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Zhou Z, Sheng X, Zhang Z, Zhao K, Zhu L, Guo G, Friedenberg SG, Hunter LS, Vandenberg-Foels WS, Hornbuckle WE, Krotscheck U, Corey E, Moise NS, Dykes NL, Li J, Xu S, Du L, Wang Y, Sandler J, Acland GM, Lust G, Todhunter RJ. Differential genetic regulation of canine hip dysplasia and osteoarthritis. PLoS One 2010; 5:e13219. [PMID: 20949002 PMCID: PMC2952589 DOI: 10.1371/journal.pone.0013219] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 09/12/2010] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Canine hip dysplasia (HD) is a common polygenic trait characterized by hip malformation that results in osteoarthritis (OA). The condition in dogs is very similar to developmental dysplasia of the human hip which also leads to OA. METHODOLOGY/PRINCIPAL FINDINGS A total of 721 dogs, including both an association and linkage population, were genotyped. The association population included 8 pure breeds (Labrador retriever, Greyhounds, German Shepherd, Newfoundland, Golden retriever, Rottweiler, Border Collie and Bernese Mountain Dog). The linkage population included Labrador retrievers, Greyhounds, and their crosses. Of these, 366 dogs were genotyped at ∼22,000 single nucleotide polymorphism (SNP) loci and a targeted screen across 8 chromosomes with ∼3,300 SNPs was performed on 551 dogs (196 dogs were common to both sets). A mixed linear model approach was used to perform an association study on this combined association and linkage population. The study identified 4 susceptibility SNPs associated with HD and 2 SNPs associated with hip OA. CONCLUSION/SIGNIFICANCE The identified SNPs included those near known genes (PTPRD, PARD3B, and COL15A1) reported to be associated with, or expressed in, OA in humans. This suggested that the canine model could provide a unique opportunity to identify genes underlying natural HD and hip OA, which are common and debilitating conditions in both dogs and humans.
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Affiliation(s)
- Zhengkui Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Xihui Sheng
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- Department of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Zhiwu Zhang
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
| | - Keyan Zhao
- Department of Computational Biology and Statistics, Cornell University, Ithaca, New York, United States of America
| | - Lan Zhu
- Department of Statistics, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Gang Guo
- Department of Animal Science, China Agricultural University, Beijing, China
| | - Steve G. Friedenberg
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Linda S. Hunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Wendy S. Vandenberg-Foels
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - William E. Hornbuckle
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Ursula Krotscheck
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Elizabeth Corey
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Nancy S. Moise
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Nathan L. Dykes
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shangzhong Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixin Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yachun Wang
- Department of Animal Science, China Agricultural University, Beijing, China
| | - Jody Sandler
- Guiding Eyes for the Blind, Yorktown Heights, New York, United States of America
| | - Gregory M. Acland
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, United States of America
| | - George Lust
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, United States of America
| | - Rory J. Todhunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
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154
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Bento-Abreu A, Van Damme P, Van Den Bosch L, Robberecht W. The neurobiology of amyotrophic lateral sclerosis. Eur J Neurosci 2010; 31:2247-65. [PMID: 20529130 DOI: 10.1111/j.1460-9568.2010.07260.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Amyotrophic lateral sclerosis is a degenerative disease affecting the motor neurons. In spite of our growing insights into its biology, it remains a lethal condition. The identification of the cause of several of the familial forms of ALS allowed generation of models to study this disease both in vitro and in vivo. Here, we summarize what is known about the pathogenic mechanisms of ALS induced by hereditary mutations, and attempt to identify the relevance of these findings for understanding the pathogenic mechanisms of the sporadic form of this disease.
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Affiliation(s)
- André Bento-Abreu
- Laboratory for Neurobiology, Experimental Neurology, K.U.Leuven, Herestraat, 3000 Leuven, Belgium.
