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Stanbury K, Schofield EC, McLaughlin B, Forman OP, Mellersh CS. Exonic Short Interspersed Nuclear Element Insertion in FAM161A Is Associated with Autosomal Recessive Progressive Retinal Atrophy in the English Shepherd. Genes (Basel) 2024; 15:952. [PMID: 39062732 PMCID: PMC11275866 DOI: 10.3390/genes15070952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Progressive retinal atrophies (PRAs) are a genetically heterogeneous group of inherited eye diseases that affect over 100 breeds of dog. The initial clinical sign is visual impairment in scotopic conditions, as a consequence of rod photoreceptor cell degeneration. Photopic vision degeneration then follows, due to progression of the disease to the cone photoreceptors, and ultimately results in complete blindness. Two full-sibling English Shepherds were diagnosed with PRA at approximately 5 years old and tested clear of all published PRA genetic variants. This study sought to identify the novel PRA-associated variant segregating in the breed. We utilised a combined approach of whole genome sequencing of the probands and homozygosity mapping of four cases and 22 controls and identified a short interspersed nuclear element within an alternatively spliced exon in FAM161A. The XP_005626197.1 c.17929_ins210 variant was homozygous in six PRA cases and heterozygous or absent in control dogs, consistent with a recessive mode of inheritance. The insertion is predicted to extend exon 4 by 39 aberrant amino acids followed by an early termination stop codon. PRA is intractable to treatment, so the development of a genetic screening test, based on the associated variant, is significant, because it provides dog breeders/owners with a means of reducing the frequency of the disease variant within this breed as well as minimising the risk of breeding puppies that will develop this blinding disease.
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Affiliation(s)
- Katherine Stanbury
- Canine Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Ellen C. Schofield
- Canine Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Bryan McLaughlin
- Canine Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Oliver P. Forman
- Wisdom Panel, Mars Petcare (Science and Diagnostics Division), Freeby Lane, Waltham on the Wolds, Leicestershire LE14 4RS, UK
| | - Cathryn S. Mellersh
- Canine Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
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2
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Murgiano L, Banjeree E, O'Connor C, Miyadera K, Werner P, Niggel JK, Aguirre GD, Casal ML. A naturally occurring canine model of syndromic congenital microphthalmia. G3 (BETHESDA, MD.) 2024; 14:jkae067. [PMID: 38682429 DOI: 10.1093/g3journal/jkae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/13/2024] [Indexed: 05/01/2024]
Abstract
In humans, the prevalence of congenital microphthalmia is estimated to be 0.2-3.0 for every 10,000 individuals, with nonocular involvement reported in ∼80% of cases. Inherited eye diseases have been widely and descriptively characterized in dogs, and canine models of ocular diseases have played an essential role in unraveling the pathophysiology and development of new therapies. A naturally occurring canine model of a syndromic disorder characterized by microphthalmia was discovered in the Portuguese water dog. As nonocular findings included tooth enamel malformations, stunted growth, anemia, and thrombocytopenia, we hence termed this disorder Canine Congenital Microphthalmos with Hematopoietic Defects. Genome-wide association study and homozygosity mapping detected a 2 Mb candidate region on canine chromosome 4. Whole-genome sequencing and mapping against the Canfam4 reference revealed a Short interspersed element insertion in exon 2 of the DNAJC1 gene (g.74,274,883ins[T70]TGCTGCTTGGATT). Subsequent real-time PCR-based mass genotyping of a larger Portuguese water dog population found that the homozygous mutant genotype was perfectly associated with the Canine Congenital Microphthalmos with Hematopoietic Defects phenotype. Biallelic variants in DNAJC21 are mostly found to be associated with bone marrow failure syndrome type 3, with a phenotype that has a certain degree of overlap with Fanconi anemia, dyskeratosis congenita, Shwachman-Diamond syndrome, Diamond-Blackfan anemia, and reports of individuals showing thrombocytopenia, microdontia, and microphthalmia. We, therefore, propose Canine Congenital Microphthalmos with Hematopoietic Defects as a naturally occurring model for DNAJC21-associated syndromes.
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Affiliation(s)
- Leonardo Murgiano
- Department of Clinical Sciences & Advanced Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Sylvia M. Van Sloun Laboratory for Canine Genomic Analysis, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Esha Banjeree
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cynthia O'Connor
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- East Bridgewater Veterinary Hospitla, East Bridgewater, MA 02333, USA
| | - Keiko Miyadera
- Department of Clinical Sciences & Advanced Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Petra Werner
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Genetic Diagnostic Laboratory, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jessica K Niggel
- Department of Clinical Sciences & Advanced Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Sylvia M. Van Sloun Laboratory for Canine Genomic Analysis, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gustavo D Aguirre
- Department of Clinical Sciences & Advanced Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Sylvia M. Van Sloun Laboratory for Canine Genomic Analysis, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Margret L Casal
- Department of Clinical Sciences & Advanced Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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3
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Cocostîrc V, Paștiu AI, Pusta DL. An Overview of Canine Inherited Neurological Disorders with Known Causal Variants. Animals (Basel) 2023; 13:3568. [PMID: 38003185 PMCID: PMC10668755 DOI: 10.3390/ani13223568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Hereditary neurological conditions documented in dogs encompass congenital, neonatal, and late-onset disorders, along with both progressive and non-progressive forms. In order to identify the causal variant of a disease, the main two approaches are genome-wide investigations and candidate gene investigation. Online Mendelian Inheritance in Animals currently lists 418 Mendelian disorders specific to dogs, of which 355 have their likely causal genetic variant identified. This review aims to summarize the current knowledge on the canine nervous system phenes and their genetic causal variant. It has been noted that the majority of these diseases have an autosomal recessive pattern of inheritance. Additionally, the dog breeds that are more prone to develop such diseases are the Golden Retriever, in which six inherited neurological disorders with a known causal variant have been documented, and the Belgian Shepherd, in which five such disorders have been documented. DNA tests can play a vital role in effectively managing and ultimately eradicating inherited diseases.
