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Meadows JRS, Kidd JM, Wang GD, Parker HG, Schall PZ, Bianchi M, Christmas MJ, Bougiouri K, Buckley RM, Hitte C, Nguyen AK, Wang C, Jagannathan V, Niskanen JE, Frantz LAF, Arumilli M, Hundi S, Lindblad-Toh K, Ginja C, Agustina KK, André C, Boyko AR, Davis BW, Drögemüller M, Feng XY, Gkagkavouzis K, Iliopoulos G, Harris AC, Hytönen MK, Kalthof DC, Liu YH, Lymberakis P, Poulakakis N, Pires AE, Racimo F, Ramos-Almodovar F, Savolainen P, Venetsani S, Tammen I, Triantafyllidis A, vonHoldt B, Wayne RK, Larson G, Nicholas FW, Lohi H, Leeb T, Zhang YP, Ostrander EA. Author Correction: Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biol 2023; 24:255. [PMID: 37936157 PMCID: PMC10631033 DOI: 10.1186/s13059-023-03101-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Affiliation(s)
- Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden.
| | - Jefrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA.
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Katia Bougiouri
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Reuben M Buckley
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Christophe Hitte
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Julia E Niskanen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Laurent A F Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E14NS, UK and Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, D-80539, Munich, Germany
| | - Meharji Arumilli
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Sruthi Hundi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catarina Ginja
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | | | - Catherine André
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Xin-Yao Feng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Konstantinos Gkagkavouzis
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Giorgos Iliopoulos
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Alexander C Harris
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Daniela C Kalthof
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Petros Lymberakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Nikolaos Poulakakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Ana Elisabete Pires
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | - Fernando Racimo
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | | | - Peter Savolainen
- Department of Gene Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, 17121, Solna, Sweden
| | - Semina Venetsani
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Imke Tammen
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Alexandros Triantafyllidis
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-7246, USA
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3TG, UK
| | - Frank W Nicholas
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA.
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Littlejohn MD, Sneddon N, Dittmer K, Keehan M, Stephen M, Drögemüller M, Garrick D. A frameshift-deletion mutation in Reelin causes cerebellar hypoplasia in White Swiss Shepherd dogs. Anim Genet 2023; 54:632-636. [PMID: 37334487 DOI: 10.1111/age.13336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/20/2023]
Abstract
Cerebellar hypoplasia is a heterogeneous neurological condition in which the cerebellum is smaller than usual or not completely developed. The condition can have genetic origins, with Mendelian-effect mutations described in several mammalian species. Here, we describe a genetic investigation of cerebellar hypoplasia in White Swiss Shepherd dogs, where two affected puppies were identified from a litter with a recent common ancestor on both sides of their pedigree. Whole genome sequencing was conducted for 10 dogs in this family, and filtering of these data based on a recessive transmission hypothesis highlighted five protein-altering candidate variants - including a frameshift-deletion of the Reelin (RELN) gene (p.Val947*). Given the status of RELN as a gene responsible for cerebellar hypoplasia in humans, sheep and mice, these data strongly suggest the loss-of-function variant as underlying these effects. This variant has not been found in other dog breeds nor in a cohort of European White Swiss Shepherds, suggesting a recent mutation event. This finding will support the genotyping of a more diverse sample of dogs, and should aid future management of the harmful allele through optimised mating schemes.
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Affiliation(s)
- Mathew D Littlejohn
- AL Rae Centre for Genetics and Breeding, Massey University, Hamilton, New Zealand
| | - Nick Sneddon
- AL Rae Centre for Genetics and Breeding, Massey University, Hamilton, New Zealand
| | - Keren Dittmer
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Mike Keehan
- Te Whatu Ora Health New Zealand, Hamilton, New Zealand
| | - Melissa Stephen
- AL Rae Centre for Genetics and Breeding, Massey University, Hamilton, New Zealand
| | | | - Dorian Garrick
- AL Rae Centre for Genetics and Breeding, Massey University, Hamilton, New Zealand
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3
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Niskanen JE, Ohlsson Å, Ljungvall I, Drögemüller M, Ernst RF, Dooijes D, van Deutekom HWM, van Tintelen JP, Snijders Blok CJB, van Vugt M, van Setten J, Asselbergs FW, Petrič AD, Salonen M, Hundi S, Hörtenhuber M, Kere J, Pyle WG, Donner J, Postma AV, Leeb T, Andersson G, Hytönen MK, Häggström J, Wiberg M, Friederich J, Eberhard J, Harakalova M, van Steenbeek FG, Wess G, Lohi H. Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human. Genome Med 2023; 15:73. [PMID: 37723491 PMCID: PMC10506233 DOI: 10.1186/s13073-023-01221-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/17/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is a life-threatening heart disease and a common cause of heart failure due to systolic dysfunction and subsequent left or biventricular dilatation. A significant number of cases have a genetic etiology; however, as a complex disease, the exact genetic risk factors are largely unknown, and many patients remain without a molecular diagnosis. METHODS We performed GWAS followed by whole-genome, transcriptome, and immunohistochemical analyses in a spontaneously occurring canine model of DCM. Canine gene discovery was followed up in three human DCM cohorts. RESULTS Our results revealed two independent additive loci associated with the typical DCM phenotype comprising left ventricular systolic dysfunction and dilatation. We highlight two novel candidate genes, RNF207 and PRKAA2, known for their involvement in cardiac action potentials, energy homeostasis, and morphology. We further illustrate the distinct genetic etiologies underlying the typical DCM phenotype and ventricular premature contractions. Finally, we followed up on the canine discoveries in human DCM patients and discovered candidate variants in our two novel genes. CONCLUSIONS Collectively, our study yields insight into the molecular pathophysiology of DCM and provides a large animal model for preclinical studies.
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Affiliation(s)
- Julia E Niskanen
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Åsa Ohlsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ingrid Ljungvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Robert F Ernst
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Dennis Dooijes
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Hanneke W M van Deutekom
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - J Peter van Tintelen
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Christian J B Snijders Blok
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Marion van Vugt
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Jessica van Setten
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Folkert W Asselbergs
- Amsterdam University Medical Centers, Department of Cardiology, University of Amsterdam, Amsterdam, The Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | | | - Milla Salonen
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Sruthi Hundi
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Matthias Hörtenhuber
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Juha Kere
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Research Programs Unit, Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - W Glen Pyle
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
- IMPART Investigator Team Canada, Dalhousie Medicine, Saint John, NB, Canada
| | - Jonas Donner
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Helsinki, Finland
| | - Alex V Postma
- Department of Human Genetics, Amsterdam University Medical Center, Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Jens Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maria Wiberg
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Jana Friederich
- LMU Small Animal Clinic, Ludwig Maximilians University of Munich, Munich, Germany
| | - Jenny Eberhard
- LMU Small Animal Clinic, Ludwig Maximilians University of Munich, Munich, Germany
| | - Magdalena Harakalova
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Frank G van Steenbeek
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, University of Utrecht, Utrecht, The Netherlands
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 108, Utrecht, 3584 CM, The Netherlands
| | - Gerhard Wess
- LMU Small Animal Clinic, Ludwig Maximilians University of Munich, Munich, Germany
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland.
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland.
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland.
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Brunetti B, Bacci B, Abbate JM, Tura G, Paciello O, Vaccaro E, Prisco F, Gandini G, Okonji S, Paola AD, Letko A, Drögemüller C, Jagannathan V, Turba ME, Ogundipe TG, Lorenzini L, Rosati M, Psalla D, Leeb T, Drögemüller M. SGCD Missense Variant in a Lagotto Romagnolo Dog with Autosomal Recessively Inherited Limb-Girdle Muscular Dystrophy. Genes (Basel) 2023; 14:1641. [PMID: 37628692 PMCID: PMC10454570 DOI: 10.3390/genes14081641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/10/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
An 8-month-old female Lagotto Romagnolo dog was presented for a 1-month history of an initial severe reluctance to move, rapidly progressing to a marked stiff gait and progressive muscular weakness and evolving to tetraparesis, which persuaded the owner to request euthanasia. A primary muscle pathology was supported by necropsy and histopathological findings. Macroscopically, the muscles were moderately atrophic, except for the diaphragm and the neck muscles, which were markedly thickened. Histologically, all the skeletal muscles examined showed atrophy, hypertrophy, necrosis with calcification of the fibers, and mild fibrosis and inflammation. On immunohistochemistry, all three dystrophin domains and sarcoglycan proteins were absent. On Western blot analysis, no band was present for delta sarcoglycan. We sequenced the genome of the affected dog and compared the data to more than 900 control genomes of different dog breeds. Genetic analysis revealed a homozygous private protein-changing variant in the SGCD gene encoding delta- sarcoglycan in the affected dog. The variant was predicted to induce a SGCD:p.(Leu242Pro) change in the protein. In silico tools predicted the change to be deleterious. Other 770 Lagotto Romagnolo dogs were genotyped for the variant and all found to be homozygous wild type. Based on current knowledge of gene function in other mammalian species, including humans, hamsters, and dogs, we propose the SGCD missense variant as the causative variant of the observed form of muscular dystrophy in the index case. The absence of the variant allele in the Lagotto Romagnolo breeding population indicates a rare allele that has appeared recently.
