosourea (ENU)-mutated C57BL/6j mice. We found that by applying a strategy of filtering raw SNV calls against known and platform-specific variants we could call true SNVs with a false-positive rate of 19.4 per cent and an estimated false-negative rate of 21.3 per cent. These error rates are small enough to enable calling a causative mutation from both homozygous and heterozygous candidate mutation lists with little or no further experimental validation. The efficacy of this approach is demonstrated by identifying the causative mutation in the Ptprc gene in a lymphocyte-deficient strain and in 11 other strains with immune disorders or obesity, without the need for meiotic mapping. Exome sequencing of first-generation mutant mice revealed hundreds of unphenotyped protein-changing mutations, 52 per cent of which are predicted to be deleterious, which now become available for breeding and experimental analysis. We show that exome sequencing data alone are sufficient to identify induced mutations. This approach transforms genetic screens in mice, establishes a general strategy for analysing rare DNA variants and opens up a large new source for experimental models of human disease.
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Affiliation(s)
- T D Andrews
- Immunogenomics Laboratory, Australian National University, GPO Box 334, Canberra City, Australian Capital Territory, 2601 , Australia.
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15
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Adams D, Baldock R, Bhattacharya S, Copp AJ, Dickinson M, Greene NDE, Henkelman M, Justice M, Mohun T, Murray SA, Pauws E, Raess M, Rossant J, Weaver T, West D. Bloomsbury report on mouse embryo phenotyping: recommendations from the IMPC workshop on embryonic lethal screening. Dis Model Mech 2013; 6:571-9. [PMID: 23519032 PMCID: PMC3634642 DOI: 10.1242/dmm.011833] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Identifying genes that are important for embryo development is a crucial first step towards understanding their many functions in driving the ordered growth, differentiation and organogenesis of embryos. It can also shed light on the origins of developmental disease and congenital abnormalities. Current international efforts to examine gene function in the mouse provide a unique opportunity to pinpoint genes that are involved in embryogenesis, owing to the emergence of embryonic lethal knockout mutants. Through internationally coordinated efforts, the International Knockout Mouse Consortium (IKMC) has generated a public resource of mouse knockout strains and, in April 2012, the International Mouse Phenotyping Consortium (IMPC), supported by the EU InfraCoMP programme, convened a workshop to discuss developing a phenotyping pipeline for the investigation of embryonic lethal knockout lines. This workshop brought together over 100 scientists, from 13 countries, who are working in the academic and commercial research sectors, including experts and opinion leaders in the fields of embryology, animal imaging, data capture, quality control and annotation, high-throughput mouse production, phenotyping, and reporter gene analysis. This article summarises the outcome of the workshop, including (1) the vital scientific importance of phenotyping embryonic lethal mouse strains for basic and translational research; (2) a common framework to harmonise international efforts within this context; (3) the types of phenotyping that are likely to be most appropriate for systematic use, with a focus on 3D embryo imaging; (4) the importance of centralising data in a standardised form to facilitate data mining; and (5) the development of online tools to allow open access to and dissemination of the phenotyping data.
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Affiliation(s)
- David Adams
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | | | | | - Andrew J. Copp
- UCL Institute of Child Health, Gower Street, London, WC1E 6BT, UK
| | | | | | | | | | - Timothy Mohun
- MRC National Institute for Medical Research, London, NW7 1AA, UK
| | | | - Erwin Pauws
- UCL Institute of Child Health, Gower Street, London, WC1E 6BT, UK
| | - Michael Raess
- Helmholtz Zentrum Munich and Infrafrontier, Ingolstädter Landstraße 1 85764 Neuherberg, Munich, Germany
| | | | - Tom Weaver
- MRC Harwell, Harwell Science and Innovation Campus, Oxford, OX11 0RD, UK
| | - David West
- CHORI, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA
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16
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Lossie AC, Lo CL, Baumgarner KM, Cramer MJ, Garner JP, Justice MJ. ENU mutagenesis reveals that Notchless homolog 1 (Drosophila) affects Cdkn1a and several members of the Wnt pathway during murine pre-implantation development. BMC Genet 2012; 13:106. [PMID: 23231322 PMCID: PMC3558363 DOI: 10.1186/1471-2156-13-106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 11/24/2012] [Indexed: 01/20/2023] Open
Abstract
Background Our interests lie in determining the genes and genetic pathways that are important for establishing and maintaining maternal-fetal interactions during pregnancy. Mutation analysis targeted to a 34 Mb domain flanked by Trp53 and Wnt3 demonstrates that this region of mouse chromosome 11 contains a large number of essential genes. Two mutant alleles (l11Jus1 and l11Jus4), which fall into the same complementation group, survive through implantation but fail prior to gastrulation. Results Through a positional cloning strategy, we discovered that these homozygous mutant alleles contain non-conservative missense mutations in the Notchless homolog 1 (Drosophila) (Nle1) gene. NLE1 is a member of the large WD40-repeat protein family, and is thought to signal via the canonical NOTCH pathway in vertebrates. However, the phenotype of the Nle1 mutant mice is much more severe than single Notch receptor mutations or even in animals in which NOTCH signaling is blocked. To test the hypothesis that NLE1 functions in multiple signaling pathways during pre-implantation development, we examined expression of multiple Notch downstream target genes, as well as select members of the Wnt pathway in wild-type and mutant embryos. We did not detect altered expression of any primary members of the Notch pathway or in Notch downstream target genes. However, our data reveal that Cdkn1a, a NOTCH target, was upregulated in Nle1 mutants, while several members of the Wnt pathway are downregulated. In addition, we found that Nle1 mutant embryos undergo caspase-mediated apoptosis as hatched blastocysts, but not as morulae or blastocysts. Conclusions Taken together, these results uncover potential novel functions for NLE1 in the WNT and CDKN1A pathways during embryonic development in mammals.
