Canine NAPEPLD-associated models of human myelin disorders.

Canine leukoencephalomyelopathy (LEMP) is a juvenile-onset neurodegenerative disorder of the CNS white matter currently described in Rottweiler and Leonberger dogs. Genome-wide association study (GWAS) allowed us to map LEMP in a Leonberger cohort to dog chromosome 18. Subsequent whole genome re-sequencing of a Leonberger case enabled the identification of a single private homozygous non-synonymous missense variant located in the highly conserved metallo-beta-lactamase domain of the N-acyl phosphatidylethanolamine phospholipase D (NAPEPLD) gene, encoding an enzyme of the endocannabinoid system. We then sequenced this gene in LEMP-affected Rottweilers and identified a different frameshift variant, which is predicted to replace the C-terminal metallo-beta-lactamase domain of the wild type protein. Haplotype analysis of SNP array genotypes revealed that the frameshift variant was present in diverse haplotypes in Rottweilers, and also in Great Danes, indicating an old origin of this second NAPEPLD variant. The identification of different NAPEPLD variants in dog breeds affected by leukoencephalopathies with heterogeneous pathological features, implicates the NAPEPLD enzyme as important in myelin homeostasis, and suggests a novel candidate gene for myelination disorders in people.

Ten inherited disorders in purebred dogs by functional breed groupings.

BACKGROUND: Analysis of 88,635 dogs seen at the University of California, Davis Veterinary Medical Teaching Hospital from 1995 to 2010 identified ten inherited conditions having greater prevalence within the purebred dog population as compared to the mixed-breed dog population: aortic stenosis, atopy/allergic dermatitis, gastric dilatation volvulus (GDV), early onset cataracts, dilated cardiomyopathy, elbow dysplasia, epilepsy, hypothyroidism, intervertebral disk disease (IVDD), and hepatic portosystemic shunt. The objective of the present study was to ascertain if disorders with higher prevalence in purebreds were restricted to particular breed group classifications within the purebred population, specifically the American Kennel Club breed grouping or groups with genomic similarities based upon allele sharing. For each disorder, healthy controls seen at the hospital during that same time period were matched for age, weight, and sex to each affected dog to determine risk of disease presentation in the purebred group as compared to that of the mixed-breed population. To enhance reliability of the analyses, sampling of matched healthy to affected dogs was repeated 50 times. For each comparison, the purebred subgroups to mixed-breed odds ratio was determined as was the mean P value used to test this ratio. RESULTS: For aortic stenosis, GDV, early onset cataracts, dilated cardiomyopathy, elbow dysplasia, epilepsy, and portosystemic shunt, most purebred groups were not statistically distinct from the mixed-breed population with higher prevalence in purebreds restricted to distinct subsets of purebred dogs. The conditions of atopy/allergic dermatitis, hypothyroidism, and IVDD were more pervasive across the purebred population with many groups having higher prevalence than the mixed-breed population. The prevalence of IVDD in purebred terrier groups was statistically lower than that observed for mixed-breed dogs. CONCLUSIONS: The results offer an assessment of the distribution of inherited disorders within purebred dogs and illustrate how mixed-breed and subpopulations of purebred dogs do not differ statistically in prevalence for certain disorders. Some disorders appear linked to common ancestors providing insight into disease allele origin whereas others may be due to selection for common structural morphology. Knowledge of the origin of a condition may aid in reducing its prevalence in the dog population as a whole.

Blood and Cerebrospinal Fluid α-Tocopherol and Selenium Concentrations in Neonatal Foals with Neuroaxonal Dystrophy.