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Affiliation(s)
- Vlad Cocostîrc
- Department of Genetics and Hereditary Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (A.I.P.); (D.L.P.)
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4
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Ciucani MM, Ramos-Madrigal J, Hernández-Alonso G, Carmagnini A, Aninta SG, Sun X, Scharff-Olsen CH, Lanigan LT, Fracasso I, Clausen CG, Aspi J, Kojola I, Baltrūnaitė L, Balčiauskas L, Moore J, Åkesson M, Saarma U, Hindrikson M, Hulva P, Bolfíková BČ, Nowak C, Godinho R, Smith S, Paule L, Nowak S, Mysłajek RW, Lo Brutto S, Ciucci P, Boitani L, Vernesi C, Stenøien HK, Smith O, Frantz L, Rossi L, Angelici FM, Cilli E, Sinding MHS, Gilbert MTP, Gopalakrishnan S. The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs. iScience 2023; 26:107307. [PMID: 37559898 PMCID: PMC10407145 DOI: 10.1016/j.isci.2023.107307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/04/2022] [Accepted: 07/04/2023] [Indexed: 08/11/2023] Open
Abstract
The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment.
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Affiliation(s)
- Marta Maria Ciucani
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Germán Hernández-Alonso
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alberto Carmagnini
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Sabhrina Gita Aninta
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Xin Sun
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Liam Thomas Lanigan
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ilaria Fracasso
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Cecilie G. Clausen
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, Finland
| | - Ilpo Kojola
- Natural Resources Institute Finland, Rovaniemi, Finland
| | | | | | - Jane Moore
- Società Amatori Cirneco dell’Etna, Modica (RG), Italy
| | - Mikael Åkesson
- Swedish University of Agricultural Sciences, Grimsö Wildlife Research Station, Department of Ecology, Riddarhyttan, Sweden
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Pavel Hulva
- Charles University, Department of Zoology, Faculty of Science, Prague 2, Czech Republic
| | | | - Carsten Nowak
- Center for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Raquel Godinho
- CIBIO/InBIO, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Steve Smith
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Ladislav Paule
- Faculty of Forestry, Technical University, Zvolen, Slovakia
| | - Sabina Nowak
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | - Robert W. Mysłajek
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | - Sabrina Lo Brutto
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technology (STEBICEF), University of Palermo, Palermo, Italy
- Museum of Zoology "P. Doderlein", SIMUA, University of Palermo, Palermo, Italy
| | - Paolo Ciucci
- Università di Roma La Sapienza, Department Biology and Biotechnologies "Charles Darwin", Roma, Italy
| | - Luigi Boitani
- Università di Roma La Sapienza, Department Biology and Biotechnologies "Charles Darwin", Roma, Italy
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Hans K. Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Oliver Smith
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - Francesco Maria Angelici
- FIZV, Via Marco Aurelio 2, Roma, Italy
- National Center for Wildlife, Al Imam Faisal Ibn Turki Ibn Abdullah, Ulaishah, Saudi Arabia
| | - Elisabetta Cilli
- Laboratory of Ancient DNA, Department of Cultural Heritage (DBC), University of Bologna, Bologna, Italy
| | - Mikkel-Holger S. Sinding
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
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5
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Flack N, Drown M, Walls C, Pratte J, McLain A, Faulk C. Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul. NAR Genom Bioinform 2023; 5:lqad033. [PMID: 37025970 PMCID: PMC10071556 DOI: 10.1093/nargab/lqad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/10/2023] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
Pallas's cat, or the manul cat (Otocolobus manul), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with O. manul's zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17097 bp mitogenome for O. manul. The primary nuclear assembly had 56× sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score for Carnivora-specific genes. High genome collinearity within Felidae permitted alignment-based scaffolding onto the fishing cat (Prionailurus viverrinus) reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; 61 differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance between Felinae nuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.
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Affiliation(s)
- Nicole Flack
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Melissa Drown
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Carrie Walls
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jay Pratte
- Bloomington Parks and Recreation, Miller Park Zoo, Bloomington, IL 61701, USA
| | - Adam McLain
- Department of Biology and Chemistry, SUNY Polytechnic Institute, Utica, NY 13502, USA
| | - Christopher Faulk
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
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6
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Leeb T, Bannasch D, Schoenebeck JJ. Identification of Genetic Risk Factors for Monogenic and Complex Canine Diseases. Annu Rev Anim Biosci 2023; 11:183-205. [PMID: 36322969 DOI: 10.1146/annurev-animal-050622-055534] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Advances in DNA sequencing and other technologies have greatly facilitated the identification of genetic risk factors for inherited diseases in dogs. We review recent technological developments based on selected examples from canine disease genetics. The identification of disease-causing variants in dogs with monogenic diseases may become a widely employed diagnostic approach in clinical veterinary medicine in the not-too-distant future. Diseases with complex modes of inheritance continue to pose challenges to researchers but have also become much more tangible than in the past. In addition to strategies for identifying genetic risk factors, we provide some thoughts on the interpretation of sequence variants that are largely inspired by developments in human clinical genetics.