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Affiliation(s)
- Amy C Lossie
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA.
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17
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Brown FC, Scott N, Rank G, Collinge JE, Vadolas J, Vickaryous N, Whitelaw N, Whitelaw E, Kile BT, Jane SM, Curtis DJ. ENU mutagenesis identifies the first mouse mutants reproducing human β-thalassemia at the genomic level. Blood Cells Mol Dis 2012; 50:86-92. [PMID: 23040355 DOI: 10.1016/j.bcmd.2012.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 09/11/2012] [Indexed: 12/24/2022]
Abstract
Forward genetic screens have been performed in many species to identify phenotypes in specific organ systems. We have undertaken a large-scale N-ethyl-N-nitrosourea (ENU) mutagenesis screen to identify dominant mutations that perturb erythropoiesis in mice. Mutant mice that displayed an erythrocyte mean cell volume (MCV) greater than three standard deviations from the population mean were identified. Two of these lines, RBC13 and RBC14, displayed a hypochromic, microcytic anemia, accompanied by a marked reticulocytosis, splenomegaly and diminished red cell survival. Timed pregnancies from heterozygous intercrosses revealed that a quarter of the embryos displayed severe anemia and did not survive beyond embryonic day (E) 18.5, consistent with homozygous β-thalassemia. Genetic complementation studies with a β-thalassemia mouse line reproduced the embryonic lethality in compound heterozygotes and a genomic custom capture array and massively parallel sequencing of the β-globin locus identified the causative mutations. The RBC13 line displayed a nonsense mutation at codon 40 in exon 2 of the β-major gene, invoking parallels with the common β(0)39 thalassemia mutation seen in humans. The RBC14 line exhibited a mutation at the polyadenylation signal of the β-major gene, exactly replicating a human β-thalassemia mutation. The RBC13 and RBC14 lines are the first β-thalassemia mouse models that reproduce human β-thalassemia at the genomic level, and as such highlight the power of ENU mutagenesis screens in generating mouse models of human disease.
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Affiliation(s)
- Fiona C Brown
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia
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18
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Smith CL, Eppig JT. The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. Mamm Genome 2012; 23:653-68. [PMID: 22961259 PMCID: PMC3463787 DOI: 10.1007/s00335-012-9421-3] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/24/2012] [Indexed: 01/16/2023]
Abstract
The Mammalian Phenotype Ontology (MP) is a structured vocabulary for describing mammalian phenotypes and serves as a critical tool for efficient annotation and comprehensive retrieval of phenotype data. Importantly, the ontology contains broad and specific terms, facilitating annotation of data from initial observations or screens and detailed data from subsequent experimental research. Using the ontology structure, data are retrieved inclusively, i.e., data annotated to chosen terms and to terms subordinate in the hierarchy. Thus, searching for "abnormal craniofacial morphology" also returns annotations to "megacephaly" and "microcephaly," more specific terms in the hierarchy path. The development and refinement of the MP is ongoing, with new terms and modifications to its organization undergoing continuous assessment as users and expert reviewers propose expansions and revisions. A wealth of phenotype data on mouse mutations and variants annotated to the MP already exists in the Mouse Genome Informatics database. These data, along with data curated to the MP by many mouse mutagenesis programs and mouse repositories, provide a platform for comparative analyses and correlative discoveries. The MP provides a standard underpinning to mouse phenotype descriptions for existing and future experimental and large-scale phenotyping projects. In this review we describe the MP as it presently exists, its application to phenotype annotations, the relationship of the MP to other ontologies, and the integration of the MP within large-scale phenotyping projects. Finally we discuss future application of the MP in providing standard descriptors of the phenotype pipeline test results from the International Mouse Phenotype Consortium projects.
