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Rietmann SJ, Loderstedt S, Matiasek K, Kiefer I, Jagannathan V, Leeb T. Intragenic duplication disrupting the reading frame of MFSD8 in Small Swiss Hounds with neuronal ceroid lipofuscinosis. Anim Genet 2024. [PMID: 39434657 DOI: 10.1111/age.13485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/16/2024] [Accepted: 10/02/2024] [Indexed: 10/23/2024]
Abstract
Neuronal ceroid lipofuscinosis (NCL) represents a heterogenous group of lysosomal storage diseases resulting in progressive neurodegeneration. We investigated two Small Swiss Hound littermates that showed progressive ataxia and loss of cognitive functions and vision starting around the age of 12 months. Both dogs had to be euthanized a few months after the onset of disease owing to the severity of their clinical signs. Pathological investigation of one affected dog revealed cerebral and cerebellar atrophy with cytoplasmic accumulation of autofluorescent material in degenerating neurons. The clinical signs in combination with the characteristic histopathology led to a tentative diagnosis of NCL. In the subsequent genetic investigation, the genome of one affected dog was sequenced. This revealed a duplication of 18 819 bp within the MFSD8 gene. The duplication breakpoints were located in intron 3 and exon 12 of the gene and were predicted to disrupt the reading frame. Both affected dogs carried the duplication in a homozygous state and there was perfect cosegregation of the genotypes with the phenotype in a large pedigree, consistent with autosomal recessive inheritance. MFSD8 loss-of-function variants are a known cause of NCL7 in human patients, dogs and other mammalian species. The existing knowledge on MFSD8 together with the experimental data strongly suggests that the identified intragenic MFSD8 duplication caused the disease in the Small Swiss Hounds. These results allow their diagnosis to be refined to NCL7 and enable genetic testing in the breed to avoid further unintentional carrier × carrier matings.
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Affiliation(s)
- Stefan J Rietmann
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | | | - Kaspar Matiasek
- Section of Clinical and Comparative Neuropathology, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ingmar Kiefer
- Department for Small Animals, Leipzig University, Leipzig, Germany
| | - Vidhya Jagannathan
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
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2
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Letko A, Quignon P, Quilleré M, Husson JC, de Citres CD, Donner J, Dréano S, Plassais J, André C. A RETREG1 variant is associated with hereditary sensory and autonomic neuropathy with acral self-mutilation in purebred German Spitz. Anim Genet 2024. [PMID: 39377488 DOI: 10.1111/age.13482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 09/05/2024] [Accepted: 09/22/2024] [Indexed: 10/09/2024]
Abstract
Hereditary sensory and autonomic neuropathies (HSAN) represent a group of genetic diseases affecting the peripheral nervous system. In humans, at least 16 loci have been associated with the disorder but do not explain the disease origin of all patients. In dogs, similar conditions have been documented for decades in various breeds with a severe impact on life quality and are often referred to as acral mutilation syndrome (AMS). Causal variants in three genes have been identified to date, suggesting larger genetic heterogeneity in the dog population. Our aim was to explain the genetic etiology of an early-onset HSAN/AMS in a purebred German Spitz. The affected dog showed progressive loss of pain sensation in the distal extremities, which led to intense licking, biting, and self-mutilation of digits and paw pads. Whole-genome sequencing identified a single candidate causal variant on chromosome 4 in the RETREG1 gene (c.656C>T, p.Pro219Leu). This missense variant was previously recognized as deleterious in a mixed breed dog family with similar clinical signs. Haplotype analyses and targeted genotyping revealed a likely German Spitz ancestry of these mixed breed dogs. Further screening of an extensive cohort of ~900 000 dogs of various breeds hinted at the variant allele origin in the German Spitz breed. Disruption of RETREG1 inhibits endoplasmic reticulum turnover and leads to neuron degeneration. Our findings provide evidence that this variant underlies the recessive form of HSAN/AMS in the German Spitz and support the use of whole-genome sequencing-based veterinary precision medicine for early diagnosis and prevention via a genetic test.
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Affiliation(s)
- Anna Letko
- Institut de Génétique et Développement de Rennes (IGDR) - UMR6290, CNRS, Université de Rennes, Rennes, France
| | - Pascale Quignon
- Institut de Génétique et Développement de Rennes (IGDR) - UMR6290, CNRS, Université de Rennes, Rennes, France
| | - Maéva Quilleré
- Institut de Génétique et Développement de Rennes (IGDR) - UMR6290, CNRS, Université de Rennes, Rennes, France
| | | | | | - Jonas Donner
- Wisdom Panel, Mars Petcare Science & Diagnostics, Helsinki, Finland
| | - Stéphane Dréano
- Institut de Génétique et Développement de Rennes (IGDR) - UMR6290, CNRS, Université de Rennes, Rennes, France
| | - Jocelyn Plassais
- Institut de Génétique et Développement de Rennes (IGDR) - UMR6290, CNRS, Université de Rennes, Rennes, France
| | - Catherine André
- Institut de Génétique et Développement de Rennes (IGDR) - UMR6290, CNRS, Université de Rennes, Rennes, France
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3
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Kiener S, Lehner G, Jagannathan V, Welle M, Leeb T. Heterozygous DSP in-frame deletion in a poodle with syndromic ichthyosis involving additional hair and tooth abnormalities. Anim Genet 2024; 55:725-732. [PMID: 39136317 DOI: 10.1111/age.13467] [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: 04/15/2024] [Revised: 06/28/2024] [Accepted: 07/29/2024] [Indexed: 10/23/2024]
Abstract
Ichthyoses comprise a large heterogeneous group of skin disorders, characterized by generalized scaly and hyperkeratotic skin. We investigated a miniature poodle with early onset generalized scaling, dry and irregularly thickened skin, paw pad hyperkeratosis and abnormalities in hair and teeth. The clinical signs of ichthyosis were confirmed by histopathological examination, which revealed mild epidermal hyperplasia and lamellar orthokeratotic hyperkeratosis. A hereditary condition was suspected and a genetic investigation was initiated. We sequenced the whole genome of the affected dog and searched for potentially causative variants in functional candidate genes for the observed phenotype. The analysis revealed a heterozygous in-frame deletion in DSP, NC_049256.1:g.8804542_8804544del resulting from a de novo mutation event as evidenced by genotyping leukocyte DNA from both parents. The 3 bp deletion is predicted to remove one aspartic acid without disrupting the open reading frame (XM_038584124.1:c.1821_1823del, XP_038440052.1:p.(Asp608del)). The DSP gene encodes desmoplakin, a desmosomal plaque protein, responsible for cell-cell adhesion to provide resistance to mechanical stress in epidermal and cardiac tissues. We hypothesize that the deletion of one amino acid in the N-terminal globular head domain acts in a dominant negative manner and thus impairs the proper connection with other proteins. Several variants in DSP in humans and cattle have been described to result in different phenotypes associated with hair and skin abnormalities, sometimes in combination with variable cardiac and/or dental manifestations. In conclusion, we characterized a new syndromic ichthyosis phenotype in a dog and identified a de novo 3 bp deletion in the DSP gene as causal variant.
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Affiliation(s)
- Sarah Kiener
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Dermfocus, University of Bern, Bern, Switzerland
| | - Georg Lehner
- Kleintierpraxis Lehner - Fachpraxis für Dermatologie, Buch, Germany
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Monika Welle
- Institute of Animal Pathology, 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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4
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Funk MW, Kidd JM. A Variant-Centric Analysis of Allele Sharing in Dogs and Wolves. Genes (Basel) 2024; 15:1168. [PMID: 39336759 PMCID: PMC11431226 DOI: 10.3390/genes15091168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 08/28/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024] Open
Abstract
Canines are an important model system for genetics and evolution. Recent advances in sequencing technologies have enabled the creation of large databases of genetic variation in canines, but analyses of allele sharing among canine groups have been limited. We applied GeoVar, an approach originally developed to study the sharing of single nucleotide polymorphisms across human populations, to assess the sharing of genetic variation among groups of wolves, village dogs, and breed dogs. Our analysis shows that wolves differ from each other at an average of approximately 2.3 million sites while dogs from the same breed differ at nearly 1 million sites. We found that 22% of the variants are common across wolves, village dogs, and breed dogs, that ~16% of variable sites are common across breed dogs, and that nearly half of the differences between two dogs of different breeds are due to sites that are common in all clades. These analyses represent a succinct summary of allele sharing across canines and illustrate the effects of canine history on the apportionment of genetic variation.
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Affiliation(s)
- Matthew W. Funk
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Jeffrey M. Kidd
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
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Wang K, Luigi-Sierra MG, Castelló A, Figueiredo-Cardoso T, Mercadé A, Martínez A, Delgado JV, Álvarez JF, Noce A, Wang M, Jordana J, Amills M. Identification of nonsense variants in the genomes of 15 Murciano-Granadina bucks and analysis of their segregation in parent-offspring trios. J Dairy Sci 2024:S0022-0302(24)01097-X. [PMID: 39218071 DOI: 10.3168/jds.2024-24952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
Nonsense variants can inactivate gene function by causing the synthesis of truncated proteins or by inducing nonsense mediated decay of messenger RNAs. The occurrence of such variants in the genomes of livestock species is modulated by multiple demographic and selective factors. Even though nonsense variants can have causal effects on embryo lethality, abortions, and disease, their genomic distribution and segregation in domestic goats have not been characterized in depth yet. In this work, we have sequenced the genomes of 15 Murciano-Granadina bucks with an average coverage of 32.92 × ± 1.45 × . Bioinformatic analysis revealed 947 nonsense variants consistently detected with SnpEff and Ensembl-VEP. These variants were especially abundant in the 3'end of the protein-coding regions. Genes related to olfactory perception, ATPase activity coupled to transmembrane movement of substances, defense to virus, hormonal response, and sensory perception of taste were particularly enriched in nonsense variants. Seventeen nonsense variants expected to have harmful effects on fitness were genotyped in parent-offspring trios. We observed that several nonsense variants predicted to be lethal based on mouse knockout data did not have such effect, a finding that could be explained by the existence of multiple mechanisms counteracting lethality. These findings demonstrate that predicting the effects of putative nonsense variants on fitness is extremely challenging. As a matter of fact, such a goal could only be achieved by generating a high quality telomere-to-telomere goat reference genome combined with carefully curated annotation and functional testing of promising candidate variants.