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Affiliation(s)
- Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland;
| | - Danika Bannasch
- Department of Population Health and Reproduction, University of California, Davis, California, USA;
| | - Jeffrey J Schoenebeck
- The Roslin Institute and Royal (Dick) School for Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom;
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7
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Srikanth K, von Pfeil DJF, Stanley BJ, Griffitts C, Huson HJ. Genome Wide Association Study with Imputed Whole Genome Sequence Data Identifies a 431 kb Risk Haplotype on CFA18 for Congenital Laryngeal Paralysis in Alaskan Sled Dogs. Genes (Basel) 2022; 13:genes13101808. [PMID: 36292693 PMCID: PMC9602090 DOI: 10.3390/genes13101808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Congenital laryngeal paralysis (CLP) is an inherited disorder that affects the ability of the dog to exercise and precludes it from functioning as a working sled dog. Though CLP is known to occur in Alaskan sled dogs (ASDs) since 1986, the genetic mutation underlying the disease has not been reported. Using a genome-wide association study (GWAS), we identified a 708 kb region on CFA 18 harboring 226 SNPs to be significantly associated with CLP. The significant SNPs explained 47.06% of the heritability of CLP. We narrowed the region to 431 kb through autozygosity mapping and found 18 of the 20 cases to be homozygous for the risk haplotype. Whole genome sequencing of two cases and a control ASD, and comparison with the genome of 657 dogs from various breeds, confirmed the homozygous status of the risk haplotype to be unique to the CLP cases. Most of the dogs that were homozygous for the risk allele had blue eyes. Gene annotation and a gene-based association study showed that the risk haplotype encompasses genes implicated in developmental and neurodegenerative disorders. Pathway analysis showed enrichment of glycoproteins and glycosaminoglycans biosynthesis, which play a key role in repairing damaged nerves. In conclusion, our results suggest an important role for the identified candidate region in CLP.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Department of Animal Science, College of Agriculture and Life Science, Cornell University, Ithaca, NY 14850, USA
| | | | - Bryden J. Stanley
- Department of Small Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | | | - Heather J. Huson
- Department of Animal Science, College of Agriculture and Life Science, Cornell University, Ithaca, NY 14850, USA
- Correspondence:
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Moura E, Tasqueti UI, Mangrich-Rocha RMV, Filho JRE, de Farias MR, Pimpão CT. Inborn Errors of Metabolism in Dogs: Historical, Metabolic, Genetic, and Clinical Aspects. Top Companion Anim Med 2022; 51:100731. [DOI: 10.1016/j.tcam.2022.100731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/11/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
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Kosushkin SA, Ustyantsev IG, Borodulina OR, Vassetzky NS, Kramerov DA. Tail Wags Dog’s SINE: Retropositional Mechanisms of Can SINE Depend on Its A-Tail Structure. BIOLOGY 2022; 11:biology11101403. [PMID: 36290307 PMCID: PMC9599045 DOI: 10.3390/biology11101403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/17/2022] [Accepted: 09/22/2022] [Indexed: 11/25/2022]
Abstract
Simple Summary The genomes of higher organisms including humans are invaded by millions of repetitive elements (transposons), which can sometimes be deleterious or beneficial for hosts. Many aspects of the mechanisms underlying the expansion of transposons in the genomes remain unclear. Short retrotransposons (SINEs) are one of the most abundant classes of genomic repeats. Their amplification relies on two major processes: transcription and reverse transcription. Here, short retrotransposons of dogs and other canids called Can SINE were analyzed. Their amplification was extraordinarily active in the wolf and, particularly, dog breeds relative to other canids. We also studied a variation of their transcription mechanism involving the polyadenylation of transcripts. An analysis of specific signals involved in this process allowed us to conclude that Can SINEs could alternate amplification with and without polyadenylation in their evolution. Understanding the mechanisms of transposon replication can shed light on the mechanisms of genome function. Abstract SINEs, non-autonomous short retrotransposons, are widespread in mammalian genomes. Their transcripts are generated by RNA polymerase III (pol III). Transcripts of certain SINEs can be polyadenylated, which requires polyadenylation and pol III termination signals in their sequences. Our sequence analysis divided Can SINEs in canids into four subfamilies, older a1 and a2 and younger b1 and b2. Can_b2 and to a lesser extent Can_b1 remained retrotranspositionally active, while the amplification of Can_a1 and Can_a2 ceased long ago. An extraordinarily high Can amplification was revealed in different dog breeds. Functional polyadenylation signals were analyzed in Can subfamilies, particularly in fractions of recently amplified, i.e., active copies. The transcription of various Can constructs transfected into HeLa cells proposed AATAAA and (TC)n as functional polyadenylation signals. Our analysis indicates that older Can subfamilies (a1, a2, and b1) with an active transcription terminator were amplified by the T+ mechanism (with polyadenylation of pol III transcripts). In the currently active Can_b2 subfamily, the amplification mechanisms with (T+) and without the polyadenylation of pol III transcripts (T−) irregularly alternate. The active transcription terminator tends to shorten, which renders it nonfunctional and favors a switch to the T− retrotransposition. The activity of a truncated terminator is occasionally restored by its elongation, which rehabilitates the T+ retrotransposition for a particular SINE copy.
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10
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A SINE Insertion in F8 Gene Leads to Severe Form of Hemophilia A in a Family of Rhodesian Ridgebacks. Genes (Basel) 2021; 12:genes12020134. [PMID: 33494213 PMCID: PMC7909816 DOI: 10.3390/genes12020134] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/30/2022] Open
Abstract
Hemophilia A is the most common coagulation factor disorder in humans and dogs. The disease is characterized by the lack or diminished activity of Factor VIII (FVIII), caused by variants in the F8 gene and inherited as an X chromosomal trait. Two related male Rhodesian Ridgebacks were diagnosed with Hemophilia A due to reduced FVIII activity. The purpose of the study was to determine the genetic cause and give breeding advice for the remaining family members in order to eradicate the variant. By Sanger sequencing a short interspersed nuclear element (SINE) insertion in exon 14 of the F8 gene was found. Perfect correlation of this genetic variant with clinical signs of hemophilia A in the family tree, and the lack of this genetic variant in more than 500 unrelated dogs of the same and other breeds, confirms the hypothesis of this SINE being the underlying genetic cause of Hemophilia A in this family. The identification of clinically unaffected female carriers allows subsequent exclusion of these animals from breeding, to avoid future production of clinically affected male offspring and more subclinical female carriers.
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Ramos-Madrigal J, Sinding MHS, Carøe C, Mak SST, Niemann J, Samaniego Castruita JA, Fedorov S, Kandyba A, Germonpré M, Bocherens H, Feuerborn TR, Pitulko VV, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Larson G, Frantz LAF, Willerslev E, Meldgaard M, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig Ø, Hansen AJ, Gilbert MTP, Gopalakrishnan S. Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages. Curr Biol 2021; 31:198-206.e8. [PMID: 33125870 PMCID: PMC7809626 DOI: 10.1016/j.cub.2020.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/28/2020] [Accepted: 10/01/2020] [Indexed: 12/30/2022]
Abstract
Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.1 Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM)1-3 and replaced local wolf populations.4 Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.35 Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.67 However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.