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19
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High throughput sequencing approaches to mutation discovery in the mouse. Mamm Genome 2012; 23:499-513. [PMID: 22991087 DOI: 10.1007/s00335-012-9424-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/19/2012] [Indexed: 12/19/2022]
Abstract
Phenotype-driven approaches in mice are powerful strategies for the discovery of genes and gene functions and for unravelling complex biological mechanisms. Traditional methods for mutation discovery are reliable and robust, but they can also be laborious and time consuming. Recently, high-throughput sequencing (HTS) technologies have revolutionised the process of forward genetics in mice by paving the way to rapid mutation discovery. However, successful application of HTS for mutation discovery relies heavily on the sequencing approach employed and strategies for data analysis. Here we review current HTS applications and resources for mutation discovery and provide an overview of the practical considerations for HTS implementation and data analysis.
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20
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Abstract
Identifying genes involved in behavioural disorders in man is a challenge as the cause is often multigenic and the phenotype is modulated by environmental cues. Mouse mutants are a valuable tool for identifying novel pathways underlying specific neurological phenotypes and exploring the influence both genetic and non-genetic factors. Many human variants causing behavioural disorders are not gene deletions but changes in levels of expression or activity of a gene product; consequently, large-scale mouse ENU mutagenesis has the advantage over the study of null mutants in that it generates a range of point mutations that frequently mirror the subtlety and heterogeneity of human genetic lesions. ENU mutants have provided novel and clinically relevant functional information on genes that influence many aspects of mammalian behaviour, from neuropsychiatric endophenotypes to circadian rhythms. This review will highlight some of the most important findings that have been made using this method in several key areas of neurological disease research.
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Affiliation(s)
- Peter L Oliver
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
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21
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Weiss J, Hurley LA, Harris RM, Finlayson C, Tong M, Fisher LA, Moran JL, Beier DR, Mason C, Jameson JL. ENU mutagenesis in mice identifies candidate genes for hypogonadism. Mamm Genome 2012; 23:346-55. [PMID: 22258617 PMCID: PMC3358541 DOI: 10.1007/s00335-011-9388-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 12/31/2011] [Indexed: 12/17/2022]
Abstract
Genome-wide mutagenesis was performed in mice to identify candidate genes for male infertility, for which the predominant causes remain idiopathic. Mice were mutagenized using N-ethyl-N-nitrosourea (ENU), bred, and screened for phenotypes associated with the male urogenital system. Fifteen heritable lines were isolated and chromosomal loci were assigned using low-density genome-wide SNP arrays. Ten of the 15 lines were pursued further using higher-resolution SNP analysis to narrow the candidate gene regions. Exon sequencing of candidate genes identified mutations in mice with cystic kidneys (Bicc1), cryptorchidism (Rxfp2), restricted germ cell deficiency (Plk4), and severe germ cell deficiency (Prdm9). In two other lines with severe hypogonadism, candidate sequencing failed to identify mutations, suggesting defects in genes with previously undocumented roles in gonadal function. These genomic intervals were sequenced in their entirety and a candidate mutation was identified in SnrpE in one of the two lines. The line harboring the SnrpE variant retains substantial spermatogenesis despite small testis size, an unusual phenotype. In addition to the reproductive defects, heritable phenotypes were observed in mice with ataxia (Myo5a), tremors (Pmp22), growth retardation (unknown gene), and hydrocephalus (unknown gene). These results demonstrate that the ENU screen is an effective tool for identifying potential causes of male infertility.
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Affiliation(s)
- Jeffrey Weiss
- Division of Endocrinology, Department of Medicine, Northwestern University Feinberg School of Medicine, 303 E. Superior Street, Chicago, IL 60611, USA.
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22
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Davisson MT, Bergstrom DE, Reinholdt LG, Donahue LR. Discovery Genetics - The History and Future of Spontaneous Mutation Research. ACTA ACUST UNITED AC 2012; 2:103-118. [PMID: 25364627 DOI: 10.1002/9780470942390.mo110200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Historically, spontaneous mutations in mice have served as valuable models of heritable human diseases, contributing substantially to our understanding of both disease mechanisms and basic biological pathways. While advances in molecular technologies have improved our ability to create mouse models of human disease through targeted mutagenesis and transgenesis, spontaneous mutations continue to provide valuable research tools for discovery of novel genes and functions. In addition, the genetic defects caused by spontaneous mutations are molecularly similar to mutations in the human genome and, therefore often produce phenotypes that more closely resemble those characteristic of human disease than do genetically engineered mutations. Due to the rarity with which spontaneous mutations arise and the animal intensive nature of their genetic analysis, large-scale spontaneous mutation analysis has traditionally been limited to large mammalian genetics institutes. More recently, ENU mutagenesis and new screening methods have increased the rate of mutant strain discovery, and high-throughput DNA sequencing has enabled rapid identification of the underlying genes and their causative mutations. Here, we discuss the continued value of spontaneous mutations for biomedical research.