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Affiliation(s)
- Barbara Brunetti
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | - Barbara Bacci
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | | | - Giorgia Tura
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | - Orlando Paciello
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (O.P.); (E.V.); (F.P.)
| | - Emanuela Vaccaro
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (O.P.); (E.V.); (F.P.)
| | - Francesco Prisco
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (O.P.); (E.V.); (F.P.)
| | - Gualtiero Gandini
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | - Samuel Okonji
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | - Andrea di Paola
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | - Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (A.L.); (C.D.); (V.J.); (T.L.); (M.D.)
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (A.L.); (C.D.); (V.J.); (T.L.); (M.D.)
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (A.L.); (C.D.); (V.J.); (T.L.); (M.D.)
| | | | - Tolulope Grace Ogundipe
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | - Luca Lorenzini
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy; (B.B.); (G.T.); (G.G.); (S.O.); (A.d.P.); (T.G.O.); (L.L.)
| | - Marco Rosati
- Section of Clinical & Comparative Neuropathology, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universitaet-Muenchen, 80539 Munich, Germany;
| | - Dimitra Psalla
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (A.L.); (C.D.); (V.J.); (T.L.); (M.D.)
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (A.L.); (C.D.); (V.J.); (T.L.); (M.D.)
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5
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Meadows JRS, Kidd JM, Wang GD, Parker HG, Schall PZ, Bianchi M, Christmas MJ, Bougiouri K, Buckley RM, Hitte C, Nguyen AK, Wang C, Jagannathan V, Niskanen JE, Frantz LAF, Arumilli M, Hundi S, Lindblad-Toh K, Ginja C, Agustina KK, André C, Boyko AR, Davis BW, Drögemüller M, Feng XY, Gkagkavouzis K, Iliopoulos G, Harris AC, Hytönen MK, Kalthoff DC, Liu YH, Lymberakis P, Poulakakis N, Pires AE, Racimo F, Ramos-Almodovar F, Savolainen P, Venetsani S, Tammen I, Triantafyllidis A, vonHoldt B, Wayne RK, Larson G, Nicholas FW, Lohi H, Leeb T, Zhang YP, Ostrander EA. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biol 2023; 24:187. [PMID: 37582787 PMCID: PMC10426128 DOI: 10.1186/s13059-023-03023-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/25/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. RESULTS We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. CONCLUSIONS We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.
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Affiliation(s)
- Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden.
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA.
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Katia Bougiouri
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Reuben M Buckley
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Christophe Hitte
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Julia E Niskanen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Laurent A F Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E14NS, UK and Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, D-80539, Munich, Germany
| | - Meharji Arumilli
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Sruthi Hundi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catarina Ginja
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | | | - Catherine André
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Xin-Yao Feng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Konstantinos Gkagkavouzis
- Department of Genetics, School of Biology, ), Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Giorgos Iliopoulos
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Alexander C Harris
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Daniela C Kalthoff
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Petros Lymberakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Nikolaos Poulakakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Ana Elisabete Pires
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | - Fernando Racimo
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | | | - Peter Savolainen
- Department of Gene Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, 17121, Solna, Sweden
| | - Semina Venetsani
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Imke Tammen
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Alexandros Triantafyllidis
- Department of Genetics, School of Biology, ), Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-7246, USA
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3TG, UK
| | - Frank W Nicholas
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA.
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6
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Drögemüller M, Klein N, Steffensen RL, Keiner M, Jagannathan V, Leeb T. PKD1 Nonsense Variant in a Lagotto Romagnolo Family with Polycystic Kidney Disease. Genes (Basel) 2023; 14:1210. [PMID: 37372390 DOI: 10.3390/genes14061210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
A female Lagotto Romagnolo dog with polycystic kidney disease (PKD) and her progeny, including PKD-affected offspring, were studied. All affected dogs appeared clinically inconspicuous, while sonography revealed the presence of renal cysts. The PKD-affected index female was used for breeding and produced two litters with six affected offspring of both sexes and seven unaffected offspring. The pedigrees suggested an autosomal dominant mode of inheritance of the trait. A trio whole genome sequencing analysis of the index female and her unaffected parents identified a de novo heterozygous nonsense variant in the coding region of the PKD1 gene. This variant, NM_001006650.1:c.7195G>T, is predicted to truncate 44% of the open reading frame of the wild-type PKD1 protein, NP_001006651.1:p.(Glu2399*). The finding of a de novo variant in an excellent functional candidate gene strongly suggests that the PKD1 nonsense variant caused the observed phenotype in the affected dogs. Perfect co-segregation of the mutant allele with the PKD phenotype in two litters supports the hypothesized causality. To the best of our knowledge, this is the second description of a PKD1-related canine form of autosomal dominant PKD that may serve as an animal model for similar hepatorenal fibrocystic disorders in humans.
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Affiliation(s)
- Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Nadine Klein
- Tierärztliche Praxis für Kleintiere, Dickstrasse 57, 53773 Hennef (Sieg), Germany
| | | | - Miriam Keiner
- Small Animal Clinic, Internal Medicine, Justus-Liebig-University, 35392 Giessen, Germany
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
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7
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Bannoehr J, Balmer P, Stoffel MH, Jagannathan V, Gaschen V, Kühni K, Sayar B, Drögemüller M, Howald D, Wiener DJ, Leeb T, Welle MM, Müller EJ, Roosje PJ. Abnormal keratinocyte differentiation in the nasal planum of Labrador Retrievers with hereditary nasal parakeratosis (HNPK). PLoS One 2020; 15:e0225901. [PMID: 32119674 PMCID: PMC7051081 DOI: 10.1371/journal.pone.0225901] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 11/14/2019] [Indexed: 01/16/2023] Open
Abstract
Hereditary nasal parakeratosis (HNPK) is an inherited disorder described in Labrador Retrievers and Greyhounds. It has been associated with breed-specific variants in the SUV39H2 gene encoding a histone 3 methyltransferase involved in epigenetic silencing. Formalin-fixed biopsies of the nasal planum of Labrador Retrievers were screened by immunofluorescence microscopy for the presence and distribution of epidermal proliferation and differentiation markers. Gene expression of these markers was further analysed using RNA sequencing (RNA-seq) and ultrastructural epidermal differences were investigated by electron microscopy. Differentiation of the nasal planum in the basal and suprabasal epidermal layers of HNPK-affected dogs (n = 6) was similar compared to control dogs (n = 6). In the upper epidermal layers, clear modifications were noticed. Loricrin protein was absent in HNPK-affected nasal planum sections in contrast to sections of the same location of control dogs. However, loricrin was present in the epidermis of paw pads and abdominal skin from HNPK dogs and healthy control dogs. The patterns of keratins K1, K10 and K14, were not markedly altered in the nasal planum of HNPK-affected dogs while the expression of the terminal differentiation marker involucrin appeared less regular. Based on RNA-seq, LOR and IVL expression levels were significantly decreased, while KRT1, KRT10 and KRT14 levels were up-regulated (log2fold-changes of 2.67, 3.19 and 1.71, respectively) in HNPK-affected nasal planum (n = 3) compared to control dogs (n = 3). Electron microscopical analysis revealed structural alterations in keratinocytes and stratum corneum, and disrupted keratinocyte adhesions and distended intercellular spaces in lesional samples (n = 3) compared to a sample of a healthy control dog (n = 1). Our findings demonstrate aberrant keratinocyte terminal differentiation of the nasal planum of HNPK-affected Labrador Retrievers and provide insights into biological consequences of this inactive SUV39H2 gene variant.
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Affiliation(s)
- Jeanette Bannoehr
- Division of Clinical Dermatology, Department of Clinical Veterinary Science, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Pierre Balmer
- Division of Clinical Dermatology, Department of Clinical Veterinary Science, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Michael H. Stoffel
- Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Véronique Gaschen
- Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Kathrin Kühni
- Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Beyza Sayar
- DermFocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Department of Clinical Research, Molecular Dermatology and Stem Cell Research, University of Bern, Bern, Switzerland
| | | | - Denise Howald
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Dominique J. Wiener
- DermFocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- DermFocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Monika M. Welle
- DermFocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Eliane J. Müller
- DermFocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Department of Clinical Research, Molecular Dermatology and Stem Cell Research, University of Bern, Bern, Switzerland
- Clinic for Dermatology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Petra J. Roosje
- Division of Clinical Dermatology, Department of Clinical Veterinary Science, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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8
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Gentilini F, Turba ME, Giancola F, Chiocchetti R, Bernardini C, Dajbychova M, Jagannathan V, Drögemüller M, Drögemüller C. A large deletion in the GP9 gene in Cocker Spaniel dogs with Bernard-Soulier syndrome. PLoS One 2019; 14:e0220625. [PMID: 31484196 PMCID: PMC6726462 DOI: 10.1371/journal.pone.0220625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/20/2019] [Indexed: 12/16/2022] Open
Abstract
Inherited bleeding disorders including abnormalities of platelet number and function rarely occur in a variety of dog breeds, but are probably underdiagnosed. Genetically characterized canine forms of platelet disorders provide valuable large animal models for understanding similar platelet disorders in people. Breed-specific disease associated genetic variants in only eight different genes are known to cause intrinsic platelet disorders in dogs. However, the causative genetic variant in many dog breeds has until now remained unknown. Four cases of a mild to severe bleeding disorder in Cocker Spaniel dogs are herein presented. The affected dogs showed a platelet adhesion defect characterized by macrothrombocytopenia with variable platelet counts resembling human Bernard-Soulier syndrome (BSS). Furthermore, the lack of functional GPIb-IX-V was demonstrated by immunocytochemistry. Whole genome sequencing of one affected dog and visual inspection of the candidate genes identified a deletion in the glycoprotein IX platelet (GP9) gene. The GP9 gene encodes a subunit of a platelet surface membrane glycoprotein complex; this functions as a receptor for von Willebrand factor, which initiates the maintenance of hemostasis after injury. Variants in human GP9 are associated with Bernard-Soulier syndrome, type C. The deletion spanned 2460 bp, and included a significant part of the single coding exon of the canine GP9 gene on dog chromosome 20. The variant results in a frameshift and premature stop codon which is predicted to truncate almost two-thirds of the encoded protein. PCR-based genotyping confirmed recessive inheritance. The homozygous variant genotype seen in affected dogs did not occur in 98 control Cocker Spaniels. Thus, it was concluded that the structural variant identified in the GP9 gene was most likely causative for the BSS-phenotype in the dogs examined. These findings provide the first large animal GP9 model for this group of inherited platelet disorders and greatly facilitate the diagnosis and identification of affected and/or normal carriers in Cocker Spaniels.