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Affiliation(s)
- Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Natural History Museum, University of Oslo, Oslo, Norway; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; Greenland Institute of Natural Resources, Nuuk, Greenland; Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Christian Carøe
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Sarah S T Mak
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Niemann
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Sergey Fedorov
- Mammoth Museum of North-Eastern Federal University, Yakutsk, Russia
| | - Alexander Kandyba
- Department of Stone Age Archeology, Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Mietje Germonpré
- Directorate Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Hervé Bocherens
- Department of Geosciences, Biogeology, University of Tübingen, Tübingen, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment, Tübingen, Germany
| | - Tatiana R Feuerborn
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Elena Y Pavlova
- Arctic and Antarctic Research Institute, St. Petersburg, Russia
| | | | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Varvara V Ivanova
- VNIIOkeangeologia Research Institute (The All-Russian Research Institute of Geology and Mineral Resources of the World Ocean), St. Petersburg, Russia
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK; Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Eske Willerslev
- Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Danish Institute for Advanced Study (D-IAS), University of Southern Denmark, Odense, Denmark; Department of Zoology, University of Cambridge, Cambridge, UK; Wellcome Trust Sanger Institute, University of Cambridge, Cambridge, UK
| | - Morten Meldgaard
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bent Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Thomas Sicheritz-Ponten
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Lutz Bachmann
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Øystein Wiig
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Anders J Hansen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; The Qimmeq Project, University of Greenland, Nuussuaq, Greenland; Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.
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12
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Letko A, Minor KM, Friedenberg SG, Shelton GD, Salvador JP, Mandigers PJJ, Leegwater PAJ, Winkler PA, Petersen-Jones SM, Stanley BJ, Ekenstedt KJ, Johnson GS, Hansen L, Jagannathan V, Mickelson JR, Drögemüller C. A CNTNAP1 Missense Variant Is Associated with Canine Laryngeal Paralysis and Polyneuropathy. Genes (Basel) 2020; 11:E1426. [PMID: 33261176 PMCID: PMC7761076 DOI: 10.3390/genes11121426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023] Open
Abstract
Laryngeal paralysis associated with a generalized polyneuropathy (LPPN) most commonly exists in geriatric dogs from a variety of large and giant breeds. The purpose of this study was to discover the underlying genetic and molecular mechanisms in a younger-onset form of this neurodegenerative disease seen in two closely related giant dog breeds, the Leonberger and Saint Bernard. Neuropathology of an affected dog from each breed showed variable nerve fiber loss and scattered inappropriately thin myelinated fibers. Using across-breed genome-wide association, haplotype analysis, and whole-genome sequencing, we identified a missense variant in the CNTNAP1 gene (c.2810G>A; p.Gly937Glu) in which homozygotes in both studied breeds are affected. CNTNAP1 encodes a contactin-associated protein important for organization of myelinated axons. The herein described likely pathogenic CNTNAP1 variant occurs in unrelated breeds at variable frequencies. Individual homozygous mutant LPPN-affected Labrador retrievers that were on average four years younger than dogs affected by geriatric onset laryngeal paralysis polyneuropathy could be explained by this variant. Pathologic changes in a Labrador retriever nerve biopsy from a homozygous mutant dog were similar to those of the Leonberger and Saint Bernard. The impact of this variant on health in English bulldogs and Irish terriers, two breeds with higher CNTNAP1 variant allele frequencies, remains unclear. Pathogenic variants in CNTNAP1 have previously been reported in human patients with lethal congenital contracture syndrome and hypomyelinating neuropathy, including vocal cord palsy and severe respiratory distress. This is the first report of contactin-associated LPPN in dogs characterized by a deleterious variant that most likely predates modern breed establishment.
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Affiliation(s)
- Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (V.J.); (C.D.)
| | - Katie M. Minor
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (K.M.M.); (J.R.M.)
| | - Steven G. Friedenberg
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA;
| | - G. Diane Shelton
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093-0709, USA; (G.D.S.); (J.P.S.)
| | - Jill Pesayco Salvador
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093-0709, USA; (G.D.S.); (J.P.S.)
| | - Paul J. J. Mandigers
- Department of Clinical Sciences, Utrecht University, 3584 CM Utrecht, The Netherlands; (P.J.J.M.); (P.A.J.L.)
| | - Peter A. J. Leegwater
- Department of Clinical Sciences, Utrecht University, 3584 CM Utrecht, The Netherlands; (P.J.J.M.); (P.A.J.L.)
| | - Paige A. Winkler
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (P.A.W.); (S.M.P.-J.); (B.J.S.)
| | - Simon M. Petersen-Jones
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (P.A.W.); (S.M.P.-J.); (B.J.S.)
| | - Bryden J. Stanley
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (P.A.W.); (S.M.P.-J.); (B.J.S.)
| | - Kari J. Ekenstedt
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA;
| | - Gary S. Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (G.S.J.); (L.H.)
| | - Liz Hansen
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (G.S.J.); (L.H.)
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (V.J.); (C.D.)
| | - James R. Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (K.M.M.); (J.R.M.)
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; (V.J.); (C.D.)
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13
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Sinding MHS, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Pitulko VV, Kuderna L, Feuerborn TR, Frantz LAF, Vieira FG, Niemann J, Samaniego Castruita JA, Carøe C, Andersen-Ranberg EU, Jordan PD, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Willerslev E, Skoglund P, Fredholm M, Wennerberg SE, Heide-Jørgensen MP, Dietz R, Sonne C, Meldgaard M, Dalén L, Larson G, Petersen B, Sicheritz-Pontén T, Bachmann L, Wiig Ø, Marques-Bonet T, Hansen AJ, Gilbert MTP. Arctic-adapted dogs emerged at the Pleistocene-Holocene transition. Science 2020; 368:1495-1499. [PMID: 32587022 PMCID: PMC7116267 DOI: 10.1126/science.aaz8599] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/06/2020] [Indexed: 12/18/2022]
Abstract
Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.