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Fenner D, Odili S, Hong HK, Kobayashi Y, Kohsaka A, Siepka SM, Vitaterna MH, Chen P, Zelent B, Grimsby J, Takahashi JS, Matschinsky FM, Bass J. Generation of N-ethyl-N-nitrosourea (ENU) diabetes models in mice demonstrates genotype-specific action of glucokinase activators. J Biol Chem 2011; 286:39560-72. [PMID: 21921030 PMCID: PMC3234779 DOI: 10.1074/jbc.m111.269100] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 08/16/2011] [Indexed: 11/06/2022] Open
Abstract
We performed genome-wide mutagenesis in C57BL/6J mice using N-ethyl-N-nitrosourea to identify mutations causing high blood glucose early in life and to produce new animal models of diabetes. Of a total of 13 new lines confirmed by heritability testing, we identified two semi-dominant pedigrees with novel missense mutations (Gck(K140E) and Gck(P417R)) in the gene encoding glucokinase (Gck), the mammalian glucose sensor that is mutated in human maturity onset diabetes of the young type 2 and the target of emerging anti-hyperglycemic agents that function as glucokinase activators (GKAs). Diabetes phenotype corresponded with genotype (mild-to-severe: Gck(+/+) < Gck(P417R/+), Gck(K140E)(/+) < Gck(P417R/P417R), Gck(P417R/K140E), and Gck(K140E/K140E)) and with the level of expression of GCK in liver. Each mutant was produced as the recombinant enzyme in Escherichia coli, and analysis of k(cat) and tryptophan fluorescence (I(320/360)) during thermal shift unfolding revealed a correlation between thermostability and the severity of hyperglycemia in the whole animal. Disruption of the glucokinase regulatory protein-binding site (GCK(K140E)), but not the ATP binding cassette (GCK(P417R)), prevented inhibition of enzyme activity by glucokinase regulatory protein and corresponded with reduced responsiveness to the GKA drug. Surprisingly, extracts from liver of diabetic GCK mutants inhibited activity of the recombinant enzyme, a property that was also observed in liver extracts from mice with streptozotocin-induced diabetes. These results indicate a relationship between genotype, phenotype, and GKA efficacy. The integration of forward genetic screening and biochemical profiling opens a pathway for preclinical development of mechanism-based diabetes therapies.
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Affiliation(s)
- Deborah Fenner
- From the Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
- the Department of Neurobiology and Physiology and
| | - Stella Odili
- the Department of Biochemistry and Biophysics, Children's Hospital of Pennsylvania and Diabetes Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Hee-Kyung Hong
- the Department of Neurobiology and Physiology and
- the Center for Sleep and Circadian Biology, Northwestern University, Evanston, Illinois 60208
| | - Yumiko Kobayashi
- From the Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
- the Department of Neurobiology and Physiology and
| | - Akira Kohsaka
- the Department of Neurobiology and Physiology and
- the Departments of Medicine and Physiology II, Wakayama Medical University, Wakayama City, 640-8265, Japan
| | - Sandra M. Siepka
- the Department of Neurobiology and Physiology and
- the Center for Sleep and Circadian Biology, Northwestern University, Evanston, Illinois 60208
| | - Martha H. Vitaterna
- the Department of Neurobiology and Physiology and
- the Center for Sleep and Circadian Biology, Northwestern University, Evanston, Illinois 60208
| | - Pan Chen
- the Department of Biochemistry and Biophysics, Children's Hospital of Pennsylvania and Diabetes Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Bogumil Zelent
- the Department of Biochemistry and Biophysics, Children's Hospital of Pennsylvania and Diabetes Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Joseph Grimsby
- the Department of Metabolic Diseases, Hoffmann-La Roche, Nutley, New Jersey 07110
| | - Joseph S. Takahashi
- the Department of Neurobiology and Physiology and
- the Department of Neuroscience and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, and
| | - Franz M. Matschinsky
- the Department of Biochemistry and Biophysics, Children's Hospital of Pennsylvania and Diabetes Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Joseph Bass
- From the Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
- the Department of Neurobiology and Physiology and
- the Center for Sleep and Circadian Biology, Northwestern University, Evanston, Illinois 60208
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Fairfield H, Gilbert GJ, Barter M, Corrigan RR, Curtain M, Ding Y, D'Ascenzo M, Gerhardt DJ, He C, Huang W, Richmond T, Rowe L, Probst FJ, Bergstrom DE, Murray SA, Bult C, Richardson J, Kile BT, Gut I, Hager J, Sigurdsson S, Mauceli E, Di Palma F, Lindblad-Toh K, Cunningham ML, Cox TC, Justice MJ, Spector MS, Lowe SW, Albert T, Donahue LR, Jeddeloh J, Shendure J, Reinholdt LG. Mutation discovery in mice by whole exome sequencing. Genome Biol 2011; 12:R86. [PMID: 21917142 PMCID: PMC3308049 DOI: 10.1186/gb-2011-12-9-r86] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 08/04/2011] [Accepted: 09/14/2011] [Indexed: 01/18/2023] Open
Abstract
We report the development and optimization of reagents for in-solution, hybridization-based capture of the mouse exome. By validating this approach in a multiple inbred strains and in novel mutant strains, we show that whole exome sequencing is a robust approach for discovery of putative mutations, irrespective of strain background. We found strong candidate mutations for the majority of mutant exomes sequenced, including new models of orofacial clefting, urogenital dysmorphology, kyphosis and autoimmune hepatitis.