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Affiliation(s)
- Fabio Gentilini
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
- * E-mail:
| | | | - Fiorella Giancola
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Roberto Chiocchetti
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Chiara Bernardini
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | | | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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9
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Henke D, Drögemüller M, Leeb T, Schweizer D, Steffen F, Demierre S, Dickinson P, Vandevelde M, Oevermann A. Familial diffuse astrocytoma (of gliomatosis cerebri type) in bearded collies. J Comp Pathol 2019. [DOI: 10.1016/j.jcpa.2018.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Dürig N, Letko A, Lepori V, Hadji Rasouliha S, Loechel R, Kehl A, Hytönen MK, Lohi H, Mauri N, Dietrich J, Wiedmer M, Drögemüller M, Jagannathan V, Schmutz SM, Leeb T. Two MC1R loss-of-function alleles in cream-coloured Australian Cattle Dogs and white Huskies. Anim Genet 2018; 49:284-290. [PMID: 29932470 DOI: 10.1111/age.12660] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2018] [Indexed: 11/27/2022]
Abstract
Loss-of-function variants in the MC1R gene cause recessive red or yellow coat-colour phenotypes in many species. The canine MC1R:c.916C>T (p.Arg306Ter) variant is widespread and found in a homozygous state in many uniformly yellow- or red-coloured dogs. We investigated cream-coloured Australian Cattle Dogs whose coat colour could not be explained by this variant. A genome-wide association study with 10 cream and 123 red Australian Cattle Dogs confirmed that the cream locus indeed maps to MC1R. Whole-genome sequencing of cream dogs revealed a single nucleotide variant within the MITF binding site of the canine MC1R promoter. We propose to designate the mutant alleles at MC1R:c.916C>T as e1 and at the new promoter variant as e2 . Both alleles segregate in the Australian Cattle Dog breed. When we considered both alleles in combination, we observed perfect association between the MC1R genotypes and the cream coat colour phenotype in a cohort of 10 cases and 324 control dogs. Analysis of the MC1R transcript levels in an e1 /e2 compound heterozygous dog confirmed that the transcript levels of the e2 allele were markedly reduced with respect to the e1 allele. We further report another MC1R loss-of-function allele in Alaskan and Siberian Huskies caused by a 2-bp deletion in the coding sequence, MC1R:c.816_817delCT. We propose to term this allele e3 . Huskies that carry two copies of MC1R loss-of-function alleles have a white coat colour.
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Affiliation(s)
- N Dürig
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - A Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - V Lepori
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - S Hadji Rasouliha
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | | | - A Kehl
- Laboklin, 97688, Bad Kissingen, Germany
| | - M K Hytönen
- Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.,Research Programs Unit, Molecular Neurology, University of Helsinki, 00014, Helsinki, Finland.,Folkhälsan Institute of Genetics, University of Helsinki, 00290, Helsinki, Finland
| | - H Lohi
- Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.,Research Programs Unit, Molecular Neurology, University of Helsinki, 00014, Helsinki, Finland.,Folkhälsan Institute of Genetics, University of Helsinki, 00290, Helsinki, Finland
| | - N Mauri
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - J Dietrich
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - M Wiedmer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - M Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - S M Schmutz
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
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11
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Minor KM, Letko A, Becker D, Drögemüller M, Mandigers PJJ, Bellekom SR, Leegwater PAJ, Stassen QEM, Putschbach K, Fischer A, Flegel T, Matiasek K, Ekenstedt KJ, Furrow E, Patterson EE, Platt SR, Kelly PA, Cassidy JP, Shelton GD, Lucot K, Bannasch DL, Martineau H, Muir CF, Priestnall SL, Henke D, Oevermann A, Jagannathan V, Mickelson JR, Drögemüller C. Canine NAPEPLD-associated models of human myelin disorders. Sci Rep 2018; 8:5818. [PMID: 29643404 PMCID: PMC5895582 DOI: 10.1038/s41598-018-23938-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/20/2018] [Indexed: 01/05/2023] Open
Abstract
Canine leukoencephalomyelopathy (LEMP) is a juvenile-onset neurodegenerative disorder of the CNS white matter currently described in Rottweiler and Leonberger dogs. Genome-wide association study (GWAS) allowed us to map LEMP in a Leonberger cohort to dog chromosome 18. Subsequent whole genome re-sequencing of a Leonberger case enabled the identification of a single private homozygous non-synonymous missense variant located in the highly conserved metallo-beta-lactamase domain of the N-acyl phosphatidylethanolamine phospholipase D (NAPEPLD) gene, encoding an enzyme of the endocannabinoid system. We then sequenced this gene in LEMP-affected Rottweilers and identified a different frameshift variant, which is predicted to replace the C-terminal metallo-beta-lactamase domain of the wild type protein. Haplotype analysis of SNP array genotypes revealed that the frameshift variant was present in diverse haplotypes in Rottweilers, and also in Great Danes, indicating an old origin of this second NAPEPLD variant. The identification of different NAPEPLD variants in dog breeds affected by leukoencephalopathies with heterogeneous pathological features, implicates the NAPEPLD enzyme as important in myelin homeostasis, and suggests a novel candidate gene for myelination disorders in people.
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Affiliation(s)
- K M Minor
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, 55108, USA
| | - A Letko
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - D Becker
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - M Drögemüller
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - P J J Mandigers
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, 3508, CM, The Netherlands
| | - S R Bellekom
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, 3508, CM, The Netherlands
| | - P A J Leegwater
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, 3508, CM, The Netherlands
| | - Q E M Stassen
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, 3508, CM, The Netherlands
| | - K Putschbach
- Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University, Munich, 80539, Germany
| | - A Fischer
- Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University, Munich, 80539, Germany
| | - T Flegel
- Department of Small Animal Medicine, University of Leipzig, Leipzig, 04103, Germany
| | - K Matiasek
- Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University, Munich, 80539, Germany
| | - K J Ekenstedt
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - E Furrow
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, 55108, USA
| | - E E Patterson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, 55108, USA
| | - S R Platt
- Small Animal Medicine and Surgery, University of Georgia, Athens, GA, 30602, USA
| | - P A Kelly
- Veterinary Sciences Centre, University College Dublin, Dublin, D04 V1W8, Ireland
| | - J P Cassidy
- Veterinary Sciences Centre, University College Dublin, Dublin, D04 V1W8, Ireland
| | - G D Shelton
- Department of Pathology, University of California, La Jolla, CA, 92093, USA
| | - K Lucot
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA, 95616, USA
| | - D L Bannasch
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA, 95616, USA
| | - H Martineau
- Pathobiology and Population Sciences, The Royal Veterinary College, North Mymms, AL9 7TA, UK
| | - C F Muir
- Pathobiology and Population Sciences, The Royal Veterinary College, North Mymms, AL9 7TA, UK
| | - S L Priestnall
- Pathobiology and Population Sciences, The Royal Veterinary College, North Mymms, AL9 7TA, UK
| | - D Henke
- Division of Clinical Neurology, University of Bern, Bern, 3001, Switzerland
| | - A Oevermann
- Division of Neurological Sciences, University of Bern, Bern, 3001, Switzerland
| | - V Jagannathan
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - J R Mickelson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, 55108, USA
| | - C Drögemüller
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland.
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12
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Koch C, Ramsauer AS, Drögemüller M, Ackermann M, Gerber V, Tobler K. Genomic comparison of bovine papillomavirus 1 isolates from bovine, equine and asinine lesional tissue samples. Virus Res 2017; 244:6-12. [PMID: 29113823 DOI: 10.1016/j.virusres.2017.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 10/18/2022]
Abstract
Several attempts have been made to categorize equid- and bovid-specific bovine papillomavirus 1 (BPV1) isolates based on sequence tags. This study includes newly determined sequence information from 33 BPV1 isolates of equine, asinine and bovine origin and investigates sequence bias due to host species. Twenty of the viral genomes were sequenced over their entire length and a further thirteen were sequenced, including flanking sequences, at two specific sites, the LCR and the E5 ORF. Alignment and analyses of the sequences did not reveal statistically significant site differences between the sequences of bovine and equid origin. None of the proposed sites of divergence noted by other authors demonstrated significant species-specific characteristics. Our results suggest that BPV1 is shared between equine, asinine and bovine host species, and that viral transfer between bovines and equids is a repeated and ongoing phenomenon.