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Affiliation(s)
- Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
- Natural History Museum, University of Oslo, Oslo, Norway
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
- Greenland Institute of Natural Resources, Nuuk, Greenland
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | | | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Lukas Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Tatiana R Feuerborn
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Filipe G Vieira
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Niemann
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- BioArch, Department of Archaeology, University of York, York, UK
| | | | - Christian Carøe
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emilie U Andersen-Ranberg
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
- Department of Clinical Veterinary Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Peter D Jordan
- Arctic Centre and Groningen Institute of Archaeology, University of Groningen, Netherlands
| | - Elena Y Pavlova
- Arctic and Antarctic Research Institute, St. Petersburg, Russia
| | | | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Varvara V Ivanova
- VNIIOkeangeologia Research Institute (The All-Russian Research Institute of Geology and Mineral Resources of the World Ocean), St. Petersburg, Russia
| | - Eske Willerslev
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Danish Institute for Advanced Study (D-IAS), University of Southern Denmark, Odense, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, University of Cambridge, Cambridge, UK
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Francis Crick Institute, London, UK
| | - Merete Fredholm
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Sanne Eline Wennerberg
- Ministry of Fisheries, Hunting and Agriculture, Government of Greenland, Nuuk, Greenland
| | | | - Rune Dietz
- Department of Bioscience, Arctic Research Centre, Aarhus University, Roskilde, Denmark
| | - Christian Sonne
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
- Department of Bioscience, Arctic Research Centre, Aarhus University, Roskilde, Denmark
- Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Morten Meldgaard
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Bent Petersen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Thomas Sicheritz-Pontén
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Lutz Bachmann
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Øystein Wiig
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain.
- Catalan Institution of Research and Advanced Studies, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
- The Qimmeq Project, University of Greenland, Nuussuaq, Greenland
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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14
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Jahns H, Vernau KM, Nolan CM, O'Neill EJ, Shiel RE, Shelton GD. Polyneuropathy in Young Siberian Huskies Caused by Degenerative and Inflammatory Diseases. Vet Pathol 2020; 57:666-674. [PMID: 32578500 DOI: 10.1177/0300985820934112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Polyneuropathy is defined as the simultaneous dysfunction of several peripheral nerves. In dogs, a number of breeds are predisposed to a variety of immune-mediated and/or degenerative inherited forms of polyneuropathy, with laryngeal paralysis and/or megaesophagus as important clinical features of many of these conditions. This case series describes degenerative and inflammatory polyneuropathies in 7 young Siberian huskies that were categorized based on clinicopathological characteristics as follows: (1) slowly progressive laryngeal paralysis and megaesophagus caused by primary axonal degeneration with large fiber loss (n = 2); (2) slowly progressive polyneuropathy without megaesophagus or laryngeal paralysis caused by primary axonal degeneration with large fiber loss (n = 2); (3) acute inflammatory demyelinating neuropathy causing sensory, motor and autonomic nerve deficits (n = 2); and (4) ganglioradiculitis (sensory neuronopathy; n = 1). Based on the predominantly young age at onset, slow progression, relatedness of affected dogs, and clinical and pathological similarities with inherited neuropathies reported in other dog breeds, a hereditary basis for the degenerative polyneuropathies in Siberian huskies is suspected. However, 5 different mutations in 3 genes known to cause polyneuropathy in other dog breeds (NDRG1, ARHGEF10, or RAB3GAP1) were not detected in the affected Siberian huskies suggesting that more genetic variants remain to be identified. This study highlights the varied underlying lesions of polyneuropathies in young Siberian huskies.
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Affiliation(s)
- Hanne Jahns
- 8797University College Dublin, Dublin, Ireland
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15
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Barthélémy I, Hitte C, Tiret L. The Dog Model in the Spotlight: Legacy of a Trustful Cooperation. J Neuromuscul Dis 2020; 6:421-451. [PMID: 31450509 PMCID: PMC6918919 DOI: 10.3233/jnd-190394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Dogs have long been used as a biomedical model system and in particular as a preclinical proof of concept for innovative therapies before translation to humans. A recent example of the utility of this animal model is the promising myotubularin gene delivery in boys affected by X-linked centronuclear myopathy after successful systemic, long-term efficient gene therapy in Labrador retrievers. Mostly, this is due to unique features that make dogs an optimal system. The continuous emergence of spontaneous inherited disorders enables the identification of reliable complementary molecular models for human neuromuscular disorders (NMDs). Dogs’ characteristics including size, lifespan and unprecedented medical care level allow a comprehensive longitudinal description of diseases. Moreover, the highly similar pathogenic mechanisms with human patients yield to translational robustness. Finally, interindividual phenotypic heterogeneity between dogs helps identifying modifiers and anticipates precision medicine issues. This review article summarizes the present list of molecularly characterized dog models for NMDs and provides an exhaustive list of the clinical and paraclinical assays that have been developed. This toolbox offers scientists a sensitive and reliable system to thoroughly evaluate neuromuscular function, as well as efficiency and safety of innovative therapies targeting these NMDs. This review also contextualizes the model by highlighting its unique genetic value, shaped by the long-term coevolution of humans and domesticated dogs. Because the dog is one of the most protected research animal models, there is considerable opposition to include it in preclinical projects, posing a threat to the use of this model. We thus discuss ethical issues, emphasizing that unlike many other models, the dog also benefits from its contribution to comparative biomedical research with a drastic reduction in the prevalence of morbid alleles in the breeding stock and an improvement in medical care.