BACKGROUND: Equine neuroaxonal dystrophy/equine degenerative myeloencephalopathy (NAD/EDM) is a neurodegenerative disorder affecting genetically predisposed foals maintained on α-tocopherol (α-TP)-deficient diet. OBJECTIVE: Intramuscular α-TP and selenium (Se) administration at 4 days of age would have no significant effect on serum or cerebrospinal fluid (CSF) α-TP in healthy foals. Serum and CSF α-TP, but not Se, would be significantly decreased in NAD/EDM-affected foals during first year of life. ANIMALS: Fourteen Quarter horse foals; 10 healthy foals supplemented with 0.02 mL/kg injectable α-TP and Se (n = 5) or saline (n = 5) at 4 days of age and 4 unsupplemented NAD/EDM-affected foals. METHODS: Complete neurologic examinations were performed, blood and CSF were collected before (4 days of age) and after supplementation at 10, 30, 60, 120, 180, 240, and 360 days of age. Additional blood collections occurred at 90, 150, 210, and 300 days. At 540 days, NAD/EDM-affected foals and 1 unsupplemented healthy foal were euthanized and necropsies performed. RESULTS: Significant decreases in blood, CSF α-TP and Se found in the first year of life in all foals, with most significant changes in serum α-TP from 4-150 days. Dam α-TP and Se significantly influenced blood concentrations in foals. Injection of α-TP and Se did not significantly increase CSF Se, blood or CSF α-TP in healthy foals. NAD/EDM-affected foals had significantly lower CSF α-TP through 120 days. CONCLUSIONS AND CLINICAL IMPORTANCE: Injection of α-TP and Se at 4 days of age does not significantly increase blood or CSF α-TP. Despite all 14 foals remaining deficient in α-TP, only the 4 genetically predisposed foals developed NAD/EDM.

Applied equine genetics.

Genome sequencing of the domestic horse and subsequent advancements in the field of equine genomics have led to an explosion in the development of tools for mapping traits and diseases and evaluating gene expression. The objective of this review is to discuss the current progress in the field of equine genomics, with specific emphasis on assembly and analysis of the reference sequence and subsequent sequencing of a Quarter Horse mare; the genomic tools currently available to researchers and their implications in genomic investigations in the horse; the genomics of Mendelian and non-Mendelian traits; the genomics of performance traits and considerations regarding genetic testing in the horse. The whole-genome sequencing of a Quarter Horse mare has provided additional variants within the equine genome that extend past single nucleotide polymorphisms to include insertions/deletions and copy number variants. Equine single nucleotide polymorphism arrays have allowed for the investigation of both simple and complex genetic traits while DNA microarrays have provided a tool for examining gene expression across various tissues and with certain disease conditions. Recently, next-generation sequencing has become more affordable and both whole-genome DNA sequencing and transcriptome-wide RNA sequencing are methodologies that are being applied to equine genomic research. Research in the field of equine genomics continues to expand rapidly as the cost of genotyping and sequencing decreases, resulting in a need for quality bioinformatics software and expertise to appropriately handle both the size and complexity of these data.

Pedigree analysis and exclusion of alpha-tocopherol transfer protein (TTPA) as a candidate gene for neuroaxonal dystrophy in the American Quarter Horse.

BACKGROUND: Equine neuroaxonal dystrophy/equine degenerative myeloencephalopathy (NAD/EDM) is a neurodegenerative disorder affecting young horses of various breeds that resembles ataxia with vitamin E deficiency in humans, an inherited disorder caused by mutations in the alpha-tocopherol transfer protein gene (TTPA). To evaluate variants found upon sequencing TTPA in the horse, the mode of inheritance for NAD/EDM had to be established. HYPOTHESIS: NAD/EDM in the American Quarter Horse (QH) is caused by a mutation in TTPA. ANIMALS: 88 clinically phenotyped (35 affected [ataxia score ≥2], 53 unaffected) QHs with a diagnosis of NAD/EDM with 6 affected and 4 unaffected cases confirmed at postmortem examination. PROCEDURES: Pedigrees and genotypes across 54,000 single nucleotide polymorphism (SNP) markers were assessed to determine heritability and mode of inheritance of NAD/EDM. TTPA sequence of exon/intron boundaries was evaluated in 2 affected and 2 control horses. An association analysis was performed by 71 SNPs surrounding TTPA and 8 SNPs within TTPA that were discovered by sequencing. RT-PCR for TTPA was performed on mRNA from the liver of 4 affected and 4 control horses. RESULTS: Equine NAD/EDM appears to be inherited as a polygenic trait and, within this family of QHs, demonstrates high heritability. Sequencing of TTPA identified 12 variants. No significant association was found using the 79 available variants in and surrounding TTPA. RT-PCR yielded PCR products of equivalent sizes between affected cases and controls. CONCLUSIONS AND CLINICAL IMPORTANCE: NAD/EDM demonstrates heritability in this family of QHs. Variants in TTPA are not responsible for NAD/EDM in this study population.

Equine degenerative myeloencephalopathy in Lusitano horses.