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Affiliation(s)
- C Koch
- Swiss Institute of Equine Medicine, Vetsuisse Faculty Berne, University of Berne, and ALP-Haras, Länggasstrasse 124, Postfach 8466, CH-3001 Berne, Switzerland.
| | - A S Ramsauer
- Institute of Virology, Vetsuisse Faculty Zurich, University of Zurich, Winterthurerstrasse 266a, CH-8057 Zürich, Switzerland
| | - M Drögemüller
- Institute of Genetics, Vetsuisse Faculty Berne, University of Berne, Bremgartenstrasse 109a, Postfach 8466, CH-3001 Berne, Switzerland
| | - M Ackermann
- Institute of Virology, Vetsuisse Faculty Zurich, University of Zurich, Winterthurerstrasse 266a, CH-8057 Zürich, Switzerland
| | - V Gerber
- Swiss Institute of Equine Medicine, Vetsuisse Faculty Berne, University of Berne, and ALP-Haras, Länggasstrasse 124, Postfach 8466, CH-3001 Berne, Switzerland
| | - K Tobler
- Institute of Virology, Vetsuisse Faculty Zurich, University of Zurich, Winterthurerstrasse 266a, CH-8057 Zürich, Switzerland
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13
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Marchant TW, Johnson EJ, McTeir L, Johnson CI, Gow A, Liuti T, Kuehn D, Svenson K, Bermingham ML, Drögemüller M, Nussbaumer M, Davey MG, Argyle DJ, Powell RM, Guilherme S, Lang J, Ter Haar G, Leeb T, Schwarz T, Mellanby RJ, Clements DN, Schoenebeck JJ. Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2. Curr Biol 2017; 27:1573-1584.e6. [PMID: 28552356 PMCID: PMC5462623 DOI: 10.1016/j.cub.2017.04.057] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/14/2017] [Accepted: 04/27/2017] [Indexed: 12/30/2022]
Abstract
In morphological terms, “form” is used to describe an object’s shape and size. In dogs, facial form is stunningly diverse. Facial retrusion, the proximodistal shortening of the snout and widening of the hard palate is common to brachycephalic dogs and is a welfare concern, as the incidence of respiratory distress and ocular trauma observed in this class of dogs is highly correlated with their skull form. Progress to identify the molecular underpinnings of facial retrusion is limited to association of a missense mutation in BMP3 among small brachycephalic dogs. Here, we used morphometrics of skull isosurfaces derived from 374 pedigree and mixed-breed dogs to dissect the genetics of skull form. Through deconvolution of facial forms, we identified quantitative trait loci that are responsible for canine facial shapes and sizes. Our novel insights include recognition that the FGF4 retrogene insertion, previously associated with appendicular chondrodysplasia, also reduces neurocranium size. Focusing on facial shape, we resolved a quantitative trait locus on canine chromosome 1 to a 188-kb critical interval that encompasses SMOC2. An intronic, transposable element within SMOC2 promotes the utilization of cryptic splice sites, causing its incorporation into transcripts, and drastically reduces SMOC2 gene expression in brachycephalic dogs. SMOC2 disruption affects the facial skeleton in a dose-dependent manner. The size effects of the associated SMOC2 haplotype are profound, accounting for 36% of facial length variation in the dogs we tested. Our data bring new focus to SMOC2 by highlighting its clinical implications in both human and veterinary medicine. A population-based genetics study of dogs that required diagnostic imaging Resolution of a QTL associated with face length reduction (brachycephaly) Association of brachycephaly with a retrotransposon that disrupts SMOC2 splicing The SMOC2 locus explains up to 36% of face length variation in dogs
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Affiliation(s)
- Thomas W Marchant
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Edward J Johnson
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Lynn McTeir
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Craig I Johnson
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Adam Gow
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Tiziana Liuti
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Dana Kuehn
- Friendship Hospital for Animals, Washington, DC 20016, USA
| | | | - Mairead L Bermingham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Marc Nussbaumer
- Naturhistorisches Museum, Bernastrasse 15, 3005 Bern, Switzerland
| | - Megan G Davey
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - David J Argyle
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Roger M Powell
- Powell Torrance Diagnostic Services, Manor Farm Business Park, Higham Gobion, Hertfordshire SG5 3HR, UK
| | - Sérgio Guilherme
- Davies Veterinary Specialists, Manor Farm Business Park, Higham Gobion, Hertfordshire SG5 3HR, UK
| | - Johann Lang
- Division of Clinical Radiology, Department of Clinical Veterinary Medicine, University of Bern, 3001 Bern, Switzerland
| | - Gert Ter Haar
- Department of Clinical Sciences and Services, Royal Veterinary College, Hertfordshire AL9 7TA, UK
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001 Bern, Switzerland
| | - Tobias Schwarz
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Richard J Mellanby
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Dylan N Clements
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Jeffrey J Schoenebeck
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
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14
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Hirz M, Drögemüller M, Schänzer A, Jagannathan V, Dietschi E, Goebel HH, Hecht W, Laubner S, Schmidt MJ, Steffen F, Hilbe M, Köhler K, Drögemüller C, Herden C. Neuronal ceroid lipofuscinosis (NCL) is caused by the entire deletion of CLN8 in the Alpenländische Dachsbracke dog. Mol Genet Metab 2017; 120:269-277. [PMID: 28024876 DOI: 10.1016/j.ymgme.2016.12.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 11/20/2022]
Abstract
Neuronal ceroid lipofuscinoses (NCLs) are inherited lysosomal storage diseases that have been described in a variety of dog breeds, where they are caused by different mutations in different genes. However, the causative gene defect in the breed Alpenländische Dachsbracke remained unknown so far. Here we present two confirmed cases of NCL in Alpenländische Dachsbracke dogs from different litters of the same sire with a different dam harboring the same underlying novel mutation in the CLN8 gene. Case 1, a 2-year-old male Alpenländische Dachsbracke was presented with neurological signs including disorientation, character changes including anxiety states and aggressiveness, sudden blindness and reduction of food intake. Magnetic resonance imaging (MRI) scans showed cerebral atrophy with dilation of all cerebral ventricles, thinning of the intermediate mass of the thalamus and widening of the cerebral sulci. Postmortem examination of the central nervous system (CNS) showed neuronal loss in the cerebral cortex, cerebellum and spinal cord with massive intracellular deposits of ceroid pigment. Additional ceroid-lipofuscin deposits were observed in the enteric nervous system and in macrophages within spleen, lymph nodes and lung. Ultrastructural analyses confirmed NCL with the presence of osmiophilic membrane bounded lamellar-like structures. Case 2, a 1,5-year old female Alpenländische Dachsbracke was presented with progressive generalized forebrain disease including mental changes such as fearful reactions to various kinds of external stimuli and disorientation. The dog also displayed seizures, absence of menace reactions and negative cotton-ball test with normal pupillary light reactions. The clinical and post mortem examination yielded similar results in the brain as in Case 1. Whole genome sequencing of Case 1 and PCR results of both cases revealed a homozygous deletion encompassing the entire CLN8 gene as the most likely causative mutation for the NCL form observed in both cases. The deletion follows recessive inheritance since the dam and a healthy male littermate of Case 1 were tested as heterozygous carriers. This is the first detailed description of CLN8 gene associated NCL in Alpenländische Dachsbracke dogs and thus provides a novel canine CLN8 model for this lysosomal storage disease. The presence of ceroid lipofuscin in extracerebral tissues may help to confirm the diagnosis of NCL in vivo, especially in new dog breeds where the underlying mutation is not known.
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Affiliation(s)
- M Hirz
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, Germany.
| | - M Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Switzerland
| | - A Schänzer
- Institute of Neuropathology, Justus-Liebig-University Giessen, Germany
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Switzerland
| | - E Dietschi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Switzerland
| | - H H Goebel
- Institute of Neuropathology Charité, University Berlin, Germany
| | - W Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, Germany
| | - S Laubner
- Clinic for Small Animals - Surgery, Justus-Liebig-University Giessen, Germany
| | - M J Schmidt
- Clinic for Small Animals - Surgery, Justus-Liebig-University Giessen, Germany
| | - F Steffen
- Clinic for Small Animals - Neurology, Vetsuisse Faculty, University of Zurich, Switzerland
| | - M Hilbe
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland
| | - K Köhler
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, Germany
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Switzerland
| | - C Herden
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, Germany
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15
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Nolte A, Bello A, Drögemüller M, Leeb T, Brockhaus E, Baumgärtner W, Wohlsein P. Neuronal ceroid lipofuscinosis in an adult American Staffordshire Terrier. Tierarztl Prax Ausg K Kleintiere Heimtiere 2016; 44:431-437. [PMID: 27778018 DOI: 10.15654/tpk-150766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 06/07/2016] [Indexed: 11/13/2022]
Abstract
A female, 5-year-old American Staffordshire Terrier with severe progressive neurological deficits, particularly in terms of ataxia and keeping balance, was examined pathomorphologically and a genetic analysis was performed. In neurons of various localizations of the central nervous system an accumulation of a finely granular pale eosinophilic or light brown material was found. In addition, the cerebellum revealed marked degeneration and loss of Purkinje and inner granule cells. The accumulated PAS-positive, argyrophilic, autofluorescent material showed ultrastructurally a lamellar appearance suggestive of lipofuscin. Genetic analysis revealed the presence of a sequence variant in the ARSG gene encoding the lysosomal enzyme arylsulfatase G. This case report describes an adult-onset of a neuronal ceroid lipofuscinosis that shows similarities with a human disorder termed Kufs disease.
