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Azevedo L, Amaro AP, Niza-Ribeiro J, Lopes-Marques M. Naturally occurring genetic diseases caused by de novo variants in domestic animals. Anim Genet 2024; 55:319-327. [PMID: 38323510 DOI: 10.1111/age.13403] [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: 08/25/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/08/2024]
Abstract
With the advent of next-generation sequencing, an increasing number of cases of de novo variants in domestic animals have been reported in scientific literature primarily associated with clinically severe phenotypes. The emergence of new variants at each generation is a crucial aspect in understanding the pathology of early-onset diseases in animals and can provide valuable insights into similar diseases in humans. With the aim of collecting deleterious de novo variants in domestic animals, we searched the scientific literature and compiled reports on 42 de novo variants in 31 genes in domestic animals. No clear disease-associated phenotype has been established in humans for three of these genes (NUMB, ANKRD28 and KCNG1). For the remaining 28 genes, a strong similarity between animal and human phenotypes was recognized from available information in OMIM and OMIA, revealing the importance of comparative studies and supporting the use of domestic animals as natural models for human diseases, in line with the One Health approach.
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Affiliation(s)
- Luísa Azevedo
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Andreia P Amaro
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - João Niza-Ribeiro
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
- Population Studies Department, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- EPIUnit-Epidemiology Research Unit, ISPUP-Institute of Public Health of the University of Porto, Porto, Portugal
| | - Mónica Lopes-Marques
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
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2
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Saito M, Otsu W, Miyadera K, Nishimura Y. Recent advances in the understanding of cilia mechanisms and their applications as therapeutic targets. Front Mol Biosci 2023; 10:1232188. [PMID: 37780208 PMCID: PMC10538646 DOI: 10.3389/fmolb.2023.1232188] [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: 05/31/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023] Open
Abstract
The primary cilium is a single immotile microtubule-based organelle that protrudes into the extracellular space. Malformations and dysfunctions of the cilia have been associated with various forms of syndromic and non-syndromic diseases, termed ciliopathies. The primary cilium is therefore gaining attention due to its potential as a therapeutic target. In this review, we examine ciliary receptors, ciliogenesis, and ciliary trafficking as possible therapeutic targets. We first discuss the mechanisms of selective distribution, signal transduction, and physiological roles of ciliary receptors. Next, pathways that regulate ciliogenesis, specifically the Aurora A kinase, mammalian target of rapamycin, and ubiquitin-proteasome pathways are examined as therapeutic targets to regulate ciliogenesis. Then, in the photoreceptors, the mechanism of ciliary trafficking which takes place at the transition zone involving the ciliary membrane proteins is reviewed. Finally, some of the current therapeutic advancements highlighting the role of large animal models of photoreceptor ciliopathy are discussed.
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Affiliation(s)
- Masaki Saito
- Department of Molecular Physiology and Pathology, School of Pharma-Sciences, Teikyo University, Tokyo, Japan
| | - Wataru Otsu
- Department of Biomedical Research Laboratory, Gifu Pharmaceutical University, Gifu, Japan
| | - Keiko Miyadera
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Yuhei Nishimura
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
- Mie University Research Center for Cilia and Diseases, Tsu, Mie, Japan
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3
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Joyce H, Burmeister LM, Wright H, Fleming L, Oliver JAC, Mellersh C. Identification of a variant in NDP associated with X-linked retinal dysplasia in the English cocker spaniel dog. PLoS One 2021; 16:e0251071. [PMID: 33945575 PMCID: PMC8096109 DOI: 10.1371/journal.pone.0251071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 04/19/2021] [Indexed: 01/09/2023] Open
Abstract
Purpose Three related male English Cocker Spaniels (ECS) were reported to be congenitally blind. Examination of one of these revealed complete retinal detachment. A presumptive diagnosis of retinal dysplasia (RD) was provided and pedigree analysis was suggestive of an X-linked mode of inheritance. We sought to investigate the genetic basis of RD in this family of ECS. Methods Following whole genome sequencing (WGS) of the one remaining male RD-affected ECS, two distinct investigative approaches were employed: a candidate gene approach and a whole genome approach. In the candidate gene approach, COL9A2, COL9A3, NHEJ1, RS1 and NDP genes were investigated based on their known associations with RD and retinal detachment in dogs and humans. In the whole genome approach, affected WGS was compared with 814 unaffected canids to identify candidate variants, which were filtered based on appropriate segregation and predicted pathogenic effects followed by subsequent investigation of gene function. Candidate variants were tested for appropriate segregation in the ECS family and association with disease was assessed using samples from a total of 180 ECS. Results The same variant in NDP (c.653_654insC, p.Met114Hisfs*16) that was predicted to result in 15 aberrant amino acids before a premature stop in norrin protein, was identified independently by both approaches and was shown to segregate appropriately within the ECS family. Association of this variant with X-linked RD was significant (P = 0.0056). Conclusions For the first time, we report a variant associated with canine X-linked RD. NDP variants are already known to cause X-linked RD, along with other abnormalities, in human Norrie disease. Thus, the dog may serve as a useful large animal model for research.