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Affiliation(s)
| | | | - Mary Barter
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Rebecca R Corrigan
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza R804, Houston, Texas 77030, USA
| | | | - Yueming Ding
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | | | | | - Chao He
- National Center for Genome Analysis (CNAG), Parc Científic de Barcelona, Torre I, Baldiri Reixac, 408028 Barcelona, Spain
| | - Wenhui Huang
- Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | | | - Lucy Rowe
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Frank J Probst
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza R804, Houston, Texas 77030, USA
| | | | | | - Carol Bult
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Joel Richardson
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Benjamin T Kile
- University of Washington, Department of Pediatrics, Division of Craniofacial Medicine and Seattle Children's Craniofacial Center, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Ivo Gut
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Jorg Hager
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Snaevar Sigurdsson
- Broad Institute of Massachusetts Institute of Technology and Harvard, 5 Cambridge Center, Cambridge, MA 02142, USA
| | - Evan Mauceli
- Broad Institute of Massachusetts Institute of Technology and Harvard, 5 Cambridge Center, Cambridge, MA 02142, USA
| | - Federica Di Palma
- Broad Institute of Massachusetts Institute of Technology and Harvard, 5 Cambridge Center, Cambridge, MA 02142, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of Massachusetts Institute of Technology and Harvard, 5 Cambridge Center, Cambridge, MA 02142, USA
| | - Michael L Cunningham
- University of Washington, Department of Genome Sciences, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle, WA 98195-5065, USA
| | - Timothy C Cox
- University of Washington, Department of Genome Sciences, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle, WA 98195-5065, USA
| | - Monica J Justice
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza R804, Houston, Texas 77030, USA
| | - Mona S Spector
- National Center for Genome Analysis (CNAG), Parc Científic de Barcelona, Torre I, Baldiri Reixac, 408028 Barcelona, Spain
| | - Scott W Lowe
- National Center for Genome Analysis (CNAG), Parc Científic de Barcelona, Torre I, Baldiri Reixac, 408028 Barcelona, Spain
| | | | | | | | - Jay Shendure
- University of Washington, Department of Genome Sciences, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle, WA 98195-5065, USA
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Samuels ME. Saturation of the human phenome. Curr Genomics 2011; 11:482-99. [PMID: 21532833 PMCID: PMC3048311 DOI: 10.2174/138920210793175886] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2010] [Revised: 06/22/2010] [Accepted: 06/22/2010] [Indexed: 12/26/2022] Open
Abstract
The phenome is the complete set of phenotypes resulting from genetic variation in populations of an organism. Saturation of a phenome implies the identification and phenotypic description of mutations in all genes in an organism, potentially constrained to those encoding proteins. The human genome is believed to contain 20-25,000 protein coding genes, but only a small fraction of these have documented mutant phenotypes, thus the human phenome is far from complete. In model organisms, genetic saturation entails the identification of multiple mutant alleles of a gene or locus, allowing a consistent description of mutational phenotypes for that gene. Saturation of several model organisms has been attempted, usually by targeting annotated coding genes with insertional transposons (Drosophila melanogaster, Mus musculus) or by sequence directed deletion (Saccharomyces cerevisiae) or using libraries of antisense oligonucleotide probes injected directly into animals (Caenorhabditis elegans, Danio rerio). This paper reviews the general state of the human phenome, and discusses theoretical and practical considerations toward a saturation analysis in humans. Throughout, emphasis is placed on high penetrance genetic variation, of the kind typically asociated with monogenic versus complex traits.