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Affiliation(s)
- Inès Barthélémy
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, École nationale vétérinaire d'Alfort, Maisons-Alfort, France
| | - Christophe Hitte
- CNRS, University of Rennes 1, UMR 6290, IGDR, Faculty of Medicine, SFR Biosit, Rennes, France
| | - Laurent Tiret
- U955 - IMRB, Team 10 - Biology of the neuromuscular system, Inserm, UPEC, EFS, École nationale vétérinaire d'Alfort, Maisons-Alfort, France
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16
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Jagannathan V, Drögemüller C, Leeb T. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 2019; 50:695-704. [PMID: 31486122 PMCID: PMC6842318 DOI: 10.1111/age.12834] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2019] [Indexed: 12/16/2022]
Abstract
The domestic dog serves as an excellent model to investigate the genetic basis of disease. More than 400 heritable traits analogous to human diseases have been described in dogs. To further canine medical genetics research, we established the Dog Biomedical Variant Database Consortium (DBVDC) and present a comprehensive list of functionally annotated genome variants that were identified with whole genome sequencing of 582 dogs from 126 breeds and eight wolves. The genomes used in the study have a minimum coverage of 10× and an average coverage of ~24×. In total, we identified 23 133 692 single-nucleotide variants (SNVs) and 10 048 038 short indels, including 93% undescribed variants. On average, each individual dog genome carried ∼4.1 million single-nucleotide and ~1.4 million short-indel variants with respect to the reference genome assembly. About 2% of the variants were located in coding regions of annotated genes and loci. Variant effect classification showed 247 141 SNVs and 99 562 short indels having moderate or high impact on 11 267 protein-coding genes. On average, each genome contained heterozygous loss-of-function variants in 30 potentially embryonic lethal genes and 97 genes associated with developmental disorders. More than 50 inherited disorders and traits have been unravelled using the DBVDC variant catalogue, enabling genetic testing for breeding and diagnostics. This resource of annotated variants and their corresponding genotype frequencies constitutes a highly useful tool for the identification of potential variants causative for rare inherited disorders in dogs.
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Affiliation(s)
- V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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17
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Granger N, Luján Feliu-Pascual A, Spicer C, Ricketts S, Hitti R, Forman O, Hersheson J, Houlden H. Charcot-Marie-Tooth type 4B2 demyelinating neuropathy in miniature Schnauzer dogs caused by a novel splicing SBF2 (MTMR13) genetic variant: a new spontaneous clinical model. PeerJ 2019; 7:e7983. [PMID: 31772832 PMCID: PMC6875392 DOI: 10.7717/peerj.7983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/02/2019] [Indexed: 01/23/2023] Open
Abstract
Background Charcot-Marie-Tooth (CMT) disease is the most common neuromuscular disorder in humans affecting 40 out of 100,000 individuals. In 2008, we described the clinical, electrophysiological and pathological findings of a demyelinating motor and sensory neuropathy in Miniature Schnauzer dogs, with a suspected autosomal recessive mode of inheritance based on pedigree analysis. The discovery of additional cases has followed this work and led to a genome-wide association mapping approach to search for the underlying genetic cause of the disease. Methods For genome wide association screening, genomic DNA samples from affected and unaffected dogs were genotyped using the Illumina CanineHD SNP genotyping array. SBF2 and its variant were sequenced using primers and PCRs. RNA was extracted from muscle of an unaffected and an affected dog and RT-PCR performed. Immunohistochemistry for myelin basic protein was performed on peripheral nerve section specimens. Results The genome-wide association study gave an indicative signal on canine chromosome 21. Although the signal was not of genome-wide significance due to the small number of cases, the SBF2 (also known as MTMR13) gene within the region of shared case homozygosity was a strong positional candidate, as 22 genetic variants in the gene have been associated with demyelinating forms of Charcot-Marie-Tooth disease in humans. Sequencing of SBF2 in cases revealed a splice donor site genetic variant, resulting in cryptic splicing and predicted early termination of the protein based on RNA sequencing results. Conclusions This study reports the first genetic variant in Miniature Schnauzer dogs responsible for the occurrence of a demyelinating peripheral neuropathy with abnormally folded myelin. This discovery establishes a genotype/phenotype correlation in affected Miniature Schnauzers that can be used for the diagnosis of these dogs. It further supports the dog as a natural model of a human disease; in this instance, Charcot-Marie-Tooth disease. It opens avenues to search the biological mechanisms responsible for the disease and to test new therapies in a non-rodent large animal model. In particular, recent gene editing methods that led to the restoration of dystrophin expression in a canine model of muscular dystrophy could be applied to other canine models such as this before translation to humans.
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Affiliation(s)
- Nicolas Granger
- Royal Veterinary College, University of London, Hatfield, United Kingdom.,Bristol Veterinary Specialists, CVS Referrals, Bristol, United Kingdom
| | | | - Charlotte Spicer
- Department of Molecular Neuroscience, UCL Institute of Neurology & National Hospital for Neurology and Neurosurgery & London, London, United Kingdom
| | - Sally Ricketts
- Kennel Club Genetics Centre, Animal Health Trust, Newmarket, United Kingdom
| | - Rebekkah Hitti
- Kennel Club Genetics Centre, Animal Health Trust, Newmarket, United Kingdom
| | - Oliver Forman
- Kennel Club Genetics Centre, Animal Health Trust, Newmarket, United Kingdom
| | - Joshua Hersheson
- Department of Molecular Neuroscience, UCL Institute of Neurology & National Hospital for Neurology and Neurosurgery & London, London, United Kingdom
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology & National Hospital for Neurology and Neurosurgery & London, London, United Kingdom
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18
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Stassen QEM, Grinwis GCM, van Rhijn NC, Beukers M, Verhoeven-Duif NM, Leegwater PAJ. Focal epilepsy with fear-related behavior as primary presentation in Boerboel dogs. J Vet Intern Med 2018; 33:694-700. [PMID: 30580458 PMCID: PMC6430876 DOI: 10.1111/jvim.15346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 10/05/2018] [Indexed: 11/27/2022] Open
Abstract
Background Focal seizures with fear as a primary ictal manifestation, their diagnostic challenges, and impact on quality of life are well described in human medicine. Reports focusing on ictal fear‐like behavior in animals are scarce. Objective To describe the clinical and histopathological characteristics of a novel focal epilepsy in Boerboel dogs. Animals Five client‐owned Boerboel littermates presented for evaluation of sudden episodes of severe fear‐related behavior. Methods Clinical examination, complete blood cell count, routine blood biochemistry, and urinalysis were performed in all dogs. Magnetic resonance imaging (MRI) scans of the brain were performed in 3 affected Boerboels. In addition, in 2 affected Boerboels, metabolic screening, cerebrospinal fluid (CSF) analysis, and necropsy were performed. Results Onset of signs was 3 months of age in all affected Boerboels. All Boerboels howled loudly, had an extremely fearful facial expression and trembled during seizures. All affected Boerboels also had autonomic or motor signs. Results of laboratory investigations, diagnostic imaging, and metabolic screening were generally unremarkable. Histopathology showed moderate numbers of single large vacuoles in the perikaryon of neurons throughout the brain, specifically in the deeper cerebral cortical regions. Family history, pedigree analysis, and the homogenous phenotype were suggestive of autosomal recessive inheritance. Conclusions and Clinical Importance The observed paroxysmal fear‐related behavior represents a newly recognized hereditary focal epilepsy in dogs with distinctive clinical and histopathologic features. Veterinarians should be aware that sudden episodes of unusual behavior can represent focal epilepsy.