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Affiliation(s)
- Hannah Joyce
- Department of Ophthalmology, Dick White Referrals, Six Mile Bottom, Cambridgeshire, United Kingdom
- Department of Ophthalmology, Centre for Small Animal Studies, Animal Health Trust, Kentford, Newmarket, United Kingdom
- * E-mail:
| | - Louise M. Burmeister
- Department of Canine Genetics, Kennel Club Genetics Centre, Animal Health Trust, Kentford, Newmarket, United Kingdom
| | - Hattie Wright
- Department of Canine Genetics, Kennel Club Genetics Centre, Animal Health Trust, Kentford, Newmarket, United Kingdom
| | - Lorraine Fleming
- Department of Ophthalmology, Dick White Referrals, Six Mile Bottom, Cambridgeshire, United Kingdom
- Department of Ophthalmology, Centre for Small Animal Studies, Animal Health Trust, Kentford, Newmarket, United Kingdom
| | - James A. C. Oliver
- Department of Ophthalmology, Dick White Referrals, Six Mile Bottom, Cambridgeshire, United Kingdom
| | - Cathryn Mellersh
- Department of Canine Genetics, Kennel Club Genetics Centre, Animal Health Trust, Kentford, Newmarket, United Kingdom
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CCDC66 frameshift variant associated with a new form of early-onset progressive retinal atrophy in Portuguese Water Dogs. Sci Rep 2020; 10:21162. [PMID: 33273526 PMCID: PMC7712861 DOI: 10.1038/s41598-020-77980-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 11/10/2020] [Indexed: 11/17/2022] Open
Abstract
Aberrant photoreceptor function or morphogenesis leads to blinding retinal degenerative diseases, the majority of which have a genetic aetiology. A variant in PRCD previously identified in Portuguese Water Dogs (PWDs) underlies prcd (progressive rod-cone degeneration), an autosomal recessive progressive retinal atrophy (PRA) with a late onset at 3–6 years of age or older. Herein, we have identified a new form of early-onset PRA (EOPRA) in the same breed. Pedigree analysis suggested an autosomal recessive inheritance. Four PWD full-siblings affected with EOPRA diagnosed at 2–3 years of age were genotyped (173,661 SNPs) along with 2 unaffected siblings, 2 unaffected parents, and 15 unrelated control PWDs. GWAS, linkage analysis and homozygosity mapping defined a 26-Mb candidate region in canine chromosome 20. Whole-genome sequencing in one affected dog and its obligatory carrier parents identified a 1 bp insertion (CFA20:g.33,717,704_33,717,705insT (CanFam3.1); c.2262_c.2263insA) in CCDC66 predicted to cause a frameshift and truncation (p.Val747SerfsTer8). Screening of an extended PWD population confirmed perfect co-segregation of this genetic variant with the disease. Western blot analysis of COS-1 cells transfected with recombinant mutant CCDC66 expression constructs showed the mutant transcript translated into a truncated protein. Furthermore, in vitro studies suggest that the mutant CCDC66 is mislocalized to the nucleus relative to wild type CCDC66. CCDC66 variants have been associated with inherited retinal degenerations (RDs) including canine and murine ciliopathies. As genetic variants affecting the primary cilium can cause ciliopathies in which RD may be either the sole clinical manifestation or part of a syndrome, our findings further support a role for CCDC66 in retinal function and viability, potentially through its ciliary function.