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155
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Yokoyama JS, Erdman CA, Hamilton SP. Array-based whole-genome survey of dog saliva DNA yields high quality SNP data. PLoS One 2010; 5:e10809. [PMID: 20520842 PMCID: PMC2876042 DOI: 10.1371/journal.pone.0010809] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 03/14/2010] [Indexed: 12/21/2022] Open
Abstract
Background Genome-wide association scans for genetic loci underlying both Mendelian and complex traits are increasingly common in canine genetics research. However, the demand for high-quality DNA for use on such platforms creates challenges for traditional blood sample ascertainment. Though the use of saliva as a means of collecting DNA is common in human studies, alternate means of DNA collection for canine research have instead been limited to buccal swabs, from which dog DNA is of insufficient quality and yield for use on most high-throughput array-based systems. We thus investigated an animal-based saliva collection method for ease of use and quality of DNA obtained and tested the performance of saliva-extracted canine DNA on genome-wide genotyping arrays. Methodology/Principal Findings Overall, we found that saliva sample collection using this method was efficient. Extractions yielded high concentrations (∼125 ng/ul) of high-quality DNA that performed equally well as blood-extracted DNA on the Illumina Infinium canine genotyping platform, with average call rates >99%. Concordance rates between genotype calls of saliva- versus blood-extracted DNA samples from the same individual were also >99%. Additionally, in silico calling of copy number variants was successfully performed and verified by PCR. Conclusions/Significance Our findings validate the use of saliva-obtained samples for genome-wide association studies in canines, highlighting an alternative means of collecting samples in a convenient and non-invasive manner.
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Affiliation(s)
- Jennifer S Yokoyama
- Department of Psychiatry and Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
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156
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Bannasch D, Young A, Myers J, Truvé K, Dickinson P, Gregg J, Davis R, Bongcam-Rudloff E, Webster MT, Lindblad-Toh K, Pedersen N. Localization of canine brachycephaly using an across breed mapping approach. PLoS One 2010; 5:e9632. [PMID: 20224736 PMCID: PMC2835769 DOI: 10.1371/journal.pone.0009632] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 02/19/2010] [Indexed: 12/23/2022] Open
Abstract
The domestic dog, Canis familiaris, exhibits profound phenotypic diversity and is an ideal model organism for the genetic dissection of simple and complex traits. However, some of the most interesting phenotypes are fixed in particular breeds and are therefore less tractable to genetic analysis using classical segregation-based mapping approaches. We implemented an across breed mapping approach using a moderately dense SNP array, a low number of animals and breeds carefully selected for the phenotypes of interest to identify genetic variants responsible for breed-defining characteristics. Using a modest number of affected (10–30) and control (20–60) samples from multiple breeds, the correct chromosomal assignment was identified in a proof of concept experiment using three previously defined loci; hyperuricosuria, white spotting and chondrodysplasia. Genome-wide association was performed in a similar manner for one of the most striking morphological traits in dogs: brachycephalic head type. Although candidate gene approaches based on comparable phenotypes in mice and humans have been utilized for this trait, the causative gene has remained elusive using this method. Samples from nine affected breeds and thirteen control breeds identified strong genome-wide associations for brachycephalic head type on Cfa 1. Two independent datasets identified the same genomic region. Levels of relative heterozygosity in the associated region indicate that it has been subjected to a selective sweep, consistent with it being a breed defining morphological characteristic. Genotyping additional dogs in the region confirmed the association. To date, the genetic structure of dog breeds has primarily been exploited for genome wide association for segregating traits. These results demonstrate that non-segregating traits under strong selection are equally tractable to genetic analysis using small sample numbers.
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Affiliation(s)
- Danika Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America.
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157
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Shearin AL, Ostrander EA. Leading the way: canine models of genomics and disease. Dis Model Mech 2010; 3:27-34. [PMID: 20075379 DOI: 10.1242/dmm.004358] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In recent years Canis familiaris, the domestic dog, has drawn considerable attention as a system in which to investigate the genetics of disease susceptibility, morphology and behavior. Because dogs show remarkable intrabreed homogeneity, coupled with striking interbreed heterogeneity, the dog offers unique opportunities to understand the genetic underpinnings of natural variation in mammals, a portion of which is disease susceptibility. In this review, we highlight the unique features of the dog, such as population diversity and breed structure, that make it particularly amenable to genetic studies. We highlight recent advances in understanding the architecture of the dog genome, which propel the system to the forefront of consideration when selecting a system for disease gene studies. The most notable benefit of using the dog for genetic studies is that dogs get many of the same diseases as humans, with a similar frequency, and the same genetic factors are often involved. We discuss two approaches for localizing disease genes in the dog and provide examples of ongoing studies.