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Affiliation(s)
| | | | | | | | | | | | - Peter Wohlsein
- Dr. Peter Wohlsein, Institut für Pathologie, Tierärztliche Hochschule Hannover, Bünteweg 17, 30559 Hannover, E-Mail:
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16
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Murgiano L, Waluk D, Towers R, Wiedemar N, Dietrich J, Jagannathan V, Drögemüller M, Druet T, Galichet A, Penedo MC, Müller E, Roosje P, Welle M, Leeb T. P6015 An intronic MBTPS2 variant results in a splicing defect in horses with brindle coat texture. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4155a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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17
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Kyöstilä K, Syrjä P, Jagannathan V, Chandrasekar G, Jokinen TS, Seppälä EH, Becker D, Drögemüller M, Dietschi E, Drögemüller C, Lang J, Steffen F, Rohdin C, Jäderlund KH, Lappalainen AK, Hahn K, Wohlsein P, Baumgärtner W, Henke D, Oevermann A, Kere J, Lohi H, Leeb T. A missense change in the ATG4D gene links aberrant autophagy to a neurodegenerative vacuolar storage disease. PLoS Genet 2015; 11:e1005169. [PMID: 25875846 PMCID: PMC4398399 DOI: 10.1371/journal.pgen.1005169] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/20/2015] [Indexed: 11/22/2022] Open
Abstract
Inherited neurodegenerative disorders are debilitating diseases that occur across different species. We have performed clinical, pathological and genetic studies to characterize a novel canine neurodegenerative disease present in the Lagotto Romagnolo dog breed. Affected dogs suffer from progressive cerebellar ataxia, sometimes accompanied by episodic nystagmus and behavioral changes. Histological examination revealed unique pathological changes, including profound neuronal cytoplasmic vacuolization in the nervous system, as well as spheroid formation and cytoplasmic aggregation of vacuoles in secretory epithelial tissues and mesenchymal cells. Genetic analyses uncovered a missense change, c.1288G>A; p.A430T, in the autophagy-related ATG4D gene on canine chromosome 20 with a highly significant disease association (p = 3.8 x 10-136) in a cohort of more than 2300 Lagotto Romagnolo dogs. ATG4D encodes a poorly characterized cysteine protease belonging to the macroautophagy pathway. Accordingly, our histological analyses indicated altered autophagic flux in affected tissues. The knockdown of the zebrafish homologue atg4da resulted in a widespread developmental disturbance and neurodegeneration in the central nervous system. Our study describes a previously unknown canine neurological disease with particular pathological features and implicates the ATG4D protein as an important autophagy mediator in neuronal homeostasis. The canine phenotype serves as a model to delineate the disease-causing pathological mechanism(s) and ATG4D function, and can also be used to explore treatment options. Furthermore, our results reveal a novel candidate gene for human neurodegeneration and enable the development of a genetic test for veterinary diagnostic and breeding purposes. Neurodegenerative disorders affect millions of people worldwide. We describe a novel neurodegenerative disease in a canine model, characterized by progressive cerebellar ataxia and cellular vacuolization. Our genetic analyses identified a single nucleotide change in the autophagy-related ATG4D gene in affected dogs. The ATG4D gene has not been linked to inherited diseases before. The autophagy-lysosome pathway plays an important role in degrading and recycling different cellular components. Disturbed autophagy has been reported in several different diseases but mutations in core autophagy components are rare. Histological analyses of affected canine brain tissues revealed altered autophagic flux, and a knockdown of the gene in the zebrafish model caused marked neurodevelopmental alterations and neurodegeneration. Our findings identify a new disease-causing pathway and implicate the ATG4D protease as an important mediator for neuronal homeostasis. Furthermore, our study establishes a large animal model to investigate the role of ATG4D in autophagy and to test possible treatment options.
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Affiliation(s)
- Kaisa Kyöstilä
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Department of Molecular Genetics, Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Pernilla Syrjä
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Tarja S. Jokinen
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Eija H. Seppälä
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Department of Molecular Genetics, Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Doreen Becker
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Elisabeth Dietschi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Johann Lang
- Department of Clinical Veterinary Medicine, Division of Clinical Radiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Frank Steffen
- Neurology Service, Department of Small Animals, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Cecilia Rohdin
- University Animal Hospital, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Karin H. Jäderlund
- Department of Companion Animal Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
| | - Anu K. Lappalainen
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Kerstin Hahn
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Diana Henke
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Anna Oevermann
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Juha Kere
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Department of Molecular Genetics, Folkhälsan Institute of Genetics, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Department of Molecular Genetics, Folkhälsan Institute of Genetics, Helsinki, Finland
- * E-mail:
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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18
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Pacholewska A, Drögemüller M, Klukowska-Rötzler J, Lanz S, Hamza E, Dermitzakis ET, Marti E, Gerber V, Leeb T, Jagannathan V. The transcriptome of equine peripheral blood mononuclear cells. PLoS One 2015; 10:e0122011. [PMID: 25790166 PMCID: PMC4366165 DOI: 10.1371/journal.pone.0122011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 02/06/2015] [Indexed: 11/26/2022] Open
Abstract
Complete transcriptomic data at high resolution are available only for a few model organisms with medical importance. The gene structures of non-model organisms are mostly computationally predicted based on comparative genomics with other species. As a result, more than half of the horse gene models are known only by projection. Experimental data supporting these gene models are scarce. Moreover, most of the annotated equine genes are single-transcript genes. Utilizing RNA sequencing (RNA-seq) the experimental validation of predicted transcriptomes has become accessible at reasonable costs. To improve the horse genome annotation we performed RNA-seq on 561 samples of peripheral blood mononuclear cells (PBMCs) derived from 85 Warmblood horses. The mapped sequencing reads were used to build a new transcriptome assembly. The new assembly revealed many alternative isoforms associated to known genes or to those predicted by the Ensembl and/or Gnomon pipelines. We also identified 7,531 transcripts not associated with any horse gene annotated in public databases. Of these, 3,280 transcripts did not have a homologous match to any sequence deposited in the NCBI EST database suggesting horse specificity. The unknown transcripts were categorized as coding and noncoding based on predicted coding potential scores. Among them 230 transcripts had high coding potential score, at least 2 exons, and an open reading frame of at least 300 nt. We experimentally validated 9 new equine coding transcripts using RT-PCR and Sanger sequencing. Our results provide valuable detailed information on many transcripts yet to be annotated in the horse genome.
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Affiliation(s)
- Alicja Pacholewska
- Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern and Agroscope, Bern, Switzerland; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Jolanta Klukowska-Rötzler
- Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern and Agroscope, Bern, Switzerland; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Division of Pediatric Hematology/Oncology, Department of Pediatrics, Bern University Hospital, Bern, Switzerland
| | - Simone Lanz
- Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern and Agroscope, Bern, Switzerland
| | - Eman Hamza
- Clinical Immunology Group, Department of Clinical Research and Veterinary Public Health, University of Bern, Bern, Switzerland
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Eliane Marti
- Clinical Immunology Group, Department of Clinical Research and Veterinary Public Health, University of Bern, Bern, Switzerland
| | - Vincent Gerber
- Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern and Agroscope, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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19
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Gerber M, Fischer A, Jagannathan V, Drögemüller M, Drögemüller C, Schmidt MJ, Bernardino F, Manz E, Matiasek K, Rentmeister K, Leeb T. A deletion in the VLDLR gene in Eurasier dogs with cerebellar hypoplasia resembling a Dandy-Walker-like malformation (DWLM). PLoS One 2015; 10:e0108917. [PMID: 25668033 PMCID: PMC4323105 DOI: 10.1371/journal.pone.0108917] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/26/2014] [Indexed: 11/18/2022] Open
Abstract
Dandy-Walker-like malformation (DWLM) is the result of aberrant brain development and mainly characterized by cerebellar hypoplasia. DWLM affected dogs display a non-progressive cerebellar ataxia. Several DWLM cases were recently observed in the Eurasier dog breed, which strongly suggested a monogenic autosomal recessive inheritance in this breed. We performed a genome-wide association study (GWAS) with 9 cases and 11 controls and found the best association of DWLM with markers on chromosome 1. Subsequent homozygosity mapping confirmed that all 9 cases were homozygous for a shared haplotype in this region, which delineated a critical interval of 3.35 Mb. We sequenced the genome of an affected Eurasier and compared it with the Boxer reference genome and 47 control genomes of dogs from other breeds. This analysis revealed 4 private non-synonymous variants in the critical interval of the affected Eurasier. We genotyped these variants in additional dogs and found perfect association for only one of these variants, a single base deletion in the VLDLR gene encoding the very low density lipoprotein receptor. This variant, VLDLR:c.1713delC is predicted to cause a frameshift and premature stop codon (p.W572Gfs*10). Variants in the VLDLR gene have been shown to cause congenital cerebellar ataxia and mental retardation in human patients and Vldlr knockout mice also display an ataxia phenotype. Our combined genetic data together with the functional knowledge on the VLDLR gene from other species thus strongly suggest that VLDLR:c.1713delC is indeed causing DWLM in Eurasier dogs.