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Hitti-Malin RJ, Burmeister LM, Ricketts SL, Lewis TW, Pettitt L, Boursnell M, Schofield EC, Sargan D, Mellersh CS. A LINE-1 insertion situated in the promoter of IMPG2 is associated with autosomal recessive progressive retinal atrophy in Lhasa Apso dogs. BMC Genet 2020; 21:100. [PMID: 32894063 PMCID: PMC7487703 DOI: 10.1186/s12863-020-00911-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 08/30/2020] [Indexed: 12/30/2022] Open
Abstract
Background Canine progressive retinal atrophies are a group of hereditary retinal degenerations in dogs characterised by depletion of photoreceptor cells in the retina, which ultimately leads to blindness. PRA in the Lhasa Apso (LA) dog has not previously been clinically characterised or described in the literature, but owners in the UK are advised to have their dog examined through the British Veterinary Association/ Kennel Club/ International Sheep Dog Society (BVA/KC/ISDS) eye scheme annually, and similar schemes that are in operation in other countries. After the exclusion of 25 previously reported canine retinal mutations in LA PRA-affected dogs, we sought to identify the genetic cause of PRA in this breed. Results Analysis of whole-exome sequencing data of three PRA-affected LA and three LA without signs of PRA did not identify any exonic or splice site variants, suggesting the causal variant was non-exonic. We subsequently undertook a genome-wide association study (GWAS), which identified a 1.3 Mb disease-associated region on canine chromosome 33, followed by whole-genome sequencing analysis that revealed a long interspersed element-1 (LINE-1) insertion upstream of the IMPG2 gene. IMPG2 has previously been implicated in human retinal disease; however, until now no canine PRAs have been associated with this gene. The identification of this PRA-associated variant has enabled the development of a DNA test for this form of PRA in the breed, here termed PRA4 to distinguish it from other forms of PRA described in other breeds. This test has been used to determine the genotypes of over 900 LA dogs. A large cohort of genotyped dogs was used to estimate the allele frequency as between 0.07–0.1 in the UK LA population. Conclusions Through the use of GWAS and subsequent sequencing of a PRA case, we have identified a LINE-1 insertion in the retinal candidate gene IMPG2 that is associated with a form of PRA in the LA dog. Validation of this variant in 447 dogs of 123 breeds determined it was private to LA dogs. We envisage that, over time, the developed DNA test will offer breeders the opportunity to avoid producing dogs affected with this form of PRA.
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Affiliation(s)
- Rebekkah J Hitti-Malin
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK. .,Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.
| | - Louise M Burmeister
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - Sally L Ricketts
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - Thomas W Lewis
- The Kennel Club, London, W1J 8AB, UK.,School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Louise Pettitt
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - Mike Boursnell
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - Ellen C Schofield
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - David Sargan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Cathryn S Mellersh
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
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Winkler PA, Occelli LM, Petersen-Jones SM. Large Animal Models of Inherited Retinal Degenerations: A Review. Cells 2020; 9:cells9040882. [PMID: 32260251 PMCID: PMC7226744 DOI: 10.3390/cells9040882] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
Studies utilizing large animal models of inherited retinal degeneration (IRD) have proven important in not only the development of translational therapeutic approaches, but also in improving our understanding of disease mechanisms. The dog is the predominant species utilized because spontaneous IRD is common in the canine pet population. Cats are also a source of spontaneous IRDs. Other large animal models with spontaneous IRDs include sheep, horses and non-human primates (NHP). The pig has also proven valuable due to the ease in which transgenic animals can be generated and work is ongoing to produce engineered models of other large animal species including NHP. These large animal models offer important advantages over the widely used laboratory rodent models. The globe size and dimensions more closely parallel those of humans and, most importantly, they have a retinal region of high cone density and denser photoreceptor packing for high acuity vision. Laboratory rodents lack such a retinal region and, as macular disease is a critical cause for vision loss in humans, having a comparable retinal region in model species is particularly important. This review will discuss several large animal models which have been used to study disease mechanisms relevant for the equivalent human IRD.