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Affiliation(s)
- Ke Wang
- Centre de Recerca Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.; Chinese Academy of Tropical Agricultural Sciences, Zhanjiang Experimental Station, Zhanjiang, Guangdong, 524000, China.; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - María Gracia Luigi-Sierra
- Centre de Recerca Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Anna Castelló
- Centre de Recerca Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Taina Figueiredo-Cardoso
- Centre de Recerca Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Anna Mercadé
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain
| | | | | | - Antonia Noce
- Centre de Recerca Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Mingjing Wang
- Centre de Recerca Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Marcel Amills
- Centre de Recerca Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain..
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Cook SR, Schwarz C, Guevar J, Assenmacher CA, Sheehy M, Fanzone N, Church ME, Murgiano L, Casal ML, Jagannathan V, Gutierrez-Quintana R, Lowrie M, Steffen F, Leeb T, Ekenstedt KJ. Canine RNF170 Single Base Deletion in a Naturally Occurring Model for Human Neuroaxonal Dystrophy. Mov Disord 2024. [PMID: 39177409 DOI: 10.1002/mds.29977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 07/15/2024] [Accepted: 07/29/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND Neuroaxonal dystrophy (NAD) is a group of inherited neurodegenerative disorders characterized primarily by the presence of spheroids (swollen axons) throughout the central nervous system. In humans, NAD is heterogeneous, both clinically and genetically. NAD has also been described to naturally occur in large animal models, such as dogs. A newly recognized disorder in Miniature American Shepherd dogs (MAS), consisting of a slowly progressive neurodegenerative syndrome, was diagnosed as NAD via histopathology. OBJECTIVES To describe the clinical and pathological phenotype together with the identification of the underlying genetic cause. METHODS Clinical and postmortem evaluations, together with a genome-wide association study and autozygosity mapping approach, followed by whole-genome sequencing. RESULTS Affected dogs were typically young adults and displayed an abnormal gait characterized by pelvic limb weakness and ataxia. The underlying genetic cause was identified as a 1-bp (base pair) deletion in RNF170 encoding ring finger protein 170, which perfectly segregates in an autosomal recessive pattern. This deletion is predicted to create a frameshift (XM_038559916.1:c.367delG) and early truncation of the RNF170 protein (XP_038415844.1:(p.Ala123Glnfs*11)). The age of this canine RNF170 variant was estimated at ~30 years, before the reproductive isolation of the MAS breed. CONCLUSIONS RNF170 variants were previously identified in human patients with autosomal recessive spastic paraplegia-85 (SPG85); this clinical phenotype shows similarities to the dogs described herein. We therefore propose that this novel MAS NAD could serve as an excellent large animal model for equivalent human diseases, particularly since affected dogs demonstrate a relatively long lifespan, which represents an opportunity for therapeutic trials. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Shawna R Cook
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | - Cleo Schwarz
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Julien Guevar
- AniCura Thun, Neurology Department, Burgerstrasse, Switzerland
| | - Charles-Antoine Assenmacher
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maeve Sheehy
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | - Nathan Fanzone
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Molly E Church
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Leonardo Murgiano
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Margret L Casal
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rodrigo Gutierrez-Quintana
- Small Animal Hospital, School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Mark Lowrie
- Movement Referrals: Independent Veterinary Specialists, Preston Brook, UK
| | - Frank Steffen
- Neurology Service, Department of Small Animals, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Kari J Ekenstedt
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
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Rietmann SJ, Nowell S, Keating MK, Bauer C, Jagannathan V, Leeb T. Heterozygous COL5A1 deletion in a cat with classical Ehlers-Danlos syndrome. Anim Genet 2024; 55:705-707. [PMID: 38745376 DOI: 10.1111/age.13446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024]
Affiliation(s)
- Stefan J Rietmann
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Sarah Nowell
- Animal Dermatology Group, Inc, Greenville, South Carolina, USA
| | | | - Cynthia Bauer
- Animal Dermatology Group, Inc, Greenville, South Carolina, USA
| | - Vidhya Jagannathan
- Institute of Genetics, 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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Bellamy KKL, Skedsmo FS, Hultman J, Jansen JH, Lingaas F. Neuronal ceroid lipofuscinosis in a Schapendoes dog is caused by a missense variant in CLN6. Anim Genet 2024; 55:612-620. [PMID: 38866396 DOI: 10.1111/age.13457] [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: 05/03/2024] [Revised: 05/03/2024] [Accepted: 05/28/2024] [Indexed: 06/14/2024]
Abstract
Neuronal ceroid lipofuscinosis (NCL) is a group of neurodegenerative disorders that occur in humans, dogs, and several other species. NCL is characterised clinically by progressive deterioration of cognitive and motor function, epileptic seizures, and visual impairment. Most forms present early in life and eventually lead to premature death. Typical pathological changes include neuronal accumulation of autofluorescent, periodic acid-Schiff- and Sudan black B-positive lipopigments, as well as marked loss of neurons in the central nervous system. Here, we describe a 19-month-old Schapendoes dog, where clinical signs were indicative of lysosomal storage disease, which was corroborated by pathological findings consistent with NCL. Whole genome sequencing of the affected dog and both parents, followed by variant calling and visual inspection of known NCL genes, identified a missense variant in CLN6 (c.386T>C). The variant is located in a highly conserved region of the gene and predicted to be harmful, which supports a causal relationship. The identification of this novel CLN6 variant enables pre-breeding DNA-testing to prevent future cases of NCL6 in the Schapendoes breed, and presents a potential natural model for NCL6 in humans.
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Affiliation(s)
| | - Fredrik S Skedsmo
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Josefin Hultman
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Johan Høgset Jansen
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Frode Lingaas
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
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Rietmann SJ, Lange A, Soto S, Thom N, Manz E, Jagannathan V, Mayer U, Leeb T. KRT5 in-frame deletion in a family of German Shepherd dogs with split paw pad disease resembling localized epidermolysis bullosa simplex in human patients. Anim Genet 2024; 55:692-696. [PMID: 38742646 DOI: 10.1111/age.13444] [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: 04/05/2024] [Revised: 04/05/2024] [Accepted: 04/27/2024] [Indexed: 05/16/2024]
Abstract
Split paw pad disease is a scarcely defined phenotype characterized by skin lesions on the paw pads of dogs. We studied a family of German Shepherd dogs, in which four dogs developed intermittent paw pad lesions and lameness. The paw pads of two of the affected dogs were biopsied and demonstrated cleft formation in the stratum spinosum and stratum corneum, the outermost layers of the epidermis. Whole genome sequencing data from an affected dog revealed a private heterozygous 18 bp in frame deletion in the KRT5 gene. The deletion NM_001346035.1:c.988_1005del or NP_001332964.1:p.(Asn330_Asp335del) is predicted to lead to a loss of six amino acids in the L12 linker domain of the encoded keratin 5. KRT5 variants in human patients lead to various subtypes of epidermolysis bullosa simplex (EBS). Localized EBS is the mildest of the KRT5-related human diseases and may be caused by variants affecting the L12 linker domain of keratin 5. We therefore think that the detected KRT5 deletion in dogs represents a candidate causal variant for the observed skin lesions in dogs. However, while the clinical phenotype of KRT5-mutant dogs of this study closely resembles human patients with localized EBS, there are differences in the histopathology. EBS is defined by cleft formation within the basal layer of the epidermis while the cleft formation in the dogs described herein occurred in the outermost layers, a hallmark of split paw pad disease. Our study provides a basis for further studies into the exact relation of split paw pad disease and EBS.
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Affiliation(s)
- Stefan J Rietmann
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Anja Lange
- Anicura Kleintierspezialisten Augsburg GmbH, Augsburg, Germany
| | - Sara Soto
- DermFocus, University of Bern, Bern, Switzerland
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nina Thom
- Small Animal Clinic, Justus-Liebig-University of Giessen, Giessen, Germany
| | | | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Ursula Mayer
- Anicura Kleintierspezialisten Augsburg GmbH, Augsburg, Germany
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
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10
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Kiener S, Wildermuth B, Meertens NM, Jagannathan V, Leeb T. Heterozygous deletion of the NSDHL gene in an Appenzeller Mountain Dog with verrucous epidermal keratinocytic nevi. Anim Genet 2024; 55:697-699. [PMID: 38659285 DOI: 10.1111/age.13436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024]
Affiliation(s)
- Sarah Kiener
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Dermfocus, University of Bern, Bern, Switzerland
| | | | - Nadine M Meertens
- Pathology Department, Royal GD Animal Health, Deventer, The Netherlands
| | - Vidhya Jagannathan
- Institute of Genetics, 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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11
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Christen M, Gregor KM, Böttcher-Künneke A, Lombardo MS, Baumgärtner W, Jagannathan V, Puff C, Leeb T. Intragenic MFSD8 duplication and histopathological findings in a rabbit with neuronal ceroid lipofuscinosis. Anim Genet 2024; 55:588-598. [PMID: 38712841 DOI: 10.1111/age.13441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 03/20/2024] [Accepted: 04/22/2024] [Indexed: 05/08/2024]
Abstract
Neuronal ceroid lipofuscinoses (NCL) are among the most prevalent neurodegenerative disorders of early life in humans. Disease-causing variants have been described for 13 different NCL genes. In this study, a refined pathological characterization of a female rabbit with progressive neurological signs reminiscent of NCL was performed. Cytoplasmic pigment present in neurons was weakly positive with Sudan black B and autofluorescent. Immunohistology revealed astrogliosis, microgliosis and axonal degeneration. During the subsequent genetic investigation, the genome of the affected rabbit was sequenced and examined for private variants in NCL candidate genes. The analysis revealed a homozygous ~10.7 kb genomic duplication on chromosome 15 comprising parts of the MFSD8 gene, NC_013683.1:g.103,727,963_103,738,667dup. The duplication harbors two internal protein coding exons and is predicted to introduce a premature stop codon into the transcript, truncating ~50% of the wild-type MFSD8 open reading frame encoding the major facilitator superfamily domain containing protein 8, XP_002717309.2:p.(Glu235Leufs*23). Biallelic loss-of-function variants in MFSD8 have been described to cause NCL7 in human patients, dogs and a single cat. The available clinical and pathological data, together with current knowledge about MFSD8 variants and their functional impact in other species, point to the MFSD8 duplication as a likely causative defect for the observed phenotype in the affected rabbit.