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Affiliation(s)
- Martina Gerber
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Andrea Fischer
- Section of Neurology, Clinic of Small Animal Medicine, Ludwig-Maximilians-University, 80539 Munich, Germany
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Martin J. Schmidt
- Department of Veterinary Clinical Science, Small Animal Clinic, Justus-Liebig-University, 35392 Giessen, Germany
| | - Filipa Bernardino
- Section of Neurology, Clinic of Small Animal Medicine, Ludwig-Maximilians-University, 80539 Munich, Germany
| | | | - Kaspar Matiasek
- Section of Clinical and Comparative Neuropathology, Institute of Veterinary Pathology at the Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University, 80539 Munich, Germany
| | - Kai Rentmeister
- Tierärztliche Praxis für Neurologie, 97337 Dettelbach, Germany
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
- * E-mail:
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20
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Drögemüller M, Jagannathan V, Dolf G, Butenhoff K, Kottmann-Berger S, Wess G, Leeb T. A single codon insertion in the PICALM gene is not associated with subvalvular aortic stenosis in Newfoundland dogs. Hum Genet 2014; 134:127-9. [PMID: 25391634 DOI: 10.1007/s00439-014-1506-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 10/28/2014] [Indexed: 10/24/2022]
Affiliation(s)
- Michaela Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland
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Drögemüller M, Jagannathan V, Welle MM, Graubner C, Straub R, Gerber V, Burger D, Signer-Hasler H, Poncet PA, Klopfenstein S, von Niederhäusern R, Tetens J, Thaller G, Rieder S, Drögemüller C, Leeb T. Congenital hepatic fibrosis in the Franches-Montagnes horse is associated with the polycystic kidney and hepatic disease 1 (PKHD1) gene. PLoS One 2014; 9:e110125. [PMID: 25295861 PMCID: PMC4190318 DOI: 10.1371/journal.pone.0110125] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 09/15/2014] [Indexed: 12/20/2022] Open
Abstract
Congenital hepatic fibrosis has been described as a lethal disease with monogenic autosomal recessive inheritance in the Swiss Franches-Montagnes horse breed. We performed a genome-wide association study with 5 cases and 12 controls and detected an association on chromosome 20. Subsequent homozygosity mapping defined a critical interval of 952 kb harboring 10 annotated genes and loci including the polycystic kidney and hepatic disease 1 (autosomal recessive) gene (PKHD1). PKHD1 represents an excellent functional candidate as variants in this gene were identified in human patients with autosomal recessive polycystic kidney and hepatic disease (ARPKD) as well as several mouse and rat mutants. Whereas most pathogenic PKHD1 variants lead to polycystic defects in kidney and liver, a small subset of the human ARPKD patients have only liver symptoms, similar to our horses with congenital hepatic fibrosis. The PKHD1 gene is one of the largest genes in the genome with multiple alternative transcripts that have not yet been fully characterized. We sequenced the genomes of an affected foal and 46 control horses to establish a comprehensive list of variants in the critical interval. We identified two missense variants in the PKHD1 gene which were strongly, but not perfectly associated with congenital hepatic fibrosis. We speculate that reduced penetrance and/or potential epistatic interactions with hypothetical modifier genes may explain the imperfect association of the detected PKHD1 variants. Our data thus indicate that horses with congenital hepatic fibrosis represent an interesting large animal model for the liver-restricted subtype of human ARPKD.
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Affiliation(s)
- Michaela Drögemüller
- Institute of Genetics, University of Bern, Bern, Switzerland
- Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL and Agroscope, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, University of Bern, Bern, Switzerland
- Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL and Agroscope, Bern, Switzerland
| | - Monika M. Welle
- Institute of Animal Pathology, University of Bern, Bern, Switzerland
| | - Claudia Graubner
- Swiss Institute of Equine Medicine, University of Bern and Agroscope, Bern, Switzerland
| | - Reto Straub
- Swiss Institute of Equine Medicine, University of Bern and Agroscope, Bern, Switzerland
| | - Vinzenz Gerber
- Swiss Institute of Equine Medicine, University of Bern and Agroscope, Bern, Switzerland
| | - Dominik Burger
- Swiss Institute of Equine Medicine, University of Bern and Agroscope, Bern, Switzerland
| | - Heidi Signer-Hasler
- Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL and Agroscope, Bern, Switzerland
- Bern University of Applied Sciences HAFL, Zollikofen, Switzerland
| | | | | | - Ruedi von Niederhäusern
- Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL and Agroscope, Bern, Switzerland
- Agroscope, Swiss National Stud Farm, Avenches, Switzerland
| | - Jens Tetens
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Kiel, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Kiel, Germany
| | - Stefan Rieder
- Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL and Agroscope, Bern, Switzerland
- Agroscope, Swiss National Stud Farm, Avenches, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, University of Bern, Bern, Switzerland
- Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL and Agroscope, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, University of Bern, Bern, Switzerland
- Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL and Agroscope, Bern, Switzerland
- * E-mail:
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22
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Kook PH, Drögemüller M, Leeb T, Hinden S, Ruetten M, Howard J. Hepatic fungal infection in a young beagle with unrecognised hereditary cobalamin deficiency (Imerslund-Gräsbeck syndrome). J Small Anim Pract 2014; 56:138-41. [PMID: 25131805 DOI: 10.1111/jsap.12251] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 05/16/2014] [Accepted: 06/07/2014] [Indexed: 12/24/2022]
Abstract
A 12-month-old beagle presented for anorexia, pyrexia and vomiting. The dog had been treated intermittently with antibiotics and corticosteroids for inappetence and lethargy since five months of age. Previous laboratory abnormalities included macrocytosis and neutropenia. At presentation, the dog was lethargic, febrile and thin. Laboratory examination findings included anaemia, a left shift, thrombocytopenia, hypoglycaemia and hyperbilirubinaemia. Multiple, small, hypoechoic, round hepatic lesions were observed on abdominal ultrasound. Cytological examination of hepatic fine needle aspirates revealed a fungal infection and associated pyogranulomatous inflammation. The dog's general condition deteriorated despite supportive measures and treatment with fluconazole, and owners opted for euthanasia before hypocobalaminaemia was identified. Subsequent genomic analysis revealed a CUBN:c.786delC mutation in a homozygous state, confirming hereditary cobalamin malabsorption (Imerslund-Gräsbeck syndrome). Similar to human infants, dogs with Imerslund-Gräsbeck syndrome may rarely be presented for infectious diseases, distracting focus from the underlying primary disorder.
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Affiliation(s)
- P H Kook
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, 8057, Zurich, Switzerland
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23
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Drögemüller M, Jagannathan V, Becker D, Drögemüller C, Schelling C, Plassais J, Kaerle C, Dufaure de Citres C, Thomas A, Müller EJ, Welle MM, Roosje P, Leeb T. A mutation in the FAM83G gene in dogs with hereditary footpad hyperkeratosis (HFH). PLoS Genet 2014; 10:e1004370. [PMID: 24832243 PMCID: PMC4022470 DOI: 10.1371/journal.pgen.1004370] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 03/25/2014] [Indexed: 01/04/2023] Open
Abstract
Hereditary footpad hyperkeratosis (HFH) represents a palmoplantar hyperkeratosis, which is inherited as a monogenic autosomal recessive trait in several dog breeds, such as e.g. Kromfohrländer and Irish Terriers. We performed genome-wide association studies (GWAS) in both breeds. In Kromfohrländer we obtained a single strong association signal on chromosome 5 (praw = 1.0×10−13) using 13 HFH cases and 29 controls. The association signal replicated in an independent cohort of Irish Terriers with 10 cases and 21 controls (praw = 6.9×10−10). The analysis of shared haplotypes among the combined Kromfohrländer and Irish Terrier cases defined a critical interval of 611 kb with 13 predicted genes. We re-sequenced the genome of one affected Kromfohrländer at 23.5× coverage. The comparison of the sequence data with 46 genomes of non-affected dogs from other breeds revealed a single private non-synonymous variant in the critical interval with respect to the reference genome assembly. The variant is a missense variant (c.155G>C) in the FAM83G gene encoding a protein with largely unknown function. It is predicted to change an evolutionary conserved arginine into a proline residue (p.R52P). We genotyped this variant in a larger cohort of dogs and found perfect association with the HFH phenotype. We further studied the clinical and histopathological alterations in the epidermis in vivo. Affected dogs show a moderate to severe orthokeratotic hyperplasia of the palmoplantar epidermis. Thus, our data provide the first evidence that FAM83G has an essential role for maintaining the integrity of the palmoplantar epidermis. The palms and soles of mammals are covered by the palmoplantar epidermis, which has to bear immense mechanical forces and has therefore a special composition in comparison to the epidermis on regular skin. We studied a Mendelian disease in dogs, termed hereditary footpad hyperkeratosis (HFH). HFH affected dogs develop deep fissures in the paw pads, which are the consequence of a pathological thickening of the outermost layer of the epidermis. We mapped the disease causing genetic variant in the Kromfohrländer and Irish Terrier breeds to a 611 kb interval on chromosome 5. HFH affected Kromfohrländer and Irish Terriers shared the same haplotype indicating descent from a common founder. We re-sequenced the genome of an affected dog and compared it to genome sequences of 46 control dogs. The HFH affected dog had only one private non-synonymous variant in the critical interval, a missense variant of the FAM83G gene. We genotyped this variant in more than 500 dogs and found perfect association with the HFH phenotype. Our data very strongly suggest that the FAM83G variant is causative for HFH. FAM83G is a protein with unknown biochemical function. Our study thus provides the first link between this protein and the palmoplantar epidermis.