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A putative silencer variant in a spontaneous canine model of retinitis pigmentosa. PLoS Genet 2020; 16:e1008659. [PMID: 32150541 PMCID: PMC7082071 DOI: 10.1371/journal.pgen.1008659] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 03/19/2020] [Accepted: 02/06/2020] [Indexed: 01/19/2023] Open
Abstract
Retinitis pigmentosa (RP) is the leading cause of blindness with nearly two million people affected worldwide. Many genes have been implicated in RP, yet in 30–80% of the RP patients the genetic cause remains unknown. A similar phenotype, progressive retinal atrophy (PRA), affects many dog breeds including the Miniature Schnauzer. We performed clinical, genetic and functional experiments to identify the genetic cause of PRA in the breed. The age of onset and pattern of disease progression suggested that at least two forms of PRA, types 1 and 2 respectively, affect the breed, which was confirmed by genome-wide association study that implicated two distinct genomic loci in chromosomes 15 and X, respectively. Whole-genome sequencing revealed a fully segregating recessive regulatory variant in type 1 PRA. The associated variant has a very recent origin based on haplotype analysis and lies within a regulatory site with the predicted binding site of HAND1::TCF3 transcription factor complex. Luciferase assays suggested that mutated regulatory sequence increases expression. Case-control retinal expression comparison of six best HAND1::TCF3 target genes were analyzed with quantitative reverse-transcriptase PCR assay and indicated overexpression of EDN2 and COL9A2 in the affected retina. Defects in both EDN2 and COL9A2 have been previously associated with retinal degeneration. In summary, our study describes two genetically different forms of PRA and identifies a fully penetrant variant in type 1 form with a possible regulatory effect. This would be among the first reports of a regulatory variant in retinal degeneration in any species, and establishes a new spontaneous dog model to improve our understanding of retinal biology and gene regulation while the affected breed will benefit from a reliable genetic testing. Retinitis pigmentosa (RP) is a blinding eye disease that affects nearly two million people worldwide. Several genes and variants have been associated with the disease, but still 30–80% of the patients lack genetic diagnosis. There is currently no standard treatment for RP, and much is expected from gene therapy. A similar disease, called progressive retinal atrophy (PRA), affects many dog breeds. We performed clinical, genetic and functional analyses to find the genetic cause for PRA in Miniature Schnauzers. We discovered two forms of PRA in the breed, named type 1 and 2, and show that they are genetically distinct as they map to different chromosomes, 15 and X, respectively. Further genetic, bioinformatic and functional analyses discovered a fully penetrant recessive variant in a putative silencer region for type 1 PRA. Silencer regions are important for gene regulation and we found that two of its predicted target genes, EDN2 and COL9A2, were overexpressed in the retina of the affected dog. Defects in both EDN2 and COL9A2 have been associated with retinal degeneration. This study provides new insights to retinal biology while the genetic test guides better breeding choices.
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8
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A SIX6 Nonsense Variant in Golden Retrievers with Congenital Eye Malformations. Genes (Basel) 2019; 10:genes10060454. [PMID: 31207931 PMCID: PMC6628151 DOI: 10.3390/genes10060454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/04/2019] [Accepted: 06/11/2019] [Indexed: 12/22/2022] Open
Abstract
Causative genetic variants for more than 30 heritable eye disorders in dogs have been reported. For other clinically described eye disorders, the genetic cause is still unclear. We investigated four Golden Retriever litters segregating for highly variable congenital eye malformations. Several affected puppies had unilateral or bilateral retina dysplasia and/or optic nerve hypoplasia. The four litters shared the same father or grandfather suggesting a heritable condition with an autosomal dominant mode of inheritance. The genome of one affected dog was sequenced and compared to 601 control genomes. A heterozygous private nonsense variant, c.487C>T, was found in the SIX6 gene. This variant is predicted to truncate about a third of the open reading frame, p.(Gln163*). We genotyped all available family members and 464 unrelated Golden Retrievers. All three available cases were heterozygous. Five additional close relatives including the common sire were also heterozygous, but did not show any obvious eye phenotypes. The variant was absent from the 464 unrelated Golden Retrievers and 17 non-affected siblings of the cases. The SIX6 protein is a homeobox transcription factor with a known role in eye development. In humans and other species, SIX6 loss of function variants were reported to cause congenital eye malformations. This strongly suggests that the c.487C>T variant detected contributed to the observed eye malformations. We hypothesize that the residual amount of functional SIX6 protein likely to be expressed in heterozygous dogs is sufficient to explain the observed incomplete penetrance and the varying severity of the eye defects in the affected dogs.