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Affiliation(s)
- Mark E Samuels
- Centre de Recherche de Ste-Justine, 3175, Côte Ste-Catherine, Montréal QC H3T 1C5, Canada
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Dettman E, Simko SJ, Ayanga B, Carofino B, Margolin J, Morse HC, Justice MJ. Prdm14 initiates lymphoblastic leukemia after expanding a population of cells resembling common lymphoid progenitors. Oncogene 2011; 30:2859-73. [PMID: 21339739 PMCID: PMC3121925 DOI: 10.1038/onc.2011.12] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 11/23/2010] [Accepted: 01/06/2011] [Indexed: 12/17/2022]
Abstract
Understanding the heterogeneous genetic mechanisms of tumor initiation in lymphoid leukemias (LL) will lead to improvements in prognostic classification and treatment regimens. In previous studies of mouse leukemias, we showed that retroviral insertion at the ecotropic viral insertion site 32 locus leads to increased expression of Prdm14, a pluripotency gene implicated in the self-renewal capacity of embryonic stem cells and the early stages of breast cancer. Here, we show that PRDM14 is also overexpressed in ∼25% of human lymphoid neoplasms, with increased frequencies in T-cell acute LL and hyperdiploid precursor B-cell acute LL. To test if Prdm14 overexpression could initiate leukemia, mice were transduced with bone marrow cells transfected with a Prdm14 expression vector. LLs developed in 96% of female mice and 42% of male mice. Before the onset of leukemia, differentiation of transduced cells was biased up to 1000-fold toward cells with features of common lymphoid progenitors (CLPs), and lymphoid differentiation showed a relative block at the pro-B stage. Microarray gene expression analysis of expanded CLP-like cells before the onset of leukemia demonstrated upregulation of genes involved in pluripotency, tumor initiation, early B-lineage commitment, Wnt/Ras signaling and the epithelial-to-mesenchymal transition. Among the dysregulated genes were imprinted genes and non-coding RNAs including Dlk1 and Meg3, which are also key pluripotency mediators. Heightened expression of the estrogen-dependent oncogene, Myb, in tumors suggests a basis for the increased frequency of cancer in female mice. These data provide the first direct evidence for the association of Prdm14 with cancer initiation in an in vivo mouse model and in human lymphoid malignancies, while suggesting mechanisms for Prdm14's mode of action.
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Affiliation(s)
- E.J. Dettman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Stephen J. Simko
- Department of Pediatrics, Section of Hematology and Oncology, Baylor College of Medicine, Houston, Texas
| | - Bernard Ayanga
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Brandi Carofino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Judith Margolin
- Department of Pediatrics, Section of Hematology and Oncology, Baylor College of Medicine, Houston, Texas
| | - Herbert C. Morse
- Laboratory of Immunopathology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Monica J. Justice
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
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Generation of N-ethyl-N-nitrosourea-induced mouse mutants with deviations in hematological parameters. Mamm Genome 2011; 22:495-505. [PMID: 21553221 DOI: 10.1007/s00335-011-9328-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 04/14/2011] [Indexed: 12/31/2022]
Abstract
Research on hematological disorders relies on suitable animal models. We retrospectively evaluated the use of the hematological parameters hematocrit (HCT), hemoglobin (HGB), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), mean corpuscular volume (MCV), red blood cell count (RBC), white blood cell count (WBC), and platelet count (PLT) in the phenotype-driven Munich N-ethyl-N-nitrosourea (ENU) mouse mutagenesis project as parameters for the generation of novel animal models for human diseases. The analysis was carried out on more than 16,000 G1 and G3 offspring of chemically mutagenized inbred C3H mice to detect dominant and recessive mutations leading to deviations in the levels of the chosen parameters. Identification of animals exhibiting altered values and transmission of the phenotypic deviations to the subsequent generations led to the successful establishment of mutant lines for the parameters MCV, RBC, and PLT. Analysis of the causative mutation was started in selected lines, thereby revealing a novel mutation in the transferrin receptor gene (Tfrc) in one line. Thus, novel phenotype-driven mouse models were established to analyze the genetic components of hematological disorders.