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Affiliation(s)
- Matthias Christen
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Katharina M Gregor
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | | | - Mara S Lombardo
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Christina Puff
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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12
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Nguyen AK, Schall PZ, Kidd JM. A map of canine sequence variation relative to a Greenland wolf outgroup. Mamm Genome 2024:10.1007/s00335-024-10056-1. [PMID: 39088040 DOI: 10.1007/s00335-024-10056-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024]
Abstract
For over 15 years, canine genetics research relied on a reference assembly from a Boxer breed dog named Tasha (i.e., canFam3.1). Recent advances in long-read sequencing and genome assembly have led to the development of numerous high-quality assemblies from diverse canines. These assemblies represent notable improvements in completeness, contiguity, and the representation of gene promoters and gene models. Although genome graph and pan-genome approaches have promise, most genetic analyses in canines rely upon the mapping of Illumina sequencing reads to a single reference. The Dog10K consortium, and others, have generated deep catalogs of genetic variation through an alignment of Illumina sequencing reads to a reference genome obtained from a German Shepherd Dog named Mischka (i.e., canFam4, UU_Cfam_GSD_1.0). However, alignment to a breed-derived genome may introduce bias in genotype calling across samples. Since the use of an outgroup reference genome may remove this effect, we have reprocessed 1929 samples analyzed by the Dog10K consortium using a Greenland wolf (mCanLor1.2) as the reference. We efficiently performed remapping and variant calling using a GPU-implementation of common analysis tools. The resulting call set removes the variability in genetic differences seen across samples and breed relationships revealed by principal component analysis are not affected by the choice of reference genome. Using this sequence data, we inferred the history of population sizes and found that village dog populations experienced a 9-13 fold reduction in historic effective population size relative to wolves.
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Affiliation(s)
- Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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13
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Subramanian S, Kumar M. The Association between the Abundance of Homozygous Deleterious Variants and the Morbidity of Dog Breeds. BIOLOGY 2024; 13:574. [PMID: 39194512 DOI: 10.3390/biology13080574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 08/29/2024]
Abstract
It is well known that highly inbred dogs are more prone to diseases than less inbred or outbred dogs. This is because inbreeding increases the load of recessive deleterious variants. Using the genomes of 392 dogs belonging to 83 breeds, we investigated the association between the abundance of homozygous deleterious variants and dog health. We used the number of non-routine veterinary care events for each breed to assess the level of morbidity. Our results revealed a highly significant positive relationship between the number of homozygous deleterious variants located within the runs of homozygosity (RoH) tracts of the breeds and the level of morbidity. The dog breeds with low morbidity had a mean of 87 deleterious SNVs within the RoH, but those with very high morbidity had 187 SNVs. A highly significant correlation was also observed for the loss-of-function (LoF) SNVs within RoH tracts. The dog breeds that required more veterinary care had 2.3 times more homozygous LoF SNVs than those that required less veterinary care (112 vs. 50). The results of this study could be useful for understanding the disease burden on breed dogs and as a guide for dog breeding programs.
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Affiliation(s)
- Sankar Subramanian
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
- School of Science, Technology, and Engineering, University of the Sunshine Coast, Moreton Bay, QLD 4502, Australia
| | - Manoharan Kumar
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD 4502, Australia
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14
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Rietmann SJ, Cochet-Faivre N, Dropsy H, Jagannathan V, Chevallier L, Leeb T. EDA Missense Variant in a Cat with X-Linked Hypohidrotic Ectodermal Dysplasia. Genes (Basel) 2024; 15:854. [PMID: 39062633 PMCID: PMC11276485 DOI: 10.3390/genes15070854] [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: 04/25/2024] [Revised: 06/12/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
Hypohidrotic ectodermal dysplasia is a developmental defect characterized by sparse or absent hair, missing or malformed teeth and defects in eccrine glands. Loss-of-function variants in the X-chromosomal EDA gene have been reported to cause hypohidrotic ectodermal dysplasia in humans, mice, dogs and cattle. We investigated a male cat exhibiting diffuse truncal alopecia with a completely absent undercoat. The cat lacked several teeth, and the remaining teeth had an abnormal conical shape. Whole-genome sequencing revealed a hemizygous missense variant in the EDA gene, XM_011291781.3:c.1042G>A or XP_011290083.1:p.(Ala348Thr). The predicted amino acid exchange is located in the C-terminal TNF signaling domain of the encoded ectodysplasin. The corresponding missense variant in the human EDA gene, p.Ala349Thr, has been reported as a recurring pathogenic variant in several human patients with X-linked hypohidrotic ectodermal dysplasia. The identified feline variant therefore represents the likely cause of the hypohidrotic ectodermal dysplasia in the investigated cat, and the genetic investigation confirmed the suspected clinical diagnosis. This is the first report of an EDA-related hypohidrotic ectodermal dysplasia in cats.
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Affiliation(s)
- Stefan J. Rietmann
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (S.J.R.); (V.J.)
- Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - Noëlle Cochet-Faivre
- Unité de Dermatologie, CHUV-Animaux de Compagnie, Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France; (N.C.-F.); (H.D.)
- BIPAR, Laboratoire de Santé Animale, INRAE, Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France
| | - Helene Dropsy
- Unité de Dermatologie, CHUV-Animaux de Compagnie, Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France; (N.C.-F.); (H.D.)
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (S.J.R.); (V.J.)
| | - Lucie Chevallier
- U955-IMRB, Team 10-Biology of the Neuromuscular System, INSERM, UPEC, Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France;
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (S.J.R.); (V.J.)
- Dermfocus, University of Bern, 3001 Bern, Switzerland
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15
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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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16
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Kiener S, Åhman S, Cikota R, Jagannathan V, Blatter S, Cvitas I, Soto S, Leeb T. Heterozygous ASPRV1 frameshift variant in a Pembroke Welsh Corgi with ichthyosis. Anim Genet 2024; 55:490-492. [PMID: 38549226 DOI: 10.1111/age.13423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 05/04/2024]
Affiliation(s)
- Sarah Kiener
- 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
| | - Sohvi Blatter
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Iva Cvitas
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sara Soto
- Institute of Animal Pathology, 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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17
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Mizukami K, Dorsey-Oresto A, Raj K, Eringis A, Furrow E, Martin E, Yamanaka D, Kehl A, Kolicheski A, Jagannathan V, Leeb T, Lionakis MS, Giger U. Increased susceptibility to Mycobacterium avium complex infection in miniature Schnauzer dogs caused by a codon deletion in CARD9. Sci Rep 2024; 14:10346. [PMID: 38710903 PMCID: PMC11074286 DOI: 10.1038/s41598-024-61054-x] [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: 03/02/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
Mammals are generally resistant to Mycobacterium avium complex (MAC) infections. We report here on a primary immunodeficiency disorder causing increased susceptibility to MAC infections in a canine breed. Adult Miniature Schnauzers developing progressive systemic MAC infections were related to a common founder, and pedigree analysis was consistent with an autosomal recessive trait. A genome-wide association study and homozygosity mapping using 8 infected, 9 non-infected relatives, and 160 control Miniature Schnauzers detected an associated region on chromosome 9. Whole genome sequencing of 2 MAC-infected dogs identified a codon deletion in the CARD9 gene (c.493_495del; p.Lys165del). Genotyping of Miniature Schnauzers revealed the presence of this mutant CARD9 allele worldwide, and all tested MAC-infected dogs were homozygous mutants. Peripheral blood mononuclear cells from a dog homozygous for the CARD9 variant exhibited a dysfunctional CARD9 protein with impaired TNF-α production upon stimulation with the fungal polysaccharide β-glucan that activates the CARD9-coupled C-type lectin receptor, Dectin-1. While CARD9-deficient knockout mice are susceptible to experimental challenges by fungi and mycobacteria, Miniature Schnauzer dogs with systemic MAC susceptibility represent the first spontaneous animal model of CARD9 deficiency, which will help to further elucidate host defense mechanisms against mycobacteria and fungi and assess potential therapies for animals and humans.
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Affiliation(s)
- Keijiro Mizukami
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- RIKEN Center for Integrative Medical Sciences, Laboratory for Genotyping Development, Yokohama, Kanagawa, Japan.
| | - Angella Dorsey-Oresto
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Karthik Raj
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anna Eringis
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eva Furrow
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA
| | - Errolyn Martin
- Wildlife Center of North Georgia, Inc., Acworth, GA, USA
| | - Daisuke Yamanaka
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- Laboratory for Immunopharmacology of Microbial Products, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | | | - Ana Kolicheski
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Urs Giger
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Vetsuisse Faculty, University of Zürich, Zurich, Switzerland.
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18
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Christen M, Oevermann A, Rupp S, Vaz FM, Wever EJM, Braus BK, Jagannathan V, Kehl A, Hytönen MK, Lohi H, Leeb T. PCYT2 deficiency in Saarlooswolfdogs with progressive retinal, central, and peripheral neurodegeneration. Mol Genet Metab 2024; 141:108149. [PMID: 38277988 DOI: 10.1016/j.ymgme.2024.108149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024]
Abstract
We investigated a syndromic disease comprising blindness and neurodegeneration in 11 Saarlooswolfdogs. Clinical signs involved early adult onset retinal degeneration and adult-onset neurological deficits including gait abnormalities, hind limb weakness, tremors, ataxia, cognitive decline and behavioral changes such as aggression towards the owner. Histopathology in one affected dog demonstrated cataract, retinal degeneration, central and peripheral axonal degeneration, and severe astroglial hypertrophy and hyperplasia in the central nervous system. Pedigrees indicated autosomal recessive inheritance. We mapped the suspected genetic defect to a 15 Mb critical interval by combined linkage and autozygosity analysis. Whole genome sequencing revealed a private homozygous missense variant, PCYT2:c.4A>G, predicted to change the second amino acid of the encoded ethanolamine-phosphate cytidylyltransferase 2, XP_038402224.1:(p.Ile2Val). Genotyping of additional Saarlooswolfdogs confirmed the homozygous genotype in all eleven affected dogs and demonstrated an allele frequency of 9.9% in the population. This experiment also identified three additional homozygous mutant young dogs without overt clinical signs. Subsequent examination of one of these dogs revealed early-stage progressive retinal atrophy (PRA) and expansion of subarachnoid CSF spaces in MRI. Dogs homozygous for the pathogenic variant showed ether lipid accumulation, confirming a functional PCYT2 deficiency. The clinical and metabolic phenotype in affected dogs shows some parallels with human patients, in whom PCYT2 variants lead to a rare form of spastic paraplegia or axonal motor and sensory polyneuropathy. Our results demonstrate that PCYT2:c.4A>G in dogs cause PCYT2 deficiency. This canine model with histopathologically documented retinal, central, and peripheral neurodegeneration further deepens the knowledge of PCYT2 deficiency.