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Hitti RJ, Oliver JAC, Schofield EC, Bauer A, Kaukonen M, Forman OP, Leeb T, Lohi H, Burmeister LM, Sargan D, Mellersh CS. Whole Genome Sequencing of Giant Schnauzer Dogs with Progressive Retinal Atrophy Establishes NECAP1 as a Novel Candidate Gene for Retinal Degeneration. Genes (Basel) 2019; 10:genes10050385. [PMID: 31117272 PMCID: PMC6562617 DOI: 10.3390/genes10050385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/08/2019] [Accepted: 05/17/2019] [Indexed: 12/30/2022] Open
Abstract
Canine progressive retinal atrophies (PRA) are genetically heterogeneous diseases characterized by retinal degeneration and subsequent blindness. PRAs are untreatable and affect multiple dog breeds, significantly impacting welfare. Three out of seven Giant Schnauzer (GS) littermates presented with PRA around four years of age. We sought to identify the causal variant to improve our understanding of the aetiology of this form of PRA and to enable development of a DNA test. Whole genome sequencing of two PRA-affected full-siblings and both unaffected parents was performed. Variants were filtered based on those segregating appropriately for an autosomal recessive disorder and predicted to be deleterious. Successive filtering against 568 canine genomes identified a single nucleotide variant in the gene encoding NECAP endocytosis associated 1 (NECAP1): c.544G>A (p.Gly182Arg). Five thousand one hundred and thirty canids of 175 breeds, 10 cross-breeds and 3 wolves were genotyped for c.544G>A. Only the three PRA-affected GS were homozygous (allele frequency in GS, excluding proband family = 0.015). In addition, we identified heterozygotes belonging to Spitz and Dachshund varieties, demonstrating c.544G>A segregates in other breeds of German origin. This study, in parallel with the known retinal expression and role of NECAP1 in clathrin mediated endocytosis (CME) in synapses, presents NECAP1 as a novel candidate gene for retinal degeneration in dogs and other species.
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Affiliation(s)
- Rebekkah J Hitti
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk CB8 7UU, UK.
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK.
| | - James A C Oliver
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk CB8 7UU, UK.
| | - Ellen C Schofield
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk CB8 7UU, UK.
| | - Anina Bauer
- Institute of Genetics, University of Bern, 3001 Bern, Switzerland.
| | - Maria Kaukonen
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland.
- Department of Medical Genetics, University of Helsinki, 00014 Helsinki, Finland.
- Folkhälsan Research Center, 00290 Helsinki, Finland.
| | - Oliver P Forman
- Wisdom Health, Waltham-on-the-Wolds, Leicestershire LE14 4RS, UK.
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001 Bern, Switzerland.
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland.
- Department of Medical Genetics, University of Helsinki, 00014 Helsinki, Finland.
- Folkhälsan Research Center, 00290 Helsinki, Finland.
| | - Louise M Burmeister
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk CB8 7UU, UK.
| | - David Sargan
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK.
| | - Cathryn S Mellersh
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk CB8 7UU, UK.