BACKGROUND: Equine degenerative myeloencephalopathy (EDM) is a neurodegenerative disorder that has been previously associated with low vitamin E concentrations. OBJECTIVE: To describe the clinical, electrophysiologic, and pathologic features of EDM in a group of related Lusitano horses. ANIMALS: Fifteen Lusitano horses. PROCEDURES: Neurologic examinations were conducted, and serum vitamin E concentrations were measured. Three neurologically abnormal horses were further evaluated by ophthalmologic examination, electroretinography, electroencephalography, muscle and nerve biopsies, and post-mortem examination. RESULTS: Six horses appeared neurologically normal, 6 were neurologically abnormal, and 3 had equivocal gait abnormalities. Abnormal horses demonstrated ataxia and paresis. An inconsistent menace response was noted in 4 neurologically abnormal horses and in 1 horse with equivocal findings. All horses had low serum vitamin E concentrations (<1.5 ppm). Ophthalmologic examinations, electroretinograms, electroencephalograms, and muscle and peripheral nerve biopsies were unremarkable in 3 neurologically abnormal horses. At necropsy, major neuropathological findings in these horses were bilaterally symmetric, severe, neuro axonal degeneration in the gracilis, cuneatus medialis, cuneatus lateralis, and thoracicus nuclei and bilaterally symmetric axonal loss and demyelination mainly in the dorsolateral and ventromedial tracts of the spinal cord. A diagnosis of EDM was made based on these findings. Pedigree analysis identified 2 sires among the affected horses. CONCLUSIONS AND CLINICAL RELEVANCE: Equine degenerative myeloencephalopathy is a neurodegenerative disorder that causes ataxia and, in severe cases, paresis, in young Lusitano horses. The disease appears to have a genetic basis, and although vitamin E deficiency is a common finding, low serum vitamin E concentrations also may occur in apparently unaffected related individuals.

Expanded dog leukocyte antigen (DLA) single nucleotide polymorphism (SNP) genotyping reveals spurious class II associations.

The dog leukocyte antigen (DLA) system contains many of the functional genes of the immune system, thereby making it a candidate region for involvement in immune-mediated disorders. A number of studies have identified associations between specific DLA class II haplotypes and canine immune hemolytic anemia, thyroiditis, immune polyarthritis, type I diabetes mellitus, hypoadrenocorticism, systemic lupus erythematosus-related disease complex, necrotizing meningoencephalitis (NME) and anal furunculosis. These studies have relied on sequencing approximately 300 bases of exon 2 of each of the DLA class II genes: DLA-DRB1, DLA-DQA1 and DLA-DQB1. In the present study, an association (odds ratio=4.29) was identified by this method between Weimaraner dogs with hypertrophic osteodystrophy (HOD) and DLA-DRB1∗01501. To fine map the association with HOD, a genotyping assay of 126 coding single nucleotide polymorphisms (SNPs) from across the entire DLA, spanning a region of 2.5 Mb (3,320,000-5,830,000) on CFA12, was developed and tested on Weimaraners with HOD, as well as two additional breeds with diseases associated with DLA class II: Nova Scotia duck tolling retrievers with hypoadrenocorticism and Pug dogs with NME. No significant associations were found between Weimaraners with HOD or Nova Scotia duck tolling retrievers with hypoadrenocorticism and SNPs spanning the DLA region. In contrast, significant associations were found with NME in Pug dogs, although the associated region extended beyond the class II genes. By including a larger number of genes from a larger genomic region, a SNP genotyping assay was generated that provides coverage of the extended DLA region and may be useful in identifying and fine mapping DLA associations in dogs.

Estimated frequency of the canine hyperuricosuria mutation in different dog breeds.

BACKGROUND: Hyperuricosuria is a condition that predisposes dogs to urate urolithiasis. A mutation that causes canine hyperuricosuria was previously identified in 3 unrelated dog breeds. The occurrence of the mutation in additional breeds was not determined. HYPOTHESIS/OBJECTIVES: Identify additional breeds that have the hyperuricosuria mutation and estimate the mutant allele frequency in those breeds. ANIMALS: Three thousand five hundred and thirty dogs from 127 different breeds were screened for the hyperuricosuria mutation. METHODS: DNA samples were genotyped by pyrosequencing and allele-specific polymerase chain reaction methods. RESULTS: Mutant allele frequencies that range from 0.001 to 0.15 were identified in the American Staffordshire Terrier, Australian Shepherd, German Shepherd Dog, Giant Schnauzer, Parson (Jack) Russell Terrier, Labrador Retriever, Large Munsterlander, Pomeranian, South African Boerboel, and Weimaraner breeds. CONCLUSIONS AND CLINICAL IMPORTANCE: The hyperuricosuria mutation has been identified in several unrelated dog breeds. The mutant allele frequencies vary among breeds and can be used to determine an appropriate breeding plan for each breed. A DNA test is available and may be used by breeders to decrease the mutant allele frequency in breeds that carry the mutation. In addition, veterinarians may use the test as a diagnostic tool to identify the cause of urate urolithiasis.