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Affiliation(s)
- Matthias Christen
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Anna Oevermann
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Stefan Rupp
- Neurology Department, Tierklinik Hofheim, IVC Evidensia, Hofheim am Taunus 65719, Germany
| | - Frédéric M Vaz
- Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, the Netherlands; Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Eric J M Wever
- Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, the Netherlands; Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Bioinformatics Laboratory, Department of Epidemiology & Data Science, Amsterdam Public Health Research Institute, University of Amsterdam, 1100 DE Amsterdam UMC, the Netherlands
| | - Barbara K Braus
- Ophthalmology Department, Tierklinik Hofheim, IVC Evidensia, Hofheim am Taunus 65719, Germany
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Alexandra Kehl
- Laboklin GmbH & Co. KG, Steubenstraße 4, Bad Kissingen 97688, Germany; Comparative Experimental Pathology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki 00014, Finland; Department of Veterinary Biosciences, University of Helsinki, Helsinki 00014, Finland; Folkhälsan Research Center, Helsinki 00290, Finland
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki 00014, Finland; Department of Veterinary Biosciences, University of Helsinki, Helsinki 00014, Finland; Folkhälsan Research Center, Helsinki 00290, Finland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland.
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19
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Christen M, Gregor A, Gutierrez-Quintana R, Bongers J, Rupp A, Penderis J, Shelton GD, Jagannathan V, Zweier C, Leeb T. NDUFS7 variant in dogs with Leigh syndrome and its functional validation in a Drosophila melanogaster model. Sci Rep 2024; 14:2975. [PMID: 38316835 PMCID: PMC10844639 DOI: 10.1038/s41598-024-53314-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/30/2024] [Indexed: 02/07/2024] Open
Abstract
Two Jack-Russell Terrier × Chihuahua mixed-breed littermates with Leigh syndrome were investigated. The dogs presented with progressive ataxia, dystonia, and increased lactate levels. Brain MRI showed characteristic bilateral symmetrical T2 hyperintense lesions, histologically representing encephalomalacia. Muscle histopathology revealed accumulation of mitochondria. Whole genome sequencing identified a missense variant in a gene associated with human Leigh syndrome, NDUFS7:c.535G > A or p.(Val179Met). The genotypes at the variant co-segregated with the phenotype in the investigated litter as expected for a monogenic autosomal recessive mode of inheritance. We investigated the functional consequences of the missense variant in a Drosophila melanogaster model by expressing recombinant wildtype or mutant canine NDUFS7 in a ubiquitous knockdown model of the fly ortholog ND-20. Neither of the investigated overexpression lines completely rescued the lethality upon knockdown of the endogenous ND-20. However, a partial rescue was found upon overexpression of wildtype NDUFS7, where pupal lethality was moved to later developmental stages, which was not seen upon canine mutant overexpression, thus providing additional evidence for the pathogenicity of the identified variant. Our results show the potential of the fruit fly as a model for canine disease allele validation and establish NDUFS7:p.(Val179Met) as causative variant for the investigated canine Leigh syndrome.
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Affiliation(s)
- Matthias Christen
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Anne Gregor
- Department of Human Genetics, Inselspital, University of Bern, Bern, Switzerland
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Rodrigo Gutierrez-Quintana
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jos Bongers
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Angie Rupp
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - G Diane Shelton
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, University of Bern, Bern, Switzerland
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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20
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Rawson F, Christen M, Rose J, Paran E, Leeb T, Fadda A. Polioencephalopathy in Eurasier dogs. J Vet Intern Med 2024; 38:277-284. [PMID: 38041431 PMCID: PMC10800227 DOI: 10.1111/jvim.16945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/14/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Polioencephalopathies secondary to inborn errors of metabolism have been described in dogs, but few genetically characterized. OBJECTIVES Clinically and genetically characterize polioencephalopathy in a family of Eurasier dogs. ANIMALS Three Eurasier dogs (littermates) presented with early onset movement disorders (9 weeks in 2, 4-6 months in 1). Progressive gait abnormalities were detected in 2 of the dogs, persistent divergent strabismus in 1, whereas consciousness and behavior remained intact in all dogs. One dog was euthanized at 25 months. METHODS Video footage was assessed in all dogs, and Dogs 1 and 2 had examinations and investigations performed. Whole genome sequencing of Dog 1 and further genetic analyses in the family were performed. A cohort of 115 Eurasier controls was genotyped for specific variants. RESULTS Episodes were characterized by generalized ataxia, as well as a hypermetric thoracic limb gait, dystonia, and irregular flexion and extension movements of the thoracic limbs. Magnetic resonance imaging of the brain in Dogs 1 and 2 identified symmetrical, bilateral T2 and fluid attenuated inversion recovery hyperintense, T1 hypo to isointense, nonenhancing lesions of the caudate nucleus, lateral and medial geniculate nuclei, thalamus, hippocampus, rostral colliculus and mild generalized brain atrophy. Genetic analyses identified a homozygous mitochondrial trans-2-enoyl-CoA reductase (MECR) missense variant in all 3 dogs, and a homozygous autophagy-related gene 4D (ATG4D) missense variant in Dogs 1 and 2. CONCLUSIONS AND CLINICAL IMPORTANCE We describe a presumed hereditary and progressive polioencephalopathy in a family of Eurasier dogs. Further research is needed to establish the role of the MECR gene in dogs and the pathogenic effects of the detected variants.
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Affiliation(s)
- Faye Rawson
- Langford Veterinary ServicesUniversity of BristolBristolUK
| | - Matthias Christen
- Institute of Genetics, Vetsuisse FacultyUniversity of BernBernSwitzerland
| | | | - Emilie Paran
- Langford Veterinary ServicesUniversity of BristolBristolUK
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse FacultyUniversity of BernBernSwitzerland
| | - Angela Fadda
- Langford Veterinary ServicesUniversity of BristolBristolUK
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21
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Stanbury K, Stavinohova R, Pettitt L, Dixon C, Schofield EC, Mclaughlin B, Pettinen I, Lohi H, Ricketts SL, Oliver JA, Mellersh CS. Multiocular defect in the Old English Sheepdog: A canine form of Stickler syndrome type II associated with a missense variant in the collagen-type gene COL11A1. PLoS One 2023; 18:e0295851. [PMID: 38153936 PMCID: PMC10754463 DOI: 10.1371/journal.pone.0295851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/30/2023] [Indexed: 12/30/2023] Open
Abstract
Multiocular defect has been described in different canine breeds, including the Old English Sheepdog. Affected dogs typically present with multiple and various ocular abnormalities. We carried out whole genome sequencing on an Old English Sheepdog that had been diagnosed with hereditary cataracts at the age of five and then referred to a board-certified veterinary ophthalmologist due to owner-reported visual deterioration. An ophthalmic assessment revealed that there was bilateral vitreal degeneration, macrophthalmos, and spherophakia in addition to cataracts. Follow-up consultations revealed cataract progression, retinal detachment, uveitis and secondary glaucoma. Whole genome sequence filtered variants private to the case, shared with another Old English Sheepdog genome and predicted to be deleterious were genotyped in an initial cohort of six Old English Sheepdogs (three affected by multiocular defect and three control dogs without evidence of inherited eye disease). Only one of the twenty-two variants segregated correctly with multiocular defect. The variant is a single nucleotide substitution, located in the collagen-type gene COL11A1, c.1775T>C, that causes an amino acid change, p.Phe1592Ser. Genotyping of an additional 14 Old English Sheepdogs affected by multiocular defect revealed a dominant mode of inheritance with four cases heterozygous for the variant. Further genotyping of hereditary cataract-affected Old English Sheepdogs revealed segregation of the variant in eight out of nine dogs. In humans, variants in the COL11A1 gene are associated with Stickler syndrome type II, also dominantly inherited.
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Affiliation(s)
- Katherine Stanbury
- Kennel Club Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Louise Pettitt
- Kennel Club Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Ellen C. Schofield
- Kennel Club Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Bryan Mclaughlin
- Kennel Club Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Inka Pettinen
- Department of Veterinary Biosciences, Department of Medical and Clinical Genetics, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland
| | - Hannes Lohi
- Department of Veterinary Biosciences, Department of Medical and Clinical Genetics, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland
| | - Sally L. Ricketts
- Kennel Club Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Cathryn S. Mellersh
- Kennel Club Genetics Centre, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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22
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Brockmann M, Mensing N, von Luckner J, Müller E, Kehl A. Hemophilia A in a litter of Border Collies caused by a one base pair deletion in the F8 gene. Vet Clin Pathol 2023; 52:607-612. [PMID: 38104983 DOI: 10.1111/vcp.13312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/30/2023] [Indexed: 12/19/2023]
Abstract
In dogs, hemophilia A is known to affect different breeds. This is a case report describing hemophilia A in a litter of Border Collies. A privately owned bitch and her puppies (n = 7) were presented to the referring veterinarian after acute hematoma formation in the male offspring (n = 3) following microchip implantation. Global coagulation testing, as well as determination of factor VIII and IX activity, were carried out. Based on the results, factor VIII deficiency was suspected. Two of the affected male puppies were euthanized within a few days. Genetic testing of the mother and the surviving male puppy resulted in the description of a deletion in exon 14 of the F8 gene. This c.3206delA variant leads to a frameshift in amino acid sequence and a premature stop codon (p.Asn1069IlefsTer7). The detection of the mutation and consequent testing of related dogs revealed that the deletion most likely had occurred spontaneously in the mother and had been transmitted to several of her offspring in different litters. Identified carriers were taken out of the breeding scheme. It is concluded that genetic testing in the context of suspected genetic disease can lead to preventive measures, including timely exclusion of carriers from breeding.