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Giannuzzi D, Marconato L, Elgendy R, Ferraresso S, Scarselli E, Fariselli P, Nicosia A, Pegolo S, Leoni G, Laganga P, Leone VF, Giantin M, Troise F, Dacasto M, Aresu L. Longitudinal transcriptomic and genetic landscape of radiotherapy response in canine melanoma. Vet Comp Oncol 2019; 17:308-316. [PMID: 30805995 DOI: 10.1111/vco.12473] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 02/20/2019] [Accepted: 02/25/2019] [Indexed: 12/22/2022]
Abstract
Canine malignant melanoma (MM) is a highly aggressive tumour with a low survival rate and represents an ideal spontaneous model for the human counterpart. Considerable progress has been recently obtained, but the therapeutic success for canine melanoma is still challenging. Little is known about the mechanisms beyond pathogenesis and melanoma development, and the molecular response to radiotherapy has never been explored before. A faster and deeper understanding of cancer mutational processes and developing mechanisms are now possible through next generation sequencing technologies. In this study, we matched whole exome and transcriptome sequencing in four dogs affected by MM at diagnosis and at disease progression to identify possible genetic mechanisms associated with therapy failure. According to previous studies, a genetic similarity between canine MM and its human counterpart was observed. Several somatic mutations were functionally related to MAPK, PI3K/AKT and p53 signalling pathways, but located in genes other than BRAF, RAS and KIT. At disease progression, several mutations were related to therapy effects. Natural killer cell-mediated cytotoxicity and several immune-system-related pathways resulted activated opening a new scenario on the microenvironment in this tumour. In conclusion, this study suggests a potential role of the immune system associated to radiotherapy in canine melanoma, but a larger sample size associated with functional studies are needed.
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Affiliation(s)
- Diana Giannuzzi
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Laura Marconato
- Centro Oncologico Veterinario, Sasso Marconi, Bologna, Italy
| | - Ramy Elgendy
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | | | - Piero Fariselli
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Alfredo Nicosia
- Nouscom AG, Basel, Switzerland.,Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy.,CEINGE-Biotecnologie Avanzate s.c. a.r.l., Naples, Italy
| | - Sara Pegolo
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padua, Legnaro, Padua, Italy
| | | | - Paola Laganga
- Centro Oncologico Veterinario, Sasso Marconi, Bologna, Italy
| | - Vito F Leone
- Centro Oncologico Veterinario, Sasso Marconi, Bologna, Italy
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | | | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Padua, Italy
| | - Luca Aresu
- Department of Veterinary Science, University of Turin, Grugliasco, Turin, Italy
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Complex Structural PPT1 Variant Associated with Non-syndromic Canine Retinal Degeneration. G3-GENES GENOMES GENETICS 2019; 9:425-437. [PMID: 30541930 PMCID: PMC6385984 DOI: 10.1534/g3.118.200859] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Rod and cone photoreceptors are specialized retinal neurons that have a fundamental role in visual perception, capturing light and transducing it into a neuronal signal. Aberrant functioning of rod and/or cone photoreceptors can ultimately lead to progressive degeneration and eventually blindness. In man, many rod and rod-cone degenerative diseases are classified as forms of retinitis pigmentosa (RP). Dogs also have a comparable disease grouping termed progressive retinal atrophy (PRA). These diseases are generally due to single gene defects and follow Mendelian inheritance.We collected 51 DNA samples from Miniature Schnauzers affected by PRA (average age of diagnosis ∼3.9 ±1 years), as well as from 56 clinically normal controls of the same breed (average age ∼6.6 ±2.8 years). Pedigree analysis suggested monogenic autosomal recessive inheritance of PRA. GWAS and homozygosity mapping defined a critical interval in the first 4,796,806 bp of CFA15. Whole genome sequencing of two affected cases, a carrier and a control identified two candidate variants within the critical interval. One was an intronic SNV in HIVEP3, and the other was a complex structural variant consisting of the duplication of exon 5 of the PPT1 gene along with a conversion and insertion (named PPT1dci). PPT1dci was confirmed homozygous in a cohort of 22 cases, and 12 more cases were homozygous for the CFA15 haplotype. Additionally, the variant was found homozygous in 6 non-affected dogs of age higher than the average age of onset. The HIVEP3 variant was found heterozygous (n = 4) and homozygous wild-type (n = 1) in cases either homozygous for PPT1dci or for the mapped CFA15 haplotype. We detected the wildtype and three aberrant PPT1 transcripts in isolated white blood cell mRNA extracted from a PRA case homozygous for PPT1dci, and the aberrant transcripts involved inclusion of the duplicated exon 5 and novel exons following the activation of cryptic splice sites. No neurological signs were detected among the dogs homozygous for the PPT1dci variant. Therefore, we propose PPT1dci as causative for a non-syndromic form of PRA (PRAPPT1) that shows incomplete penetrance in Miniature Schnauzers, potentially related to the presence of the wild-type transcript. To our knowledge, this is the first case of isolated retinal degeneration associated with a PPT1 variant.