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Affiliation(s)
- Quirine E M Stassen
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Guy C M Grinwis
- Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Nieke C van Rhijn
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Martjin Beukers
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Nanda M Verhoeven-Duif
- Department of Genetics and Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Peter A J Leegwater
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Panahi Y, Azimi A, Naderi M, Jadidi K, Sahebkar A. An analytical enrichment-based review of structural genetic studies on keratoconus. J Cell Biochem 2018; 120:4748-4756. [PMID: 30260013 DOI: 10.1002/jcb.27764] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 09/06/2018] [Indexed: 12/19/2022]
Abstract
Keratoconus is a progressive bilateral corneal protrusion that leads to irregular astigmatism and impairment of vision. Keratoconus is an etiologically heterogeneous corneal dystrophy and both environmental and genetic factors play a role in its etiopathogenesis. In this analytical review, we have studied all the genes that are structurally associated with keratoconus and have tried to explain the function of each gene and its association with other eye disorders in a concise way. In addition, using gene set enrichment analysis, it was attempted to find the most important impaired metabolic pathways in keratoconus. Several genetic studies have been carried out on keratoconus and several genes have been identified as risk factors involved in the etiology of the disease. In the current study, 16 studies, including nine association studies, five genome-wide association studies, one linkage study, and one meta-analysis, were reviewed and based on the 19 genes found, enrichment was performed and the most important metabolic pathways involved in the disease were identified. The enrichment results indicated that the two pathways, interleukin 1 processing and assembly of collagen fibrils, are significantly associated with the disease. Obviously, the results of this study, in addition to providing information about the genes involved in the disease, can provide an integrated insight into the gene-based etiology of keratoconus and therapeutic opportunities thereof.
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Affiliation(s)
- Yunes Panahi
- Chemical Injuries Research Center, System Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Azimi
- Department of Ophthalmology, Poostchi Eye Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mostafa Naderi
- Chemical Injuries Research Center, System Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Khosrow Jadidi
- Chemical Injuries Research Center, System Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Neurogenic inflammation Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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Becker D, Minor KM, Letko A, Ekenstedt KJ, Jagannathan V, Leeb T, Shelton GD, Mickelson JR, Drögemüller C. A GJA9 frameshift variant is associated with polyneuropathy in Leonberger dogs. BMC Genomics 2017; 18:662. [PMID: 28841859 PMCID: PMC5574090 DOI: 10.1186/s12864-017-4081-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/21/2017] [Indexed: 01/15/2023] Open
Abstract
Background Many inherited polyneuropathies (PN) observed in dogs have clinical similarities to the genetically heterogeneous group of Charcot-Marie-Tooth (CMT) peripheral neuropathies in humans. The canine disorders collectively show a variable expression of progressive clinical signs and ages of onset, and different breed prevalences. Previously in the Leonberger breed, a variant highly associated with a juvenile-onset PN was identified in the canine orthologue of a CMT-associated gene. As this deletion in ARHGEF10 (termed LPN1) does not explain all cases, PN in this breed may encompass variants in several genes with similar clinical and histopathological features. Results A genome-wide comparison of 173 k SNP genotypes of 176 cases, excluding dogs homozygous for the ARHGEF10 variant, and 138 controls, was carried out to detect further PN-associated variants. A single suggestive significant association signal on CFA15 was found. The genome of a PN-affected Leonberger homozygous for the associated haplotype was sequenced and variants in the 7.7 Mb sized critical interval were identified. These variants were filtered against a database of variants observed in 202 genomes of various dog breeds and 3 wolves, and 6 private variants in protein-coding genes, all in complete linkage disequilibrium, plus 92 non-coding variants were revealed. Five of the coding variants were predicted to have low or moderate effect on the encoded protein, whereas a 2 bp deletion in GJA9 results in a frameshift of high impact. GJA9 encodes connexin 59, a connexin gap junction family protein, and belongs to a group of CMT-associated genes that have emerged as important components of peripheral myelinated nerve fibers. The association between the GJA9 variant and PN was confirmed in an independent cohort of 296 cases and 312 controls. Population studies showed a dominant mode of inheritance, an average age of onset of approximately 6 years, and incomplete penetrance. Conclusions This GJA9 variant represents a highly probable candidate variant for another form of PN in Leonberger dogs, which we have designated LPN2, and a new candidate gene for CMT disease. To date, approximately every third PN-diagnosed Leonberger dog can be explained by the ARHGEF10 or GJA9 variants, and we assume that additional genetic heterogeneity in this condition exists in the breed. Electronic supplementary material The online version of this article (10.1186/s12864-017-4081-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Doreen Becker
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Katie M Minor
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Kari J Ekenstedt
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA.,Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, 47907, USA
| | - 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
| | - G Diane Shelton
- Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, California, 92093, USA
| | - James R Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.