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Affiliation(s)
| | - Niels Mensing
- Tierarztpraxis Dr. Niels Mensing, Magdeburg, Germany
| | | | | | - Alexandra Kehl
- Laboklin GmbH & Co. KG, Bad Kissingen, Germany
- Comparative Experimental Pathology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
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23
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Ekenstedt KJ, Minor KM, Shelton GD, Hammond JJ, Miller AD, Taylor SM, Huang Y, Mickelson JR. A SACS deletion variant in Great Pyrenees dogs causes autosomal recessive neuronal degeneration. Hum Genet 2023; 142:1587-1601. [PMID: 37758910 PMCID: PMC10602964 DOI: 10.1007/s00439-023-02599-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023]
Abstract
ARSACS (autosomal recessive spastic ataxia of Charlevoix-Saguenay) is a human neurological disorder characterized by progressive cerebellar ataxia and peripheral neuropathy. A recently recognized disorder in Great Pyrenees dogs is similarly characterized by widespread central nervous system degeneration leading to progressive cerebellar ataxia and spasticity, combined with peripheral neuropathy. Onset of clinical signs occurred in puppies as young as 4 months of age, with slow progression over several years. A multi-generation pedigree suggested an autosomal recessive mode of inheritance. Histopathology revealed consistent cerebellar Purkinje cell degeneration, neuronal degeneration in brainstem nuclei, widespread spinal cord white matter degeneration, ganglion cell degeneration, inappropriately thin myelin sheaths or fully demyelinated peripheral nerve fibers, and normal or only mild patterns of denervation atrophy in skeletal muscles. Genome-wide single nucleotide polymorphism (SNP) genotype data was collected from 6 cases and 26 controls, where homozygosity mapping identified a 3.3 Mb region on CFA25 in which all cases were homozygous and all controls were either heterozygous or homozygous for alternate haplotypes. This region tagged the SACS gene where variants are known to cause ARSACS. Sanger sequencing of SACS in affected dogs identified a 4 bp deletion that causes a frame shift and truncates 343 amino acids from the C terminus of the encoded sacsin protein (p.Val4244AlafsTer32). Our clinical and histopathological descriptions of this canine disorder contribute to the description of human ARSACS and represents the first naturally occurring large animal model of this disorder.
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Affiliation(s)
- Kari J Ekenstedt
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, Lynn Hall, 625 Harrison Street, West Lafayette, IN, 47907, USA.
| | - Katie M Minor
- Department of Veterinary and Biomedical 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, USA
| | - James J Hammond
- Department of Neurology, Pieper Memorial Veterinary Center, Middletown, CT, 06457, USA
| | - Andrew D Miller
- Section of Anatomic Pathology, Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Susan M Taylor
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - Yanyun Huang
- Prairie Diagnostic Services, Inc., Saskatoon, SK, S7N 5B4, Canada
| | - James R Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, 55108, USA
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24
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Kiener S, Åhman S, Jagannathan V, Soto S, Leeb T. Heterozygous KRT10 missense variant in a Chihuahua with severe epidermolytic ichthyosis. Anim Genet 2023; 54:652-654. [PMID: 37332248 DOI: 10.1111/age.13341] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 06/20/2023]
Affiliation(s)
- Sarah Kiener
- 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
| | - Sara Soto
- DermFocus, University of Bern, Bern, Switzerland
- Institute of Animal Pathology, 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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25
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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] [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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26
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Soh PXY, Khatkar MS, Williamson P. Lymphoma in Border Collies: Genome-Wide Association and Pedigree Analysis. Vet Sci 2023; 10:581. [PMID: 37756103 PMCID: PMC10536503 DOI: 10.3390/vetsci10090581] [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: 08/02/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
There has been considerable interest in studying cancer in dogs and its potential as a model system for humans. One area of research has been the search for genetic risk variants in canine lymphoma, which is amongst the most common canine cancers. Previous studies have focused on a limited number of breeds, but none have included Border Collies. The aims of this study were to identify relationships between Border Collie lymphoma cases through an extensive pedigree investigation and to utilise relationship information to conduct genome-wide association study (GWAS) analyses to identify risk regions associated with lymphoma. The expanded pedigree analysis included 83,000 Border Collies, with 71 identified lymphoma cases. The analysis identified affected close relatives, and a common ancestor was identified for 54 cases. For the genomic study, a GWAS was designed to incorporate lymphoma cases, putative "carriers", and controls. A case-control GWAS was also conducted as a comparison. Both analyses showed significant SNPs in regions on chromosomes 18 and 27. Putative top candidate genes from these regions included DLA-79, WNT10B, LMBR1L, KMT2D, and CCNT1.
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Affiliation(s)
- Pamela Xing Yi Soh
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia;
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Mehar Singh Khatkar
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia;
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA 5371, Australia
| | - Peter Williamson
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia;
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW 2006, Australia;
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27
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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] [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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28
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Simon R, Kiener S, Thom N, Schäfer L, Müller J, Schlohsarczyk EK, Gärtner U, Herden C, Leeb T, Lühken G. Identification of an ADAMTS2 frameshift variant in a cat family with Ehlers-Danlos syndrome. G3 (BETHESDA, MD.) 2023; 13:jkad152. [PMID: 37462293 PMCID: PMC10468306 DOI: 10.1093/g3journal/jkad152] [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: 05/05/2023] [Accepted: 07/01/2023] [Indexed: 09/01/2023]
Abstract
We investigated 4 European domestic shorthair kittens with skin lesions consistent with the dermatosparaxis type of the Ehlers-Danlos syndrome, a connective tissue disorder. The kittens were sired by the same tomcat but were born by 3 different mothers. The kittens had easily torn skin resulting in nonhealing skin wounds. Both clinically and histologically, the skin showed thin epidermis in addition to inflammatory changes. Changes in collagen fibers were visible in electron micrographs. The complete genome of an affected kitten was sequenced. A one base pair duplication leading to a frameshift in the candidate gene ADAMTS2 was identified, p.(Ser235fs*3). All 4 affected cats carried the frameshift duplication in a homozygous state. Genotypes at this variant showed perfect cosegregation with the autosomal recessive Ehlers-Danlos syndrome phenotype in the available family. The mutant allele did not occur in 48 unrelated control cats. ADAMTS2 loss-of-function variants cause autosomal recessive forms of Ehlers-Danlos syndrome in humans, mice, dogs, cattle, and sheep. The available evidence from our investigation together with the functional knowledge on ADAMTS2 in other species allows to classify the identified ADAMTS2 variant as pathogenic and most likely causative variant for the observed Ehlers-Danlos syndrome.
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Affiliation(s)
- Rebecca Simon
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen 35390, Germany
| | - Sarah Kiener
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
- Dermfocus, University of Bern, Bern 3001, Switzerland
| | - Nina Thom
- Small Animal Clinic, Justus Liebig University, Giessen 35392, Germany
| | - Laura Schäfer
- Small Animal Clinic, Justus Liebig University, Giessen 35392, Germany
| | - Janina Müller
- Institute of Veterinary Pathology, Justus Liebig University, Giessen 35392, Germany
| | - Elfi K Schlohsarczyk
- Institute of Veterinary Pathology, Justus Liebig University, Giessen 35392, Germany
| | - Ulrich Gärtner
- Institute of Anatomy and Cell Biology, Justus Liebig University, Giessen 35385, Germany
| | - Christiane Herden
- Institute of Veterinary Pathology, Justus Liebig University, Giessen 35392, Germany
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
- Dermfocus, University of Bern, Bern 3001, Switzerland
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen 35390, Germany
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29
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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] [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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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: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [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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Cullen JN, Friedenberg SG. Whole Animal Genome Sequencing: user-friendly, rapid, containerized pipelines for processing, variant discovery, and annotation of short-read whole genome sequencing data. G3 (BETHESDA, MD.) 2023; 13:jkad117. [PMID: 37243692 PMCID: PMC10411559 DOI: 10.1093/g3journal/jkad117] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 02/24/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Abstract
Advancements in massively parallel short-read sequencing technologies and the associated decreasing costs have led to large and diverse variant discovery efforts across species. However, processing high-throughput short-read sequencing data can be challenging with potential pitfalls and bioinformatics bottlenecks in generating reproducible results. Although a number of pipelines exist that address these challenges, these are often geared toward human or traditional model organism species and can be difficult to configure across institutions. Whole Animal Genome Sequencing (WAGS) is an open-source set of user-friendly, containerized pipelines designed to simplify the process of identifying germline short (SNP and indel) and structural variants (SVs) geared toward the veterinary community but adaptable to any species with a suitable reference genome. We present a description of the pipelines [adapted from the best practices of the Genome Analysis Toolkit (GATK)], along with benchmarking data from both the preprocessing and joint genotyping steps, consistent with a typical user workflow.
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Affiliation(s)
- Jonah N Cullen
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, 1352 Boyd Ave, Saint Paul, MN 55108, USA
| | - Steven G Friedenberg
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, 1352 Boyd Ave, Saint Paul, MN 55108, USA
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Christen M, Zdora I, Leschnik M, Jagannathan V, Puff C, Hünerfauth E, Volk HA, Baumgärtner W, Koch TC, Schäfer W, Kleiter M, Leeb T. RALGAPA1 Deletion in Belgian Shepherd Dogs with Cerebellar Ataxia. Genes (Basel) 2023; 14:1520. [PMID: 37628572 PMCID: PMC10454311 DOI: 10.3390/genes14081520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Several genetically distinct forms of cerebellar ataxia exist in Belgian shepherd dogs. We investigated a litter in which two puppies developed cerebellar ataxia. The clinical signs stabilized at around six weeks of age, but remained visible into adulthood. Combined linkage and homozygosity mapping delineated a 5.5 Mb critical interval. The comparison of whole-genome sequence data of one affected dog to 929 control genomes revealed a private homozygous ~4.8 kb deletion in the critical interval, Chr8:14,468,376_14,473,136del4761. The deletion comprises exon 35 of the RALGAPA1 gene, XM_038544497.1:c.6080-2893_6944+1003del. It is predicted to introduce a premature stop codon into the transcript, truncating ~23% of the wild-type open reading frame of the encoded Ral GTPase-activating protein catalytic subunit α 1, XP_038400425.1:(p.Val2027Glnfs*7). Genotypes at the deletion showed the expected co-segregation with the phenotype in the family. Genotyping additional ataxic Belgian shepherd dogs revealed three additional homozygous mutant dogs from a single litter, which had been euthanized at five weeks of age due to their severe clinical phenotype. Histopathology revealed cytoplasmic accumulation of granular material within cerebellar Purkinje cells. Genotyping a cohort of almost 900 Belgian shepherd dogs showed the expected genotype-phenotype association and a carrier frequency of 5% in the population. Human patients with loss-of-function variants in RALGAPA1 develop psychomotor disability and early-onset epilepsy. The available clinical and histopathological data, together with current knowledge about RALGAPA1 variants and their functional impact in other species, suggest the RALGAPA1 deletion is the likely causative defect for the observed phenotype in the affected dogs.
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Affiliation(s)
- Matthias Christen
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (M.C.); (V.J.)
| | - Isabel Zdora
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (I.Z.); (C.P.); (W.B.)