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Dwyer ND, Manning DK, Moran JL, Mudbhary R, Fleming MS, Favero CB, Vock VM, O'Leary DDM, Walsh CA, Beier DR. A forward genetic screen with a thalamocortical axon reporter mouse yields novel neurodevelopment mutants and a distinct emx2 mutant phenotype. Neural Dev 2011; 6:3. [PMID: 21214893 PMCID: PMC3024922 DOI: 10.1186/1749-8104-6-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 01/07/2011] [Indexed: 12/02/2022] Open
Abstract
Background The dorsal thalamus acts as a gateway and modulator for information going to and from the cerebral cortex. This activity requires the formation of reciprocal topographic axon connections between thalamus and cortex. The axons grow along a complex multistep pathway, making sharp turns, crossing expression boundaries, and encountering intermediate targets. However, the cellular and molecular components mediating these steps remain poorly understood. Results To further elucidate the development of the thalamocortical system, we first created a thalamocortical axon reporter line to use as a genetic tool for sensitive analysis of mutant mouse phenotypes. The TCA-tau-lacZ reporter mouse shows specific, robust, and reproducible labeling of thalamocortical axons (TCAs), but not the overlapping corticothalamic axons, during development. Moreover, it readily reveals TCA pathfinding abnormalities in known cortical mutants such as reeler. Next, we performed an unbiased screen for genes involved in thalamocortical development using random mutagenesis with the TCA reporter. Six independent mutant lines show aberrant TCA phenotypes at different steps of the pathway. These include ventral misrouting, overfasciculation, stalling at the corticostriatal boundary, and invasion of ectopic cortical cell clusters. An outcross breeding strategy coupled with a genomic panel of single nucleotide polymorphisms facilitated genetic mapping with small numbers of mutant mice. We mapped a ventral misrouting mutant to the Emx2 gene, and discovered that some TCAs extend to the olfactory bulbs in this mutant. Mapping data suggest that other lines carry mutations in genes not previously known for roles in thalamocortical development. Conclusions These data demonstrate the feasibility of a forward genetic approach to understanding mammalian brain morphogenesis and wiring. A robust axonal reporter enabled sensitive analysis of a specific axon tract inside the mouse brain, identifying mutant phenotypes at multiple steps of the pathway, and revealing a new aspect of the Emx2 mutant. The phenotypes highlight vulnerable choice points and latent tendencies of TCAs, and will lead to a refined understanding of the elements and interactions required to form the thalamocortical system. See Commentary: http://www.biomedcentral.com/1741-7007/9/1
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Affiliation(s)
- Noelle D Dwyer
- Howard Hughes Medical Institute, Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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Ching YH, Munroe RJ, Moran JL, Barker AK, Mauceli E, Fennell T, Dipalma F, Lindblad-Toh K, Abcunas LM, Gilmour JF, Harris TP, Kloet SL, Luo Y, McElwee JL, Mu W, Park HK, Rogal DL, Schimenti KJ, Shen L, Shindo M, Shou JY, Stenson EK, Stover PJ, Schimenti JC. High resolution mapping and positional cloning of ENU-induced mutations in the Rw region of mouse chromosome 5. BMC Genet 2010; 11:106. [PMID: 21118569 PMCID: PMC3009607 DOI: 10.1186/1471-2156-11-106] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 11/30/2010] [Indexed: 01/02/2023] Open
Abstract
Background Forward genetic screens in mice provide an unbiased means to identify genes and other functional genetic elements in the genome. Previously, a large scale ENU mutagenesis screen was conducted to query the functional content of a ~50 Mb region of the mouse genome on proximal Chr 5. The majority of phenotypic mutants recovered were embryonic lethals. Results We report the high resolution genetic mapping, complementation analyses, and positional cloning of mutations in the target region. The collection of identified alleles include several with known or presumed functions for which no mutant models have been reported (Tbc1d14, Nol14, Tyms, Cad, Fbxl5, Haus3), and mutations in genes we or others previously reported (Tapt1, Rest, Ugdh, Paxip1, Hmx1, Otoe, Nsun7). We also confirmed the causative nature of a homeotic mutation with a targeted allele, mapped a lethal mutation to a large gene desert, and localized a spermiogenesis mutation to a region in which no annotated genes have coding mutations. The mutation in Tbc1d14 provides the first implication of a critical developmental role for RAB-GAP-mediated protein transport in early embryogenesis. Conclusion This collection of alleles contributes to the goal of assigning biological functions to all known genes, as well as identifying novel functional elements that would be missed by reverse genetic approaches.
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Affiliation(s)
- Yung-Hao Ching
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
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Funato Y, Terabayashi T, Sakamoto R, Okuzaki D, Ichise H, Nojima H, Yoshida N, Miki H. Nucleoredoxin Sustains Wnt/β-Catenin Signaling by Retaining a Pool of Inactive Dishevelled Protein. Curr Biol 2010; 20:1945-52. [DOI: 10.1016/j.cub.2010.09.065] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 09/10/2010] [Accepted: 09/29/2010] [Indexed: 10/18/2022]
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Beier DR. New genetic resources for mammalian developmental biologists. F1000 BIOLOGY REPORTS 2010; 2:72. [PMID: 21173845 PMCID: PMC2989628 DOI: 10.3410/b2-72] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The utilization of homologous recombination in embryonic stem cells as a means to generate mice carrying pre-determined modifications of genomic sequences has revolutionized the study of developmental biology. Recognizing the potential efficiencies that can be obtained by high-throughput production at centralized technology centers, a number of large-scale efforts for generating mice with targeted mutations have been funded. These programs are reaching fruition, and a variety of libraries of embryonic stem cells with defined mutations are now available.