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Affiliation(s)
- Abigail L Shearin
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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158
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Liu X, Zhang X, Zhang Z. Cu,Zn-superoxide dismutase is required for cell wall structure and for tolerance to cell wall-perturbing agents in Saccharomyces cerevisiae. FEBS Lett 2010; 584:1245-50. [PMID: 20176017 DOI: 10.1016/j.febslet.2010.02.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 02/12/2010] [Accepted: 02/17/2010] [Indexed: 02/05/2023]
Abstract
Here we report that deletion of SOD1, the Cu,Zn-superoxide dismutase in Saccharomyces cerevisiae is sensitive to cell wall-perturbing agents, such as Calcofluor white and Congo red. The sensitivity was restored by retransformation with wild type SOD1 or the addition of N-acetylcysteine or reduced glutathione to the medium. Additionally, the accumulation of reactive oxygen species was observed in sod1Delta mutant in the presence of Calcofluor white or Congo red. Cell wall analysis indicated an increase of cell wall chitin and cell wall thickness in sod1Delta mutant compared to wild type. These results indicate a novel direct connection between antioxidative functions and cell wall homeostasis.
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Affiliation(s)
- Xiangyong Liu
- Department of Cell Biology, Binzhou Medical University, Yantai, China.
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161
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Trumbull KA, Beckman JS. A role for copper in the toxicity of zinc-deficient superoxide dismutase to motor neurons in amyotrophic lateral sclerosis. Antioxid Redox Signal 2009; 11:1627-39. [PMID: 19309264 PMCID: PMC2842582 DOI: 10.1089/ars.2009.2574] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Accepted: 03/22/2009] [Indexed: 10/21/2022]
Abstract
In the 16 years since mutations to copper, zinc superoxide dismutase (SOD1) were first linked to familial amyotrophic lateral sclerosis (ALS), a multitude of apparently contradictory results have prevented any general consensus to emerge about the mechanism of toxicity. A decade ago, we showed that the loss of zinc from SOD1 results in the remaining copper in SOD1 to become extremely toxic to motor neurons in culture by a mechanism requiring nitric oxide. The loss of zinc causes SOD1 to become more accessible, more redox reactive, and a better catalyst of tyrosine nitration. Although SOD1 mutant proteins have a modestly reduced affinity for zinc, wild-type SOD1 can be induced to lose zinc by dialysis at slightly acidic pH. Our zinc-deficient hypothesis offers a compelling explanation for how mutant SOD1s have an increased propensity to become selectively toxic to motor neurons and also explains how wild-type SOD1 can be toxic in nonfamilial ALS patients. One critical prediction is that a therapeutic agent directed at zinc-deficient mutant SOD1 could be even more effective in treating sporadic ALS patients. Although transgenic mice experiments have yielded contradictory evidence to the zinc-deficient hypothesis, we will review more recent studies that support a role for copper in ALS. A more careful examination of the role of copper and zinc binding to SOD1 may help counter the growing disillusion in the ALS field about understanding the pathological role of SOD1.
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Affiliation(s)
- Kari A. Trumbull
- Linus Pauling Institute, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon
| | - Joseph S. Beckman
- Linus Pauling Institute, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon
- Environmental Health Science Center, Oregon State University, Corvallis, Oregon
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163
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Prudencio M, Hart PJ, Borchelt DR, Andersen PM. Variation in aggregation propensities among ALS-associated variants of SOD1: correlation to human disease. Hum Mol Genet 2009; 18:3217-26. [PMID: 19483195 PMCID: PMC2722984 DOI: 10.1093/hmg/ddp260] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
To date, 146 different mutations in superoxide dismutase 1 (SOD1) have been identified in patients with familial amyotrophic lateral sclerosis (ALS). The mean age of disease onset in patients inheriting mutations in SOD1 is 45-47 years of age. However, although the length of disease duration is highly variable, there are examples of consistent disease durations associated with specific mutations (e. g. A4V, less than 2 years). In the present study, we have used a large set of data from SOD1-associated ALS pedigrees to identify correlations between disease features and biochemical/biophysical properties of more than 30 different variants of mutant SOD1. Using a reliable cell culture assay, we show that all ALS-associated mutations in SOD1 increase the inherent aggregation propensity of the protein. However, the relative propensity to do so varied considerably among mutants. We were not able to explain the variation in aggregation rates by differences in known protein properties such as enzyme activity, protein thermostability, mutation position or degree of change in protein charge. Similarly, we were not able to explain variability in the duration of disease in SOD1-associated ALS pedigrees by these properties. However, we find that the majority of pedigrees in which patients exhibit reproducibly short disease durations are associated with mutations that show a high inherent propensity to induce aggregation of SOD1.
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Affiliation(s)
- Mercedes Prudencio
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
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