- Center of Systems Neuroscience, Hannover Graduate School for Neurosciences, Infection Medicine, and Veterinary Sciences (HGNI), 30559 Hannover, Germany
| | - Michael Leschnik
- Department for Companion Animals and Horses, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (M.L.); (M.K.)
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (M.C.); (V.J.)
| | - Christina Puff
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (I.Z.); (C.P.); (W.B.)
| | - Enrice Hünerfauth
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (E.H.); (H.A.V.)
| | - Holger A. Volk
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (E.H.); (H.A.V.)
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (I.Z.); (C.P.); (W.B.)
| | - Tessa C. Koch
- Bundeswehr School of Dog Handling, 56766 Ulmen, Germany; (T.C.K.); (W.S.)
| | - Wencke Schäfer
- Bundeswehr School of Dog Handling, 56766 Ulmen, Germany; (T.C.K.); (W.S.)
| | - Miriam Kleiter
- Department for Companion Animals and Horses, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (M.L.); (M.K.)
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (M.C.); (V.J.)
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33
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Ripolles-Garcia A, Murgiano L, Ziolkowska N, Marinho FP, Roszak K, Iffrig S, Aguirre GD, Miyadera K. Natural disease history of a canine model of oligogenic RPGRIP1-cone-rod dystrophy establishes variable effects of previously and newly mapped modifier loci. Hum Mol Genet 2023; 32:2139-2151. [PMID: 36951959 PMCID: PMC10281748 DOI: 10.1093/hmg/ddad046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/23/2023] [Accepted: 03/21/2023] [Indexed: 03/24/2023] Open
Abstract
Canine RPGRIP1-cone-rod dystrophy (CRD), a model for human inherited retinal diseases (IRDs), was originally identified as autosomal recessive early-onset blindness. However, later studies revealed extensive phenotypic variability among RPGRIP1 mutants. This led to the identification of a homozygous MAP9 variant as a modifier associated with early-onset disease. Based on further phenotypic variation affecting cone photoreceptor function, we report mapping of L3 as an additional modifier locus, within a 4.1-Mb locus on canine chromosome 30. We establish the natural disease history of RPGRIP1-CRD based on up to 9-year long-term functional and structural retinal data from 58 dogs including 44 RPGRIP1 mutants grouped according to the modifier status. RPGRIP1 mutants affected by both MAP9 and L3 modifiers exhibited the most severe phenotypes with rapid disease progression. MAP9 alone was found to act as an overall accelerator of rod and cone diseases, while L3 had a cone-specific effect. Ultrastructural analysis of photoreceptors revealed varying degrees of rod and cone damage, while the connecting cilia appeared structurally preserved in all groups. We conclude that RPGRIP1-CRD is an oligogenic disease with at least three loci contributing to the pathogenesis. While the RPGRIP1 variant is required for developing the disease, MAP9 and L3 modifiers exacerbate the phenotype, individually and cumulatively. Oligogenic canine RPGRIP1-CRD illustrates the impact of multiple genetic modifiers on disease phenotype and thus has the potential to reveal new targets for broad-spectrum therapies for oligogenic or polygenic forms of human IRDs.
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Affiliation(s)
- Ana Ripolles-Garcia
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leonardo Murgiano
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Natalia Ziolkowska
- Department of Histology and Embryology, Faculty of Veterinary Medicine, University of Warmia and Mazury, Olsztyn 10-719, Poland
| | - Felipe Pompeo Marinho
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Karolina Roszak
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sommer Iffrig
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gustavo D Aguirre
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Keiko Miyadera
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Wade CM, Nuttall R, Liu S. Comprehensive analysis of geographic and breed-purpose influences on genetic diversity and inherited disease risk in the Doberman dog breed. Canine Med Genet 2023; 10:7. [PMID: 37277858 DOI: 10.1186/s40575-023-00130-3] [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: 04/27/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Publicly available phenotype data and genotyping array data from two citizen science projects: "Doberman Health Surveys" and "The Doberman Diversity Project" were analyzed to explore relative homozygosity, diversity, and disorder risk according to geographical locale and breeding purpose in the Doberman. RESULTS From the phenotypic data cohort, life expectancy of a Doberman at birth is 9.1 years. The leading causes of death were heart disease (accounting for 28% of deaths) and cancers (collectively accounting for 14% of deaths). By genotyping, the world Doberman population exists as four major cohorts (European exhibition-bred, Americas exhibition-bred, European work, Americas pet/informal). Considering the entire Doberman population, four genomic regions longer than 500 Kb are fixed in 90% or more of 3,226 dogs included in this study. The four fixed regions reside on two autosomal chromosomes: CFA3:0.8-2.3 Mb (1.55 Mb); CFA3: 57.9-59.8 Mb (1.8 Mb); CFA31:0-1.2 Mb (1.2 Mb); and CFA31:4.80-6.47 Mb (1.67 Mb). Using public variant call files including variants for eight Doberman pinschers, we observed 30 potentially functional alternate variants that were evolutionarily diverged relative to the wider sequenced dog population within the four strongly homozygous chromosomal regions. Effective population size (Ne) is a statistical measure of breed diversity at the time of sampling that approximates the number of unique individuals. The major identified sub-populations of Dobermans demonstrated Ne in the range 70-236. The mean level of inbreeding in the Doberman breed is 40% as calculated by the number of array variants in runs of homozygosity divided by the assayed genome size (excluding the X chromosome). The lowest observed level of inbreeding in the Dobermans assayed was 15% in animals that were first generation mixes of European and USA bred Dobermans. Array variant analysis shows that inter-crossing between European and USA-bred Dobermans has capacity to re-introduce variation at many loci that are strongly homozygous. CONCLUSIONS We conclude that efforts to improve breed diversity first should focus on regions with the highest fixation levels, but managers must ensure that mutation loads are not worsened by increasing the frequencies of rarer haplotypes in the identified regions. The analysis of global data identified regions of strong fixation that might impact known disorder risks in the breed. Plausible gene candidates for future analysis of the genetic basis of cardiac disease and cancer were identified in the analysis.
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Affiliation(s)
- Claire M Wade
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia.
| | | | - Sophie Liu
- Doberman Diversity Project, Oakland, CA, USA
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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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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36
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Christen M, Gutierrez-Quintana R, James M, Faller KME, Lowrie M, Rusbridge C, Bossens K, Mellersh C, Pettitt L, Heinonen T, Lohi H, Jagannathan V, Leeb T. A TNR Frameshift Variant in Weimaraner Dogs with an Exercise-Induced Paroxysmal Movement Disorder. Mov Disord 2023; 38:1094-1099. [PMID: 37023257 DOI: 10.1002/mds.29391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/30/2023] [Accepted: 03/10/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Some paroxysmal movement disorders remain without an identified genetic cause. OBJECTIVES The aim was to identify the causal genetic variant for a paroxysmal dystonia-ataxia syndrome in Weimaraner dogs. METHODS Clinical and diagnostic investigations were performed. Whole genome sequencing of one affected dog was used to identify private homozygous variants against 921 control genomes. RESULTS Four Weimaraners were presented for episodes of abnormal gait. Results of examinations and diagnostic investigations were unremarkable. Whole genome sequencing revealed a private frameshift variant in the TNR (tenascin-R) gene in an affected dog, XM_038542431.1:c.831dupC, which is predicted to truncate more than 75% of the open read frame. Genotypes in a cohort of 4 affected and 70 unaffected Weimaraners showed perfect association with the disease phenotype. CONCLUSIONS We report the association of a TNR variant with a paroxysmal dystonia-ataxia syndrome in Weimaraners. It might be relevant to include sequencing of this gene in diagnosing humans with unexplained paroxysmal movement disorders. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Matthias Christen
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rodrigo Gutierrez-Quintana
- Small Animal Hospital, School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | | | - Kiterie M E Faller
- Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Roslin, United Kingdom
| | - Mark Lowrie
- Dovecote Veterinary Hospital, Derby, United Kingdom
| | - Clare Rusbridge
- School of Veterinary Medicine, University of Surrey, Surrey, United Kingdom
| | - Kenny Bossens
- Nesto Veterinary Referral Center Orion, Herentals, Belgium
| | - Cathryn Mellersh
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Louise Pettitt
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Tiina Heinonen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki, and Folkhälsan Research Center, Helsinki, Finland
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki, and Folkhälsan Research Center, Helsinki, Finland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Dell'Apa D, Fumeo M, Volta A, Bernardini M, Fidanzio F, Buffagni V, Christen M, Jagannathan V, Leeb T, Bianchi E. Case report: Sacral agenesis in two boxer dogs: clinical presentation, diagnostic investigations, and outcome. Front Vet Sci 2023; 10:1201484. [PMID: 37303726 PMCID: PMC10248164 DOI: 10.3389/fvets.2023.1201484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Two boxer dogs from the same litter were presented at 3 months of age for urinary and fecal incontinence. Both dogs had an abnormal tail consisting of a small stump, an atonic anal sphincter, and absent perineal reflex and sensation. Neurological evaluation was indicative of a lesion of the cauda equina or sacral spinal cord. Radiology and CT scan of the spine displayed similar findings in the two dogs that were indicative of sacral agenesis. Indeed, they had 6 lumbar vertebrae followed by a lumbosacral transitional vertebra, lacking a complete spinous process, and a hypoplastic vertebra carrying 2 hypoplastic sacral transverse processes as the only remnant of the sacral bone. Caudal vertebrae were absent in one of the dogs. On MRI, one dog had a dural sac occupying the entire spinal canal and ending in a subfascial fat structure. In the other dog, the dural sac finished in an extracanalar, subfascial, well-defined cystic structure, communicating with the subarachnoid space, and consistent with a meningocele. Sacral agenesis-that is the partial or complete absence of the sacral bones-is a neural tube defect occasionally reported in humans with spina bifida occulta. Sacral agenesis has been described in human and veterinary medicine in association with conditions such as caudal regression syndrome, perosomus elumbis, and Currarino syndrome. These neural tube defects are caused by genetic and/or environmental factors. Despite thorough genetic investigation, no candidate variants in genes with known functional impact on bone development or sacral development could be found in the affected dogs. To the best of the authors' knowledge, this is the first report describing similar sacral agenesis in two related boxer dogs.