Association of a dog leukocyte antigen class II haplotype with hypoadrenocorticism in Nova Scotia Duck Tolling Retrievers.

Canine hypoadrenocorticism (Addison's disease) is due to a deficiency of corticosteroids and mineralocorticoids produced by the adrenals. Although this is a relatively uncommon disease in the general dog population, some breeds, including the Nova Scotia Duck Tolling Retriever (NSDTR), are at increased risk for developing hypoadrenocorticism. A prior study has shown that the increased risk is due to a heritable component. This potentially lethal disorder is hypothesized to have an autoimmune etiology, thus the aim of this study was to determine whether genetic susceptibility to hypoadrenocorticism in NSDTRs is associated with genes of the canine major histocompatibility complex [MHC; dog leukocyte antigen system (DLA)]. Samples were collected from NSDTRs diagnosed with hypoadrenocorticism and healthy siblings or country-matched controls. The DLA class II alleles and haplotypes were determined and compared between cases and controls. We found seven different haplotypes of which the haplotype DLA-DRB1*01502/DQA*00601/DQB1*02301 was significantly more prevalent in the diseased dogs (P = 0.044). In addition, these affected dogs also were more likely to be homozygous across the DLA class II region than the control dogs (OR = 6.7, CI = 1.5-29.3, P = 0.011). We also found that homozygous dogs, regardless of their haplotype, tended to have earlier disease onset compared with heterozygous dogs. These data indicate a limited MHC diversity in North American NSDTRs and suggest that the MHC may play a role in the development of hypoadrenocorticism in the NSDTR, supporting the autoimmune origin of the disease.

Characterization of variation in the canine suppressor of cytokine signaling-2 (SOCS2) gene.

Suppressor of cytokine signaling 2 (SOCS2) is a negative regulator of growth hormone signaling. The deletion of SOCS2 in mice results in a 30-50% increase in post-natal growth. In an effort to identify polymorphisms in the SOCS2 gene that may be associated with body size in dogs, we characterized the canine SOCS2 gene and analyzed its genetic diversity among small and large dog breeds. The study was carried out on a total of 520 dogs from 66 different breeds. Dogs were classified as large or small based on height and weight as determined by their respective American Kennel Club breed standards. The SH2 and SOCS domains of the canine SOCS2 gene were sequenced in 32 dogs from different breeds. Only one non-synonymous sequence variant (DQ415457:g.326G>T) was detected which corresponds to an amino acid change (Asp127Tyr). All samples were genotyped by PCR/RFLP and the allele frequencies were determined for each dog breed. The T allele was distributed primarily among European large dog breeds with a gene frequency ranging from 0.72 to 0.04. The nature of the nucleotide change and the effect on the protein together with the finding of a QTL related to body size in the same CFA15 region by other researchers suggest canine SOCS2 as a potential candidate gene for body size in dogs. Future studies will be needed to clarify the role of the 326G>T polymorphism and its interaction with genes like growth hormone and insulin-like growth factor 1.

Characterization of variation in the canine suppressor of cytokine signaling-2 (SOCS2) gene

Suppressor of cytokine signaling 2 (SOCS2) is a negative regulator of growth hormone signaling. The deletion of SOCS2 in mice results in a 30-50% increase in post-natal growth. In an effort to identify polymorphisms in the SOCS2 gene that may be associated with body size in dogs, we characterized the canine SOCS2 gene and analyzed its genetic diversity among small and large dog breeds. The study was carried out on a total of 520 dogs from 66 different breeds. Dogs were classified as large or small based on height and weight as determined by their respective American Kennel Club breed standards. The SH2 and SOCS domains of the canine SOCS2 gene were sequenced in 32 dogs from different breeds. Only one non-synonymous sequence variant (DQ415457:g.326G>T) was detected which corresponds to an amino acid change (Asp127Tyr). All samples were genotyped by PCR/RFLP and the allele frequencies were determined for each dog breed. The T allele was distributed primarily among European large dog breeds with a gene frequency ranging from 0.72 to 0.04. The nature of the nucleotide change and the effect on the protein together with the finding of a QTL related to body size in the same CFA15 region by other researchers suggest canine SOCS2 as a potential candidate gene for body size in dogs. Future studies will be needed to clarify the role of the 326G>T polymorphism and its interaction with genes like growth hormone and insulin-like growth factor 1

Development of a new canine osteosarcoma cell line.