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Affiliation(s)
- Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland; DermFocus, University of Bern, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland; DermFocus, University of Bern, Bern, Switzerland
| | - Doreen Becker
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland; DermFocus, University of Bern, Bern, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland; DermFocus, University of Bern, Bern, Switzerland
| | - Claude Schelling
- Clinic for Reproductive Medicine, University of Zurich, Zurich, Switzerland
| | - Jocelyn Plassais
- CNRS, UMR 6290, Institut Génétique et Développement de Rennes, Rennes, France; Université Rennes 1, UEB, Biosit, Faculté de Médecine, Rennes, France
| | - Cécile Kaerle
- Antagene, Animal Genetics Laboratory, La Tour de Salvagny, France
| | | | - Anne Thomas
- Antagene, Animal Genetics Laboratory, La Tour de Salvagny, France
| | - Eliane J Müller
- DermFocus, University of Bern, Bern, Switzerland; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Monika M Welle
- DermFocus, University of Bern, Bern, Switzerland; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Petra Roosje
- DermFocus, University of Bern, Bern, Switzerland; Division of Clinical Dermatology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland; DermFocus, University of Bern, Bern, Switzerland
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Kook PH, Drögemüller M, Leeb T, Howard J, Ruetten M. Degenerative liver disease in young Beagles with hereditary cobalamin malabsorption because of a mutation in the cubilin gene. J Vet Intern Med 2014; 28:666-71. [PMID: 24467303 PMCID: PMC4858026 DOI: 10.1111/jvim.12295] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 10/18/2013] [Accepted: 12/04/2013] [Indexed: 12/20/2022] Open
Affiliation(s)
- P H Kook
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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25
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Drögemüller M, Jagannathan V, Howard J, Bruggmann R, Drögemüller C, Ruetten M, Leeb T, Kook PH. A frameshift mutation in the cubilin gene (CUBN) in Beagles with Imerslund-Gräsbeck syndrome (selective cobalamin malabsorption). Anim Genet 2013; 45:148-50. [DOI: 10.1111/age.12094] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2013] [Indexed: 12/23/2022]
Affiliation(s)
- Michaela Drögemüller
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
| | - Judith Howard
- Department of Clinical Veterinary Medicine; University of Bern; 3001 Bern Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit; University of Bern; 3001 Bern Switzerland
| | - Cord Drögemüller
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
| | - Maja Ruetten
- Institute of Veterinary Pathology; Vetsuisse Faculty; University of Zurich; 8057 Zurich Switzerland
| | - Tosso Leeb
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
| | - Peter H. Kook
- Clinic for Small Animal Internal Medicine; Vetsuisse Faculty; University of Zurich; 8057 Zurich Switzerland
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26
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Jagannathan V, Bannoehr J, Plattet P, Hauswirth R, Drögemüller C, Drögemüller M, Wiener DJ, Doherr M, Owczarek-Lipska M, Galichet A, Welle MM, Tengvall K, Bergvall K, Lohi H, Rüfenacht S, Linek M, Paradis M, Müller EJ, Roosje P, Leeb T. A mutation in the SUV39H2 gene in Labrador Retrievers with hereditary nasal parakeratosis (HNPK) provides insights into the epigenetics of keratinocyte differentiation. PLoS Genet 2013; 9:e1003848. [PMID: 24098150 PMCID: PMC3789836 DOI: 10.1371/journal.pgen.1003848] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 08/16/2013] [Indexed: 11/19/2022] Open
Abstract
Hereditary nasal parakeratosis (HNPK), an inherited monogenic autosomal recessive skin disorder, leads to crusts and fissures on the nasal planum of Labrador Retrievers. We performed a genome-wide association study (GWAS) using 13 HNPK cases and 23 controls. We obtained a single strong association signal on chromosome 2 (p(raw) = 4.4×10⁻¹⁴). The analysis of shared haplotypes among the 13 cases defined a critical interval of 1.6 Mb with 25 predicted genes. We re-sequenced the genome of one case at 38× coverage and detected 3 non-synonymous variants in the critical interval with respect to the reference genome assembly. We genotyped these variants in larger cohorts of dogs and only one was perfectly associated with the HNPK phenotype in a cohort of more than 500 dogs. This candidate causative variant is a missense variant in the SUV39H2 gene encoding a histone 3 lysine 9 (H3K9) methyltransferase, which mediates chromatin silencing. The variant c.972T>G is predicted to change an evolutionary conserved asparagine into a lysine in the catalytically active domain of the enzyme (p.N324K). We further studied the histopathological alterations in the epidermis in vivo. Our data suggest that the HNPK phenotype is not caused by hyperproliferation, but rather delayed terminal differentiation of keratinocytes. Thus, our data provide evidence that SUV39H2 is involved in the epigenetic regulation of keratinocyte differentiation ensuring proper stratification and tight sealing of the mammalian epidermis.
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Affiliation(s)
- Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Jeanette Bannoehr
- DermFocus, University of Bern, Bern, Switzerland
- Division of Clinical Dermatology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Philippe Plattet
- Division of Neuroscience, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Regula Hauswirth
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Dominique J. Wiener
- DermFocus, University of Bern, Bern, Switzerland
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Marcus Doherr
- Veterinary Public Health Institute, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Marta Owczarek-Lipska
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Arnaud Galichet
- DermFocus, University of Bern, Bern, Switzerland
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Monika M. Welle
- DermFocus, University of Bern, Bern, Switzerland
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Katarina Tengvall
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Kerstin Bergvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hannes Lohi
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences and Department of Medical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | | | | | - Manon Paradis
- Department of Clinical Sciences, Faculté de Médecine Vétérinaire, University of Montreal, St-Hyacinthe, Québec, Canada
| | - Eliane J. Müller
- DermFocus, University of Bern, Bern, Switzerland
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Petra Roosje
- DermFocus, University of Bern, Bern, Switzerland
- Division of Clinical Dermatology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
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Abstract
Interleukin-26 (IL26) is a member of the IL10 cytokine family. The IL26 gene is located between two other well-known cytokines genes of this family encoding interferon-gamma (IFNG) and IL22 in an evolutionary conserved gene cluster. In contrast to humans and most other mammals, mice lack a functional Il26 gene. We analyzed the genome sequences of other vertebrates for the presence or absence of functional IL26 orthologs and found that the IL26 gene has also become inactivated in several equid species. We detected a one-base pair frameshift deletion in exon 2 of the IL26 gene in the domestic horse (Equus caballus), Przewalski horse (Equus przewalskii) and donkey (Equus asinus). The remnant IL26 gene in the horse is still transcribed and gives rise to at least five alternative transcripts. None of these transcripts share a conserved open reading frame with the human IL26 gene. A comparative analysis across diverse vertebrates revealed that the IL26 gene has also independently been inactivated in a few other mammals, including the African elephant and the European hedgehog. The IL26 gene thus appears to be highly variable, and the conserved open reading frame has been lost several times during mammalian evolution.
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Affiliation(s)
- M Shakhsi-Niaei
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland; Genetics Group, Science Faculty, University of Shahrekord, Rahbar Boulevard, Shahrekord, Iran
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Hirschvogel K, Matiasek K, Flatz K, Drögemüller M, Drögemüller C, Reiner B, Fischer A. Magnetic resonance imaging and genetic investigation of a case of Rottweiler leukoencephalomyelopathy. BMC Vet Res 2013; 9:57. [PMID: 23531239 PMCID: PMC3614464 DOI: 10.1186/1746-6148-9-57] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Accepted: 03/14/2013] [Indexed: 11/12/2022] Open
Abstract
Background Leukoencephalomyelopathy is an inherited neurodegenerative disorder that affects the white matter of the spinal cord and brain and is known to occur in the Rottweiler breed. Due to the lack of a genetic test for this disorder, post mortem neuropathological examinations are required to confirm the diagnosis. Leukoencephalopathy with brain stem and spinal cord involvement and elevated lactate levels is a rare, autosomal recessive disorder in humans that was recently described to have clinical features and magnetic resonance imaging (MRI) findings that are similar to the histopathologic lesions that define leukoencephalomyelopathy in Rottweilers. Leukoencephalopathy with brain stem and spinal cord involvement is caused by mutations in the DARS2 gene, which encodes a mitochondrial aspartyl-tRNA synthetase. The objective of this case report is to present the results of MRI and candidate gene analysis of a case of Rottweiler leukoencephalomyelopathy to investigate the hypothesis that leukoencephalomyelopathy in Rottweilers could serve as an animal model of human leukoencephalopathy with brain stem and spinal cord involvement. Case presentation A two-and-a-half-year-old male purebred Rottweiler was evaluated for generalised progressive ataxia with hypermetria that was most evident in the thoracic limbs. MRI (T2-weighted) demonstrated well-circumscribed hyperintense signals within both lateral funiculi that extended from the level of the first to the sixth cervical vertebral body. A neurodegenerative disorder was suspected based on the progressive clinical course and MRI findings, and Rottweiler leukoencephalomyelopathy was subsequently confirmed via histopathology. The DARS2 gene was investigated as a causative candidate, but a sequence analysis failed to identify any disease-associated variants in the DNA sequence. Conclusion It was concluded that MRI may aid in the pre-mortem diagnosis of suspected cases of leukoencephalomyelopathy. Genes other than DARS2 may be involved in Rottweiler leukoencephalomyelopathy and may also be relevant in human leukoencephalopathy with brain stem and spinal cord involvement.