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Affiliation(s)
- Diletta Dell'Apa
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Martina Fumeo
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Antonella Volta
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Marco Bernardini
- Neurodiagnostic Unit, Anicura Portoni Rossi Veterinary Hospital, Bologna, Italy
- Department of Animal Medicine, Production and Health, Clinical Section, University of Padua, Legnaro, Italy
| | | | | | - Matthias Christen
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Vidhya Jagannathan
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Ezio Bianchi
- Department of Veterinary Science, University of Parma, Parma, Italy
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Furrow E, Tate N, Minor K, Martinson S, Larrabee S, Anttila M, Sleeper M, Henthorn P. An ABCC9 Missense Variant Is Associated with Sudden Cardiac Death and Dilated Cardiomyopathy in Juvenile Dogs. Genes (Basel) 2023; 14:genes14050988. [PMID: 37239348 DOI: 10.3390/genes14050988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Sudden cardiac death in the young (SCDY) is a devastating event that often has an underlying genetic basis. Manchester Terrier dogs offer a naturally occurring model of SCDY, with sudden death of puppies as the manifestation of an inherited dilated cardiomyopathy (DCM). We performed a genome-wide association study for SCDY/DCM in Manchester Terrier dogs and identified a susceptibility locus harboring the cardiac ATP-sensitive potassium channel gene ABCC9. Sanger sequencing revealed an ABCC9 p.R1186Q variant present in a homozygous state in all SCDY/DCM-affected dogs (n = 26). None of the controls genotyped (n = 398) were homozygous for the variant, but 69 were heterozygous carriers, consistent with autosomal recessive inheritance with complete penetrance (p = 4 × 10-42 for the association of homozygosity for ABCC9 p.R1186Q with SCDY/DCM). This variant exists at low frequency in human populations (rs776973456) with clinical significance previously deemed uncertain. The results of this study further the evidence that ABCC9 is a susceptibility gene for SCDY/DCM and highlight the potential application of dog models to predict the clinical significance of human variants.
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Affiliation(s)
- Eva Furrow
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55455, USA
| | - Nicole Tate
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55455, USA
| | - Katie Minor
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55455, USA
| | - Shannon Martinson
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE CIA 4P3, Canada
| | - Shannon Larrabee
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55455, USA
| | | | - Meg Sleeper
- College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Paula Henthorn
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Kiener S, McMahill BG, Affolter VK, Welle M, Yager JA, Jagannathan V, Leeb T. SOAT1 missense variant in two cats with sebaceous gland dysplasia. Mol Genet Genomics 2023; 298:837-843. [PMID: 37060467 DOI: 10.1007/s00438-023-02020-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/08/2023] [Indexed: 04/16/2023]
Abstract
Spontaneously arisen hereditary diseases in domestic animals provide an excellent opportunity to study the physiological functions of the altered genes. We investigated two 4-month-old sibling domestic short haired kittens with dry dark debris around the eyes, nose, and ears, dark crusting on the legs and a thin poor hair coat. Skin biopsies revealed abnormal sebaceous gland morphology with lack of normal sebocyte arrangement and differentiation. Hair follicles had a distorted silhouette, interpreted as a change secondary to the observed sebaceous gland dysplasia. Whole genome sequencing on both affected kittens and 65 genetically diverse feline genomes was performed. Filtering for variants that were present in both kittens but absent from the control genomes revealed a homozygous missense variant in SOAT1, encoding sterol O-acyltransferase 1. The protein is localized in the endoplasmic reticulum and catalyzes the formation of cholesteryl esters, an essential component of sebum and meibum. The identified SOAT1:c.1531G > A variant is predicted to change a highly conserved glycine residue within the last transmembrane domain of SOAT1, p.Gly511Arg. In mice, variants in Soat1 or complete knockout of the gene lead to the "hair interior defect" (hid) or abnormal Meibomian glands, respectively. SOAT1:c.1531G > A represents a plausible candidate variant for the observed sebaceous gland dysplasia in both kittens of this study. The variant was not present in 10 additional cats with a similar clinical and histopathological phenotype suggesting genetic heterogeneity. SOAT1 variants should be considered as potential cause in hereditary sebaceous gland dysplasias of humans and domestic animals.
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Affiliation(s)
- Sarah Kiener
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland
- Dermfocus, University of Bern, 3001, Bern, Switzerland
| | - Barbara G McMahill
- Pathology Services, IDEXX Reference Laboratories Inc., Lander, WY, 82520, USA
| | - Verena K Affolter
- Department of Pathology, Microbiology, Immunology, School of Veterinary Medicine, University California Davis, Davis, CA, 95616, USA
| | - Monika Welle
- Dermfocus, University of Bern, 3001, Bern, Switzerland
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Julie A Yager
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
- School of Veterinary Science, University of Sydney, Sydney, NSW, 2006, Australia
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001, Bern, Switzerland
| | - Tosso 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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40
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Szydlowski M. A clue to the etiology of disorders of sex development from identity-by-descent analysis in dogs with cryptic relatedness. Anim Genet 2023; 54:166-176. [PMID: 36437751 DOI: 10.1111/age.13276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/02/2022] [Accepted: 11/14/2022] [Indexed: 11/29/2022]
Abstract
Disorders of sex development (DSDs) are discrepancies between sex chromosomes and phenotypical sex. Quite common forms of DSD in canine populations include testicular and ovotesticular XX DSDs with a normal set of sex chromosomes. The objective of this study was to identify genes and putative harmful variants for canine XX DSDs. I have reanalyzed data from the whole-genome sequencing of 11 XX DSD French Bulldogs and six XX DSD American Staffordshire Terriers. Identity-by-descent analysis revealed cryptic relatedness in affected French Bulldogs. Causative genes were sought in chromosomal segments shared identical-by-descent by close relatives. In French Bulldogs, the reanalysis identified 19 regions of importance with a total length of just 65.9 Mb. Variant filtering within the regions implicated AKAP2, PIWIL1, POLR3A and SH2D4B as genes that may be involved in individual cases of testicular and ovotesticular XX DSD in French Bulldogs and American Staffordshire Terriers.
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Affiliation(s)
- Maciej Szydlowski
- Department of Genetics and Animal Breeding, Poznań University of Life Sciences, Poznań, Poland
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41
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Fitzwilliams T, Wolff‐Sneedorff JL, Fredholm M, Karlskov‐Mortensen P, Guldbrandtsen B, Bruun CS. Evaluation of the value of genetic testing for cystinuria in the Danish population of English bulldogs. Anim Genet 2023. [DOI: 10.1111/age.13321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 02/21/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023]
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42
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Kiener S, Castilla E, Jagannathan V, Welle M, Leeb T. SDR9C7
missense variant in a Chihuahua with non‐epidermolytic ichthyosis. Anim Genet 2023. [DOI: 10.1111/age.13319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/24/2023] [Accepted: 03/10/2023] [Indexed: 03/29/2023]
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Jenni S, Ludwig-Peisker O, Jagannathan V, Lapsina S, Stirn M, Hofmann-Lehmann R, Bogdanov N, Schetle N, Giger U, Leeb T, Bogdanova A. Methemoglobinemia, Increased Deformability and Reduced Membrane Stability of Red Blood Cells in a Cat with a CYB5R3 Splice Defect. Cells 2023; 12:cells12070991. [PMID: 37048064 PMCID: PMC10093206 DOI: 10.3390/cells12070991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/16/2023] [Accepted: 03/22/2023] [Indexed: 04/14/2023] Open
Abstract
Methemoglobinemia is an acquired or inherited condition resulting from oxidative stress or dysfunction of the NADH-cytochrome b5 reductase or associated pathways. This study describes the clinical, pathophysiological, and molecular genetic features of a cat with hereditary methemoglobinemia. Whole genome sequencing and mRNA transcript analyses were performed in affected and control cats. Co-oximetry, ektacytometry, Ellman's assay for reduced glutathione concentrations, and CYB5R activity were assessed. A young adult European domestic shorthair cat decompensated at induction of anesthesia and was found to have persistent methemoglobinemia of 39 ± 8% (reference range < 3%) of total hemoglobin which could be reversed upon intravenous methylene blue injection. The erythrocytic CYB5R activity was 20 ± 6% of normal. Genetic analyses revealed a single homozygous base exchange at the beginning of intron 3 of the CYB5R3 gene, c.226+5G>A. Subsequent mRNA studies confirmed a splice defect and demonstrated expression of two mutant CYB5R3 transcripts. Erythrocytic glutathione levels were twice that of controls. Mild microcytosis, echinocytes, and multiple Ca2+-filled vesicles were found in the affected cat. Erythrocytes were unstable at high osmolarities although highly deformable as follows from the changes in elongation index and maximal-tolerated osmolarity. Clinicopathological presentation of this cat was similar to other cats with CYB5R3 deficiency. We found that methemoglobinemia is associated with an increase in red blood cell fragility and deformability, glutathione overload, and morphological alterations typical for stress erythropoiesis.
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Affiliation(s)
- Sophia Jenni
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Odette Ludwig-Peisker
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Sandra Lapsina
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Martina Stirn
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Regina Hofmann-Lehmann
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Nikolay Bogdanov
- Red Blood Cell Group, Institute of Veterinary Physiology and the Center for Clinical Studies, Vetsuisse Faculty Zurich, University of Zurich, 8057 Zurich, Switzerland
| | - Nelli Schetle
- Red Blood Cell Group, Institute of Veterinary Physiology and the Center for Clinical Studies, Vetsuisse Faculty Zurich, University of Zurich, 8057 Zurich, Switzerland
| | - Urs Giger
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Anna Bogdanova
- Red Blood Cell Group, Institute of Veterinary Physiology and the Center for Clinical Studies, Vetsuisse Faculty Zurich, University of Zurich, 8057 Zurich, Switzerland
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44
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Latrille T, Rodrigue N, Lartillot N. Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale. Proc Natl Acad Sci U S A 2023; 120:e2214977120. [PMID: 36897968 PMCID: PMC10089192 DOI: 10.1073/pnas.2214977120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/11/2023] [Indexed: 03/12/2023] Open
Abstract
Adaptation in protein-coding sequences can be detected from multiple sequence alignments across species or alternatively by leveraging polymorphism data within a population. Across species, quantification of the adaptive rate relies on phylogenetic codon models, classically formulated in terms of the ratio of nonsynonymous over synonymous substitution rates. Evidence of an accelerated nonsynonymous substitution rate is considered a signature of pervasive adaptation. However, because of the background of purifying selection, these models are potentially limited in their sensitivity. Recent developments have led to more sophisticated mutation-selection codon models aimed at making a more detailed quantitative assessment of the interplay between mutation, purifying, and positive selection. In this study, we conducted a large-scale exome-wide analysis of placental mammals with mutation-selection models, assessing their performance at detecting proteins and sites under adaptation. Importantly, mutation-selection codon models are based on a population-genetic formalism and thus are directly comparable to the McDonald and Kreitman test at the population level to quantify adaptation. Taking advantage of this relationship between phylogenetic and population genetics analyses, we integrated divergence and polymorphism data across the entire exome for 29 populations across 7 genera and showed that proteins and sites detected to be under adaptation at the phylogenetic scale are also under adaptation at the population-genetic scale. Altogether, our exome-wide analysis shows that phylogenetic mutation-selection codon models and the population-genetic test of adaptation can be reconciled and are congruent, paving the way for integrative models and analyses across individuals and populations.