Establishing a canine osteosarcoma (OSA) cell line can be useful to develop in vivo and in vitro models of OSA. The goal of this study was to develop, characterize and authenticate a new canine OSA cell line and a clone. A cell line and a clone were developed with standard cell culture techniques from a naturally occurring OSA in a dog. The clonal cell line induced a tumour after injection in RAG 1-deficient mouse. Histology was consistent with OSA. The original tumour from the dog and the tumour induced in the mouse were both reactive with vimentin and osteonectin (ON). The parent cell line and clonal cell line were reactive with ON, osteocalcin and alkaline phosphatase. Loss of heterozygosity was found in the same three microsatellite markers in the parent and clonal cell lines, and the tumour tissue grown in the mouse.

Evaluation of canine COL4A3 and COL4A4 as candidates for familial renal disease in the Norwegian elkhound.

The collagen type IV alpha3 and alpha4 chains (COL4A3 and COL4A4) are part of the specialized glomerular basement membrane in the kidney. In human these genes are responsible for Alport syndrome (a type of hereditary nephritis). Histopathological similarities between kidneys of Norwegian elkhound dogs affected with familial renal disease and human Alport syndrome were the basis for a candidate gene approach in Norwegian elkhounds. Three microsatellites-tightly linked to canine COL4A3 and COL4A4--were developed. The microsatellites were used to analyze linkage between COL4A3 and COL4A4 and familial renal disease in a Norwegian elkhound pedigree segregating this disease. Presence of one recombinant between familial renal disease and COL4A3/COL4A4 suggests that these genes are not likely candidates for familial renal disease in this breed.

Exclusion of urate oxidase as a candidate gene for hyperuricosuria in the Dalmatian dog using an interbreed backcross.

Hyperuricosuria, an autosomal recessive disorder, is characterized by high levels of uric acid in the urine of Dalmatian dogs. Whereas high levels of uric acid are known to be caused by the silencing of the urate oxidase (uox) gene in humans and higher primates, the molecular basis for the Dalmatian defect is unknown. Transplantation studies show that the organ responsible for the Dalmatian phenotype is the liver, which is where urate oxidase is exclusively expressed and uric acid is converted into allantoin. We cloned and sequenced the canine uox cDNA and compared the sequence between a Dalmatian and non-Dalmatian dog. No change in cDNA sequence was identified. A Dalmatian x pointer backcross family was used to track the segregation of microsatellite markers surrounding the urate oxidase locus. The uox gene was excluded for Dalmatian hyperuricosuria based on the cDNA sequence identity and negative LOD scores.

Inheritance of urinary calculi in the Dalmatian.

Dalmatians are unique among dogs in that they excrete uric acid in their urine as the end product of purine metabolism rather than allantoin as do other breeds of dogs. Urinary calculi form from urate (salts of uric acid) and can cause urethral obstruction in male Dalmatians. Although all Dalmatians have the primary defect, only a subset develops clinical disease. We postulated that calculi formation might have a genetic component that segregates within the breed, causing some animals to form calculi and others to never form calculi despite excreting uric acid in their urine. We used a survey to ascertain the urinary calculi status based on clinical signs of adult Dalmatians aged 6 years or older, and we used pedigrees from these same animals to estimate the heritability of the clinical manifestation of urate calculi within the breed to be .87 (.75-.96). The prevalence of the disease was 34% (24.99-43.70%) among male Dalmatians in our survey. The high heritability of the disease makes it possible for breeders to effectively select against the disease.

Exclusion of galectin 9 as a candidate gene for hyperuricosuria in the Dalmatian dog.

All Dalmatian dogs have an inherited defect in purine metabolism leading to high levels of uric acid excretion in their urine (hyperuricosuria) rather than allantoin, the normal end product of purine metabolism in all other breeds of dog. Transplantation experiments have demonstrated that the defect is intrinsic to the liver and not the kidney. Uricase, the enzyme involved in the breakdown of urate into allantoin, has been shown to function in Dalmatian liver cells. Therefore, candidate genes for this defect include transporters of urate, a salt of uric acid, across cell membranes. We excluded one such urate transporter candidate, galectin 9, using a Dalmatian x Pointer backcross in which hyperuricosuria was segregating.