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Martinez-Fernandez De La Camara C, Nanda A, Salvetti AP, Fischer MD, MacLaren RE. Gene therapy for the treatment of X-linked retinitis pigmentosa. Expert Opin Orphan Drugs 2018; 6:167-177. [PMID: 30057863 PMCID: PMC6059358 DOI: 10.1080/21678707.2018.1444476] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
INTRODUCTION X-linked retinitis pigmentosa caused by mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene is the most common form of recessive RP. The phenotype is characterised by its severity and rapid disease progression. Gene therapy using adeno-associated viral vectors is currently the most promising therapeutic approach. However, the construction of a stable vector encoding the full-length RPGR transcript has previously proven to be a limiting step towards gene therapy clinical trials. Recently however, a codon optimised version of RPGR has been shown to increase the stability and fidelity of the sequence, conferring a therapeutic effect in murine and canine animal models. AREAS COVERED This manuscript reviews the natural history of X-linked retinitis pigmentosa and the research performed from the discovery of the causative gene, RPGR, to the preclinical testing of potential therapies that have led to the initiation of three clinical trials. EXPERT OPINION X-linked retinitis pigmentosa is an amenable disease to be treated by gene therapy. Codon optimisation has overcome the challenge of designing an RPGR vector without mutations, and with a therapeutic effect in different animal models. With the RPGR gene therapy clinical trials still in the early stages, the confirmation of the safety, tolerability and potency of the therapy is still ongoing.
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Affiliation(s)
| | - Anika Nanda
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
| | - Anna Paola Salvetti
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Oxford, UK
- Department of Biomedical and Clinical Sciences “Luigi Sacco”, Sacco Hospital, University of Milan, Milano, Italy
| | - M. Dominik Fischer
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Oxford, UK
- Centre for Ophthalmology Tübingen, University Eye Hospital, Tübingen, Germany
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
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Cox ML, Evans JM, Davis AG, Guo LT, Levy JR, Starr-Moss AN, Salmela E, Hytönen MK, Lohi H, Campbell KP, Clark LA, Shelton GD. Exome sequencing reveals independent SGCD deletions causing limb girdle muscular dystrophy in Boston terriers. Skelet Muscle 2017; 7:15. [PMID: 28697784 PMCID: PMC5506588 DOI: 10.1186/s13395-017-0131-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/23/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Limb-girdle muscular dystrophies (LGMDs) are a heterogeneous group of inherited autosomal myopathies that preferentially affect voluntary muscles of the shoulders and hips. LGMD has been clinically described in several breeds of dogs, but the responsible mutations are unknown. The clinical presentation in dogs is characterized by marked muscle weakness and atrophy in the shoulder and hips during puppyhood. METHODS Following clinical evaluation, the identification of the dystrophic histological phenotype on muscle histology, and demonstration of the absence of sarcoglycan-sarcospan complex by immunostaining, whole exome sequencing was performed on five Boston terriers: one affected dog and its three family members and one unrelated affected dog. RESULTS Within sarcoglycan-δ (SGCD), a two base pair deletion segregating with LGMD in the family was discovered, and a deletion encompassing exons 7 and 8 was found in the unrelated dog. Both mutations are predicted to cause an absence of SGCD protein, confirmed by immunohistochemistry. The mutations are private to each family. CONCLUSIONS Here, we describe the first cases of canine LGMD characterized at the molecular level with the classification of LGMD2F.