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Affiliation(s)
- David R Beier
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School New Research Building 77 Avenue Louis Pasteur, Boston, MA 02115 USA
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Abstract
Numerous studies indicate that reactive oxygen species (ROS) are not merely cellular by-products of respiration, but are able to modulate various signalling pathways and play certain physiological roles. Recent studies have revealed the importance of translating ROS-generation to activation/suppression of specific signalling pathways. The Wnt signalling pathway, which is essential for early development and stem cell maintenance, is also regulated by ROS. A thioredoxin-related protein, nucleoredoxin (NRX), governs ROS-stimulated Wnt signalling in a temporal manner. NRX usually interacts with Dishevelled (Dvl), an essential adaptor protein for Wnt signalling, and blocks the activation of the Wnt pathway. Oxidative stress causes dissociation of NRX from Dvl, which enables Dvl to activate the downstream Wnt signalling pathway. This study also presents the latest research findings on NRX and its related molecules.
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Affiliation(s)
- Yosuke Funato
- Laboratory of Intracellular Signaling, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Mykles DL, Ghalambor CK, Stillman JH, Tomanek L. Grand Challenges in Comparative Physiology: Integration Across Disciplines and Across Levels of Biological Organization. Integr Comp Biol 2010; 50:6-16. [DOI: 10.1093/icb/icq015] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Abstract
The generation and analysis of germline mutations in the mouse is one of the cornerstones of modern biological research. The chemical supermutagen N-ethyl-N-nitrosourea (ENU) is the most potent known mouse mutagen and can be used to generate point mutations throughout the mouse genome. The progeny of ENU-mutagenized males can be screened for autosomal dominant phenotypes, or they can be used to generate multigeneration pedigrees to screen for autosomal recessive traits. The introduction of balancer chromosomes into the breeding scheme can allow for the selective capture of mutations in a specific chromosomal region. More recent work has demonstrated that the use of animals that already have a mutation of interest can lead to the successful isolation of additional mutations that modify the original mutant phenotype. Further, modern molecular techniques ensure that mutations can be readily identified. We describe here the procedures for mutagenizing male mice with ENU and explain the various types of screens that can be performed for different kinds of induced mutations. The currently published research on ENU mutagenesis in the mouse has only scratched the surface of what is possible with this powerful technique, and further work is certain to deepen our knowledge of the role of the individual components of the mouse genome and the myriad relationships between them.
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Affiliation(s)
- Frank J Probst
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Abstract
In the past decade, forward genetic screens in the mouse have come into their own as a practical method for exploring the genetic basis of many biological processes. By looking directly for disruption in a process of interest, genetic screens have always been powerful, but completion of the genome sequence has made mouse forward genetic screens practical, as well. The sequenced genome means we can map and sequence more efficiently than before, so small focused screens are now within the reach of even small labs. N-Ethyl-N-nitrosourea (ENU) is the preferred mutagen in forward genetic screens, because it is extremely potent in the premeiotic male germ line, where it induces point mutations. This last point is crucial, as point mutations lead to all classes of mutations (e.g., null, hypomorphs, neomorphs, antimorphs, and hypermorphs), which is why forward genetic screens can implicate a gene in a particular process when a targeted deletion may not. Point mutations often mimic human disease states, yielding highly relevant animal models. Since mammals reproduce, lactate, behave, develop, and protect themselves from infection differently from other vertebrates, mammalian forward genetic screens are uniquely informative. In fact, in the past decade, forward genetics has uncovered mutations demonstrating that certain genes exist only in mammals, that specific mechanisms function only in mammals, and that particular biological processes may exist only in mammals; hence screens focused on these processes have identified unsuspected genes. As powerful as the approach is, forward genetics remains a method for the committed; the process of screening requires organization and tenacity. This chapter is intended to help those who are ready to make the commitment by providing practical advice. To this end I detail the issues surrounding screen design and screen execution, as well as mutation identification and confirmation.
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Affiliation(s)
- Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
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Abstract
The use of mutagenesis in invertebrates to generate phenotypic variants has a long and productive history. Despite the conclusive demonstration by Russell and colleagues in the 1970s that the chemical N-ethyl-N-nitrosourea (ENU) is a highly effective mutagen in mice, the application of phenotypic-driven mutagenesis as a method to study mammalian biology proceeded slowly. With the development of tools for genomic analysis, the task of positional cloning ENU-induced mutations has become quite feasible, and this approach has recently been widely applied and highly productive. It has specifically lived up to its theoretical utility as means to provide insight into the biological roles of genes that is not biased by presumptions of their function. While the power of this approach is indisputable, the effort necessary for its success remains substantial, requiring careful attention to aspects including ENU treatment, mouse husbandry, screen assay design, genetic mapping, positional cloning, and mutation validation. In this chapter we discuss practical aspects of implementing a phenotype-driven analysis of an ENU-mutagenized mouse population.
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