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A SINE Insertion in ATP1B2 in Belgian Shepherd Dogs Affected by Spongy Degeneration with Cerebellar Ataxia (SDCA2). G3-GENES GENOMES GENETICS 2017; 7:2729-2737. [PMID: 28620085 PMCID: PMC5555477 DOI: 10.1534/g3.117.043018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Spongy degeneration with cerebellar ataxia (SDCA) is a genetically heterogeneous neurodegenerative disorder with autosomal recessive inheritance in Malinois dogs, one of the four varieties of the Belgian Shepherd breed. Using a combined linkage and homozygosity mapping approach we identified an ∼10.6 Mb critical interval on chromosome 5 in a Malinois family with four puppies affected by cerebellar dysfunction. Visual inspection of the 10.6 Mb interval in whole-genome sequencing data from one affected puppy revealed a 227 bp SINE insertion into the ATP1B2 gene encoding the β2 subunit of the Na+/K+-ATPase holoenzyme (ATP1B2:c.130_131insLT796559.1:g.50_276). The SINE insertion caused aberrant RNA splicing. Immunohistochemistry suggested a reduction of ATP1B2 protein expression in the central nervous system of affected puppies. Atp1b2 knockout mice had previously been reported to show clinical and neurohistopathological findings similar to the affected Malinois puppies. Therefore, we consider ATP1B2:c.130_131ins227 the most likely candidate causative variant for a second subtype of SDCA in Malinois dogs, which we propose to term spongy degeneration with cerebellar ataxia subtype 2 (SDCA2). Our study further elucidates the genetic and phenotypic complexity underlying cerebellar dysfunction in Malinois dogs and provides the basis for a genetic test to eradicate one specific neurodegenerative disease from the breeding population in Malinois and the other varieties of the Belgian Shepherd breed. ATP1B2 thus represents another candidate gene for human inherited cerebellar ataxias, and SDCA2-affected Malinois puppies may serve as a naturally occurring animal model for this disorder.
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A Missense Variant in KCNJ10 in Belgian Shepherd Dogs Affected by Spongy Degeneration with Cerebellar Ataxia (SDCA1). G3-GENES GENOMES GENETICS 2017; 7:663-669. [PMID: 28007838 PMCID: PMC5295610 DOI: 10.1534/g3.116.038455] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Spongy degeneration with cerebellar ataxia (SDCA) is a severe neurodegenerative disease with monogenic autosomal recessive inheritance in Malinois dogs, one of the four varieties of the Belgian Shepherd breed. We performed a genetic investigation in six families and seven isolated cases of Malinois dogs with signs of cerebellar dysfunction. Linkage analysis revealed an unexpected genetic heterogeneity within the studied cases. The affected dogs from four families and one isolated case shared a ∼1.4 Mb common homozygous haplotype segment on chromosome 38. Whole genome sequence analysis of three affected and 140 control dogs revealed a missense variant in the KCNJ10 gene encoding a potassium channel (c.986T>C; p.Leu329Pro). Pathogenic variants in KCNJ10 were reported previously in humans, mice, and dogs with neurological phenotypes. Therefore, we consider KCNJ10:c.986T>C the most likely candidate causative variant for one subtype of SDCA in Malinois dogs, which we propose to term spongy degeneration with cerebellar ataxia 1 (SDCA1). However, our study also comprised samples from 12 Malinois dogs with cerebellar dysfunction which were not homozygous for this variant, suggesting a different genetic basis in these dogs. A retrospective detailed clinical and histopathological analysis revealed subtle neuropathological differences with respect to SDCA1-affected dogs. Thus, our study highlights the genetic and phenotypic complexity underlying cerebellar dysfunction in Malinois dogs and provides the basis for a genetic test to eradicate one specific neurodegenerative disease from the breeding population. These dogs represent an animal model for the human EAST syndrome.
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Mhlanga-Mutangadura T, Johnson GS, Ashwini A, Shelton GD, Wennogle SA, Johnson GC, Kuroki K, O'Brien DP. A Homozygous RAB3GAP1:c.743delC Mutation in Rottweilers with Neuronal Vacuolation and Spinocerebellar Degeneration. J Vet Intern Med 2016; 30:813-8. [PMID: 26968732 PMCID: PMC4913561 DOI: 10.1111/jvim.13921] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/28/2015] [Accepted: 02/11/2016] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND A variety of presumed hereditary, neurologic diseases have been reported in young Rottweilers. Overlapping ages of onset and clinical signs have made antemortem diagnosis difficult. One of these diseases, neuronal vacuolation and spinocerebellar degeneration (NVSD) shares clinical and histological features with polyneuropathy with ocular abnormalities and neuronal vacuolation (POANV), a recently described hereditary disease in Black Russian Terriers (BRTs). Dogs with POANV harbor mutations in RAB3GAP1 which codes for a protein involved in membrane trafficking. HYPOTHESIS Rottweilers with NVSD will be homozygous for the RAB3GAP1:c.743delC allele associated with POANV in BRTs. ANIMALS Eight Rottweilers with NVSD confirmed at necropsy, 128 Rottweilers without early onset neurologic signs, and 468 randomly selected dogs from 169 other breeds. METHODS Retrospective case-control study. Dogs were genotyped for the RAB3GAP1:c.743delC allele with an allelic discrimination assay. RESULTS All 8 NVSD-affected dogs were homozygous for the RAB3GAP1:c.743delC allele while the 128 NVSD-free Rottweilers were either homozygous for the reference allele (n = 105) or heterozygous (n = 23) and the 468 genotyped dogs from other breeds were all homozygous for the reference allele. CONCLUSIONS AND CLINICAL IMPORTANCE The RAB3GAP1:c.743delC mutation is associated with a similar phenotype in Rottweilers and BRTs. Identification of the mutation permits a DNA test that can aid in the diagnosis of NVSD and identify carriers of the trait so that breeders can avoid producing affected dogs. Disruption of membrane trafficking could explain the neuronal vacuolation seen in NVSD and other spongiform encephalopathies.
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Affiliation(s)
- T Mhlanga-Mutangadura
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO
| | - G S Johnson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO
| | - A Ashwini
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO
| | - G D Shelton
- Department of Pathology, University of California San Diego, La Jolla, CA
| | - S A Wennogle
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO
| | - G C Johnson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO
| | - K Kuroki
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO
| | - D P O'Brien
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO
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