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Affiliation(s)
- Melissa L. Cox
- CAG GmbH - Center for Animal Genetics, Paul-Ehrlich-Str. 23, 72076 Tubingen, Germany
| | - Jacquelyn M. Evans
- Department of Genetics and Biochemistry, Clemson University, 130 McGinty Ct., Clemson, SC 29634 USA
| | - Alexander G. Davis
- Department of Genetics and Biochemistry, Clemson University, 130 McGinty Ct., Clemson, SC 29634 USA
| | - Ling T. Guo
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Jennifer R. Levy
- Howard Hughes Medical Institute, Department of Molecular Physiology and Biophysics, Department of Neurology, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, 4283 Carver Biomedical Research Building, 285 Newton Road, Iowa City, Iowa 52242-1101 USA
- Department of Neurology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, 4283 Carver Biomedical Research Building, 285 Newton Road, Iowa City, Iowa 52242 USA
| | - Alison N. Starr-Moss
- Department of Genetics and Biochemistry, Clemson University, 130 McGinty Ct., Clemson, SC 29634 USA
| | - Elina Salmela
- Department of Veterinary Biosciences and Research Programs Unit, University of Helsinki, Haartmaninkatu 8, FI-00290 Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Marjo K. Hytönen
- Department of Veterinary Biosciences and Research Programs Unit, University of Helsinki, Haartmaninkatu 8, FI-00290 Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Hannes Lohi
- Department of Veterinary Biosciences and Research Programs Unit, University of Helsinki, Haartmaninkatu 8, FI-00290 Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Kevin P. Campbell
- Howard Hughes Medical Institute, Department of Molecular Physiology and Biophysics, Department of Neurology, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, 4283 Carver Biomedical Research Building, 285 Newton Road, Iowa City, Iowa 52242-1101 USA
- Department of Neurology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, 4283 Carver Biomedical Research Building, 285 Newton Road, Iowa City, Iowa 52242 USA
| | - Leigh Anne Clark
- Department of Genetics and Biochemistry, Clemson University, 130 McGinty Ct., Clemson, SC 29634 USA
| | - G. Diane Shelton
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
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Tsuboi M, Watanabe M, Nibe K, Yoshimi N, Kato A, Sakaguchi M, Yamato O, Tanaka M, Kuwamura M, Kushida K, Ishikura T, Harada T, Chambers JK, Sugano S, Uchida K, Nakayama H. Identification of the PLA2G6 c.1579G>A Missense Mutation in Papillon Dog Neuroaxonal Dystrophy Using Whole Exome Sequencing Analysis. PLoS One 2017; 12:e0169002. [PMID: 28107443 PMCID: PMC5249094 DOI: 10.1371/journal.pone.0169002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 12/09/2016] [Indexed: 12/29/2022] Open
Abstract
Whole exome sequencing (WES) has become a common tool for identifying genetic causes of human inherited disorders, and it has also recently been applied to canine genome research. We conducted WES analysis of neuroaxonal dystrophy (NAD), a neurodegenerative disease that sporadically occurs worldwide in Papillon dogs. The disease is considered an autosomal recessive monogenic disease, which is histopathologically characterized by severe axonal swelling, known as “spheroids,” throughout the nervous system. By sequencing all eleven DNA samples from one NAD-affected Papillon dog and her parents, two unrelated NAD-affected Papillon dogs, and six unaffected control Papillon dogs, we identified 10 candidate mutations. Among them, three candidates were determined to be “deleterious” by in silico pathogenesis evaluation. By subsequent massive screening by TaqMan genotyping analysis, only the PLA2G6 c.1579G>A mutation had an association with the presence or absence of the disease, suggesting that it may be a causal mutation of canine NAD. As a human homologue of this gene is a causative gene for infantile neuroaxonal dystrophy, this canine phenotype may serve as a good animal model for human disease. The results of this study also indicate that WES analysis is a powerful tool for exploring canine hereditary diseases, especially in rare monogenic hereditary diseases.
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Affiliation(s)
- Masaya Tsuboi
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Manabu Watanabe
- Laboratory of Functional Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazumi Nibe
- Japan Animal Referral Medical Center, Kanagawa, Japan
| | | | | | - Masahiro Sakaguchi
- Laboratory of Veterinary Microbiology I, School of Veterinary Medicine, Azabu University, Kanagawa, Japan
| | - Osamu Yamato
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Miyuu Tanaka
- Laboratory of Veterinary Pathology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Mitsuru Kuwamura
- Laboratory of Veterinary Pathology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Kazuya Kushida
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Takashi Ishikura
- Thermo Fisher Scientific, Life Technologies Japan Ltd., Tokyo, Japan
| | - Tomoyuki Harada
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - James Kenn Chambers
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Sumio Sugano
- Laboratory of Functional Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazuyuki Uchida
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
| | - Hiroyuki Nakayama
- Laboratory of Veterinary Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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