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Affiliation(s)
- Katrin Hirschvogel
- Department of Veterinary Clinical Sciences Ludwig-Maximilians-Universitaet, Neurology Service, Clinic of Small Animal Medicine, Munich, Germany
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Mausberg TB, Wess G, Simak J, Keller L, Drögemüller M, Drögemüller C, Webster MT, Stephenson H, Dukes-McEwan J, Leeb T. A locus on chromosome 5 is associated with dilated cardiomyopathy in Doberman Pinschers. PLoS One 2011; 6:e20042. [PMID: 21625443 PMCID: PMC3098859 DOI: 10.1371/journal.pone.0020042] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 04/11/2011] [Indexed: 01/22/2023] Open
Abstract
Dilated cardiomyopathy (DCM) is a heterogeneous group of heart diseases with a strong genetic background. Currently, many human DCM cases exist where no causative mutation can be identified. DCM also occurs with high prevalence in several large dog breeds. In the Doberman Pinscher a specific DCM form characterized by arrhythmias and/or echocardiographic changes has been intensively studied by veterinary cardiologists. We performed a genome-wide association study in Doberman Pinschers. Using 71 cases and 70 controls collected in Germany we identified a genome-wide significant association to DCM on chromosome 5. We validated the association in an independent cohort collected in the United Kingdom. There is no known DCM candidate gene under the association signal. Therefore, DCM in Doberman Pinschers offers the chance of identifying a novel DCM gene that might also be relevant for human health.
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Affiliation(s)
| | - Gerhard Wess
- Clinic of Small Animal Medicine, LMU University, Munich, Germany
| | - Julia Simak
- Clinic of Small Animal Medicine, LMU University, Munich, Germany
| | - Lisa Keller
- Clinic of Small Animal Medicine, LMU University, Munich, Germany
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Matthew T. Webster
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Hannah Stephenson
- Small Animal Teaching Hospital, University of Liverpool, Liverpool, United Kingdom
| | - Joanna Dukes-McEwan
- Small Animal Teaching Hospital, University of Liverpool, Liverpool, United Kingdom
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- * E-mail:
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30
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Alves L, Hülsmeyer V, Jaggy A, Fischer A, Leeb T, Drögemüller M. Polymorphisms in the ABCB1 gene in phenobarbital responsive and resistant idiopathic epileptic Border Collies. J Vet Intern Med 2011; 25:484-9. [PMID: 21488961 DOI: 10.1111/j.1939-1676.2011.0718.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Variation in the ABCB1 gene is believed to play a role in drug resistance in epilepsy. HYPOTHESIS/OBJECTIVES Variation in the ABCB1 gene encoding the permeability-glycoprotein could have an influence on phenobarbital (PB) resistance, which occurs with high frequency in idiopathic epileptic Border Collies (BCs). ANIMALS Two hundred and thirty-six client-owned BCs from Switzerland and Germany including 25 with idiopathic epilepsy, of which 13 were resistant to PB treatment. METHODS Prospective and retrospective case-control study. Data were collected retrospectively regarding disease status, antiepileptic drug (AED) therapy, and drug responsiveness. The frequency of a known mutation in the ABCB1 gene (4 base-pair deletion in the ABCB1 gene [c.296_299del]) was determined in all BCs. Additionally, the ABCB1 coding exons and flanking sequences were completely sequenced to search for additional variation in 41 BCs. Association analyses were performed in 2 case-control studies: idiopathic epileptic and control BCs and PB-responsive and resistant idiopathic epileptic BCs. RESULTS One of 236 BCs (0.4%) was heterozygous for the mutation in the ABCB1 gene (c.296_299del). A total of 23 variations were identified in the ABCB1 gene: 4 in exons and 19 in introns. The G-allele of the c.-6-180T > G variation in intron 1 was significantly more frequent in epileptic BCs resistant to PB treatment than in epileptic BCs responsive to PB treatment (P(raw) = .0025). CONCLUSIONS AND CLINICAL IMPORTANCE A variation in intron 1 of the ABCB1 gene is associated with drug responsiveness in BCs. This might indicate that regulatory mutations affecting the expression level of ABCB1 could exist, which may influence the reaction of a dog to AEDs.
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Affiliation(s)
- L Alves
- Department of Clinical Veterinary Medicine, Division of Clinical Neurology, Vetsuisse Faculty, University of Bern, Switzerland.
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31
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Swinburne JE, Bogle H, Klukowska-Rötzler J, Drögemüller M, Leeb T, Temperton E, Dolf G, Gerber V. A whole-genome scan for recurrent airway obstruction in Warmblood sport horses indicates two positional candidate regions. Mamm Genome 2010; 20:504-15. [PMID: 19760324 DOI: 10.1007/s00335-009-9214-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Accepted: 08/17/2009] [Indexed: 11/25/2022]
Abstract
Recurrent airway obstruction (RAO), or heaves, is a naturally occurring asthma-like disease that is related to sensitisation and exposure to mouldy hay and has a familial basis with a complex mode of inheritance. A genome-wide scanning approach using two half-sibling families was taken in order to locate the chromosome regions that contribute to the inherited component of this condition in these families. Initially, a panel of 250 microsatellite markers, which were chosen as a well-spaced, polymorphic selection covering the 31 equine autosomes, was used to genotype the two half-sibling families, which comprised in total 239 Warmblood horses. Subsequently, supplementary markers were added for a total of 315 genotyped markers. Each half-sibling family is focused around a severely RAO-affected stallion, and the phenotype of each individual was assessed for RAO and related signs, namely, breathing effort at rest, breathing effort at work, coughing, and nasal discharge, using an owner-based questionnaire. Analysis using a regression method for half-sibling family structures was performed using RAO and each of the composite clinical signs separately; two chromosome regions (on ECA13 and ECA15) showed a genome-wide significant association with RAO at P < 0.05. An additional 11 chromosome regions showed a more modest association. This is the first publication that describes the mapping of genetic loci involved in RAO. Several candidate genes are located in these regions, a number of which are interleukins. These are important signalling molecules that are intricately involved in the control of the immune response and are therefore good positional candidates.
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Drögemüller C, Rossi M, Gentile A, Testoni S, Jörg H, Stranzinger G, Drögemüller M, Glowatzki-Mullis ML, Leeb T. Arachnomelia in Brown Swiss cattle maps to chromosome 5. Mamm Genome 2008; 20:53-9. [DOI: 10.1007/s00335-008-9157-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 11/12/2008] [Indexed: 10/21/2022]
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Drögemüller M, Tetens J, Dalrymple B, Goldammer T, Wu CH, Cockett NE, Leeb T, Drögemüller C. A comparative radiation hybrid map of sheep chromosome 10. Cytogenet Genome Res 2008; 121:35-40. [PMID: 18544924 DOI: 10.1159/000124379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2008] [Indexed: 11/19/2022] Open
Abstract
Comparative radiation hybrid (RH) maps of individual ovine chromosomes are essential to identify genes governing traits of economic importance in sheep, a livestock species for which whole genome sequence data are not yet available. The USUoRH5000 radiation hybrid panel was used to generate a RH map of sheep chromosome 10 (OAR10) with 59 markers that span 1,422 cR over an estimated 92 Mb of the chromosome, thus providing markers every 2 Mb (equivalent to every 24 cR). The markers were derived from 46 BAC end sequences (BESs), a single EST, and 12 microsatellites. Comparative analysis showed that OAR10 shares remarkable conservation of gene order along the entire length of cattle chromosome 12 and that OAR10 contains four major homologous synteny blocks, each related to segments of the homologous human chromosome 13. Extending the comparison to the horse, dog, mouse, and chicken genome showed that these blocks share conserved synteny across species.
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Affiliation(s)
- M Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Berne, Berne, Switzerland
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Posedi J, Drögemüller M, Schnieder T, Höglund J, Lichtenfels JR, von Samson-Himmelstjerna G. Microchip capillary electrophoresis-based genetic comparison of closely related cyathostomin nematode parasites of horses using randomly amplified polymorphic DNA polymerase chain reaction. Parasitol Res 2004; 92:421-9. [PMID: 14963773 DOI: 10.1007/s00436-003-1067-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Accepted: 12/04/2003] [Indexed: 10/26/2022]
Abstract
The microchip-based capillary electrophoresis technology represents a valuable recent development for the analysis of complex DNA banding patterns. We have used this technology for the differentiation of the closely related cyathostomin species Cylicocyclus elongatus and C. insigne from the horse. We found that the Agilent 2100 bioanalyser in combination with the DNA 7500 Lab Chip were suited to perform a phylogenetic DNA fingerprinting analysis of the parasite species studied. The analysis of the electrophoretic data was optimised and it was possible to resolve a phylogenetic tree where all 12 individual worms of the two Cylicocyclus species studied were assigned to their species as determined by microscopic identification based on morphological traits. Thus, our data indicated that the procedure described here provides an additional powerful tool that can be employed for species delineation of closely related strains or species, such as the two taxa of Cylicocyclus investigated in the present study. Furthermore, by determining the second internal transcribed spacer region of three and nine individual worms for C. elongatus and C. insigne, respectively, low intraspecific variations of only up to 0.3% were demonstrated.
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Affiliation(s)
- Janez Posedi
- Institute of Parasitology, Hannover School of Veterinary Medicine, Buenteweg 17, 30559 Hannover, Germany
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