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Affiliation(s)
- Thibault Latrille
- Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et Biologie Evolutive, UMR5558, 69100Villeurbanne, France
- École Normale Supérieure de Lyon, Université de Lyon, 69342Lyon, France
- Department of Computational Biology, Université de Lausanne, 1015Lausanne, Switzerland
| | - Nicolas Rodrigue
- Department of Biology, Institute of Biochemistry, and School of Mathematics and Statistics, Carleton University, K1S 5B6Ottawa, Canada
| | - Nicolas Lartillot
- Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et Biologie Evolutive, UMR5558, 69100Villeurbanne, France
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45
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Kiener S, Yang C, Rich N, Jagannathan V, Mauldin EA, Leeb T. Heterozygous ATP2A2 missense variant identified in a Shih Tzu with Darier disease. Anim Genet 2023. [PMID: 36883421 DOI: 10.1111/age.13314] [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: 01/27/2023] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 03/09/2023]
Abstract
Darier disease is caused by heterozygous loss of function variants in the ATP2A2 gene encoding the endoplasmic/sarcoplasmic reticulum Ca2+ pump ATP2A2. Defective intracellular calcium signaling in the epidermis results in a loss of desmosomal adhesion and the development of characteristic skin lesions. In this study, we investigated a Shih Tzu that developed erythematous papules on the ventrum and, over time, the dorsal neck and a nodule in the right ear canal with secondary ear infection. Histopathologic examination demonstrated discrete foci of acantholysis affecting suprabasal layers of the epidermis. Whole genome sequencing of the affected dog identified a heterozygous missense variant, p.N809H, affecting an evolutionarily conserved amino acid residue of the ATP2A2 protein. The highly characteristic clinical and histopathologic findings together with a plausible variant in the only known functional candidate gene establish the diagnosis of canine Darier disease in the studied dog and highlight the potential of genetic analyses as complementary diagnostic approach in veterinary medicine.
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Affiliation(s)
- Sarah Kiener
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,DermFocus, University of Bern, Bern, Switzerland
| | - Ching Yang
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Naomi Rich
- Animal Skin and Allergy Clinic, Lynnwood, Washington, USA
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Elizabeth A Mauldin
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,DermFocus, University of Bern, Bern, Switzerland
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46
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Genomic Diversity and Runs of Homozygosity in Bernese Mountain Dogs. Genes (Basel) 2023; 14:genes14030650. [PMID: 36980922 PMCID: PMC10048372 DOI: 10.3390/genes14030650] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Bernese mountain dogs are a large dog breed formed in the early 1900s in Switzerland. While originally farm dogs that were used for pulling carts, guarding, and driving cattle, today they are considered multi-purpose companion and family dogs. The breed is predisposed to several complex diseases, such as histiocytic sarcoma, degenerative myelopathy, or hip dysplasia. Using whole-genome sequencing (WGS) data, we assessed the genomic architecture of 33 unrelated dogs from four countries: France, Sweden, Switzerland, and the United States. Analysis of runs of homozygosity (ROH) identified 12,643 ROH with an average length of 2.29 Mb and an average inbreeding coefficient of 0.395. Multidimensional scaling analysis of the genetic relatedness revealed limited clustering of European versus USA dogs, suggesting exchanges of breeding stock between continents. Furthermore, only two mtDNA haplotypes were detected in the 33 studied dogs, both of which are widespread throughout multiple dog breeds. WGS-based ROH analyses revealed several fixed or nearly fixed regions harboring discreet morphological trait-associated as well as disease-associated genetic variants. Several genes involved in the regulation of immune cells were found in the ROH shared by all dogs, which is notable in the context of the breed’s strong predisposition to hematopoietic cancers. High levels of inbreeding and relatedness, strongly exaggerated in the last 30 years, have likely led to the high prevalence of specific genetic disorders in this breed.
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47
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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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48
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Christen M, Ludwig-Peisker O, Jagannathan V, Hetzel U, Schönball U, Leeb T. STK36 splice site variant in an Australian Shepherd dog with primary ciliary dyskinesia. Anim Genet 2023; 54:412-415. [PMID: 36786090 DOI: 10.1111/age.13306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 01/20/2023] [Accepted: 02/01/2023] [Indexed: 02/15/2023]
Abstract
Primary ciliary dyskinesia (PCD) represents a group of diseases characterized by impaired movement of cilia and subsequent health problems in diverse organ systems, notably the respiratory tract. Almost 50 candidate genes for PCD are known in humans. In this study, we investigated an Australian Shepherd dog with a history of recurrent respiratory infections and nasal discharge. A transmission electron microscopy investigation led to the diagnosis of PCD with central pair defect, in which the normal 9:2 arrangement of respiratory cilia was altered and reduced to a 9:0 arrangement. Whole genome sequencing data from the affected dog was obtained and searched for variants in PCD candidate genes that were not present in 918 control genomes from different breeds. This revealed a homozygous single base pair exchange at a splice site of STK36, XM_038585732.1:c.2868-1G>A. The mutant allele was absent from 281 additionally genotyped Australian Shepherd dogs. RT-PCR confirmed aberrant splicing in the affected dog with the skipping of exon 20 and the insertion of a cryptic exon, which is predicted to lead to a premature stop codon and truncation of 36% of the STK36 wild-type open reading frame, XP_038441660.1:(p.Met957Profs*11). STK36 variants were previously reported to cause PCD in humans and mice. The knowledge from other species together with the absence of the mutant allele in more than 1000 control dogs suggests STK36:c.2868-1G>A as the most likely candidate variant for PCD in the investigated case.
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Affiliation(s)
- Matthias Christen
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Udo Hetzel
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | | | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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49
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Dystrophin ( DMD) Missense Variant in Cats with Becker-Type Muscular Dystrophy. Int J Mol Sci 2023; 24:ijms24043192. [PMID: 36834603 PMCID: PMC9964367 DOI: 10.3390/ijms24043192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/20/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Muscular dystrophy due to dystrophin deficiency in humans is phenotypically divided into a severe Duchenne and milder Becker type. Dystrophin deficiency has also been described in a few animal species, and few DMD gene variants have been identified in animals. Here, we characterize the clinical, histopathological, and molecular genetic aspects of a family of Maine Coon crossbred cats with clinically mild and slowly progressive muscular dystrophy. Two young adult male littermate cats exhibited abnormal gait and muscular hypertrophy with macroglossia. Serum creatine kinase activities were highly increased. Histopathologically, dystrophic skeletal muscle exhibited marked structural changes including atrophic, hypertrophic, and necrotic muscle fibers. Immunohistochemistry showed irregularly reduced expression of dystrophin but the staining of other muscle proteins such as β- and γ-sarcoglycans as well as desmin was also diminished. Whole genome sequencing of one affected cat and genotyping of the littermate found both to be hemizygous mutant at a single DMD missense variant (c.4186C>T). No other protein-changing variants in candidate genes for muscular dystrophy were detected. In addition, one clinically healthy male littermate was hemizygous wildtype, while the queen and one female littermate were clinically healthy, but heterozygous. The predicted amino acid exchange (p.His1396Tyr) resides in a conserved central rod spectrin domain of dystrophin. Various protein modeling programs did not predict major disruption of the dystrophin protein by this substitution, but the altered charge of the region may still affect protein function. This study represents the first genotype-to-phenotype correlation of Becker-type dystrophin deficiency in companion animals.
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50
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Abitbol M, Jagannathan V, Lopez M, Courtin A, Dufaure de Citres C, Gache V, Leeb T. A CDH23 missense variant in Beauceron dogs with non-syndromic deafness. Anim Genet 2023; 54:73-77. [PMID: 36308003 PMCID: PMC10092623 DOI: 10.1111/age.13273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/04/2022] [Accepted: 10/17/2022] [Indexed: 01/07/2023]
Abstract
Congenital coat-colour-related deafness is common among certain canine breeds especially those exhibiting extreme white spotting or merle patterning. We identified a non-syndromic deafness in Beauceron dogs characterised by a bilateral hearing loss in puppies that is not linked to coat colour. Pedigree analysis suggested an autosomal recessive transmission. By combining homozygosity mapping with whole genome sequencing and variant filtering in affected dogs we identified a CDH23:c.700C>T variant. The variant, located in the CHD23 (cadherin related 23) gene, was predicted to induce a CDH23:p.(Pro234Ser) change in the protein. Proline-234 of CDH23 protein is highly conserved across different vertebrate species. In silico tools predicted the CDH23:p.(Pro234Ser) change to be deleterious. CDH23 encodes a calcium-dependent transmembrane glycoprotein localised near the tips of hair-cell stereocilia in the mammalian inner ear. Intact function of these cilia is mandatory for the transformation of the acoustical wave into a neurological signal, leading to sensorineural deafness when impaired. By genotyping a cohort of 90 control Beauceron dogs sampled in France, we found a 3.3% carrier frequency. The CDH23:c.[700C>T] allele is easily detectable with a genetic test to avoid at-risk matings.
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Affiliation(s)
- Marie Abitbol
- Univ Lyon, VetAgro Sup, Marcy-l'Etoile, France.,Institut NeuroMyoGène INMG-PNMG, CNRS UMR5261, INSERM U1315, Faculté de Médecine, Rockefeller, Université Claude Bernard Lyon 1, Lyon, France
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Marie Lopez
- Cabinet Vétérinaire Le Semnoz, Seynod, France
| | - Ambre Courtin
- Société Centrale Canine, Aubervilliers, France.,Ecole Nationale Vétérinaire d'Alfort, INSERM, IMRB, Univ Paris-Est Créteil, Maisons-Alfort, France
| | | | - Vincent Gache
- Institut NeuroMyoGène INMG-PNMG, CNRS UMR5261, INSERM U1315, Faculté de Médecine, Rockefeller, Université Claude Bernard Lyon 1, Lyon, France
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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