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Hopper RG, Bromberg RB, Salzman MM, Peterson KD, Rogers C, Cameron S, Mowat FM. Dual sensory impairments in companion dogs: Prevalence and relationship to cognitive impairment. PLoS One 2024; 19:e0310299. [PMID: 39413072 PMCID: PMC11482676 DOI: 10.1371/journal.pone.0310299] [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: 05/07/2024] [Accepted: 08/29/2024] [Indexed: 10/18/2024] Open
Abstract
PURPOSE Many older dogs (Canis lupus familiaris) develop cognitive impairment. Dog owners often describe impairments in multiple sensory functions, yet the relationships between sensory and cognitive function in older dogs is not well understood. METHODS We performed assessments of dog vision and hearing, both clinically (n = 91, electroretinography and brainstem auditory evoked potential) and via validated questionnaire (n = 238). We determined prevalence of sole and dual hearing/vision impairments in younger (<8 years) and older (≥8 years) dogs. Impairment cutoffs were determined using data from young dogs. We assessed the relationships between questionnaire-assessed vision and/or hearing impairments and cognitive impairment using logistic regression. RESULTS Younger and older dog groups had similar distributions of sex and purebred/mixed breed status. Sex had no relationship to prevalence of sensory impairments. Older dogs had higher prevalence of hearing, vision, and dual sensory impairments, assessed both clinically and by questionnaire (P<0.001), and cognitive impairment assessed by questionnaire (P<0.001). Dogs had higher prevalence of reported cognitive impairment when owners reported dual vision and hearing impairments (79-94%, versus 25-27% in dogs with no sensory impairments), which was most consistent in dogs aged ≥8 years. In these older dogs, dual vision/hearing impairments were associated with a significantly increased risk of cognitive impairment (1.8-2.0 odds ratio). CONCLUSION Dogs aged ≥8 years are at higher risk for dual hearing/vision impairments and associated cognitive impairments. The causal relationship between these impairments is not defined, but clinical consideration of these multimorbidity risks should be made in older dogs.
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Affiliation(s)
- Ryan G. Hopper
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Rachel B. Bromberg
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michele M. Salzman
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kyle D. Peterson
- Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Callie Rogers
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Starr Cameron
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Freya M. Mowat
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Salzman MM, Takimoto T, Foster ML, Mowat FM. Differential gene expression between central and peripheral retinal regions in dogs and comparison with humans. Exp Eye Res 2024; 245:109980. [PMID: 38914302 PMCID: PMC11250724 DOI: 10.1016/j.exer.2024.109980] [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: 02/12/2024] [Revised: 06/09/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024]
Abstract
The dog retina contains a central macula-like region, and there are reports of central retinal disorders in dogs with shared genetic etiologies with humans. Defining central/peripheral gene expression profiles may provide insight into the suitability of dogs as models for human disorders. We determined central/peripheral posterior eye gene expression profiles in dogs and interrogated inherited retinal and macular disease-associated genes for differential expression between central and peripheral regions. Bulk tissue RNA sequencing was performed on 8 mm samples of the dog central and superior peripheral regions, sampling retina and retinal pigmented epithelium/choroid separately. Reads were mapped to CanFam3.1, read counts were analyzed to determine significantly differentially expressed genes (DEGs). A similar analytic pipeline was used with a published bulk-tissue RNA sequencing human dataset. Pathways and processes involved in significantly DEGs were identified (Database for Annotation, Visualization and Integrated Discovery). Dogs and humans shared the extent and direction of central retinal differential gene expression, with multiple shared biological pathways implicated in differential expression. Many genes implicated in heritable retinal disorders in dogs and humans were differentially expressed between central and periphery. Approximately half of genes associated with human age-related macular degeneration were differentially expressed in human and dog tissues. We have identified similarities and differences in central/peripheral gene expression profiles between dogs and humans which can be applied to further define the relevance of dogs as models for human retinal disorders.
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Affiliation(s)
- Michele M Salzman
- Dept. Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, USA
| | - Tetsuya Takimoto
- Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, USA; Division of Gene Regulation, Division of Data Science, Research Promotion Headquarters, Fujita Health University, Toyoake, Japan
| | - Melanie L Foster
- Dept. Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Freya M Mowat
- Dept. Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, USA; Dept. Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA; Dept. Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
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3
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Simon KE, Russell K, Mondino A, Yang CC, Case BC, Anderson Z, Whitley C, Griffith E, Gruen ME, Olby NJ. A randomized, controlled clinical trial demonstrates improved owner-assessed cognitive function in senior dogs receiving a senolytic and NAD+ precursor combination. Sci Rep 2024; 14:12399. [PMID: 38811634 PMCID: PMC11137034 DOI: 10.1038/s41598-024-63031-w] [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: 02/17/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024] Open
Abstract
Age-related decline in mobility and cognition are associated with cellular senescence and NAD + depletion in dogs and people. A combination of a novel NAD + precursor and senolytic, LY-D6/2, was examined in this randomized controlled trial. Seventy dogs with mild to moderate cognitive impairment were enrolled and allocated into placebo, low or full dose groups. Primary outcomes were change in cognitive impairment measured with the owner-reported Canine Cognitive Dysfunction Rating (CCDR) scale and change in activity measured with physical activity monitors. Fifty-nine dogs completed evaluations at the 3-month primary endpoint, and 51 reached the 6-month secondary endpoint. There was a significant difference in CCDR score across treatment groups from baseline to the primary endpoint (p = 0.02) with the largest decrease in the full dose group. No difference was detected between groups using in house cognitive testing. There were no significant differences between groups in changes in measured activity. The proportion of dogs that improved in frailty and owner-reported activity levels and happiness was higher in the full dose group than other groups, however this difference was not significant. Adverse events occurred equally across groups. All groups showed improvement in cognition, frailty, and activity suggesting placebo effect and benefits of trial participation. We conclude that LY-D6/2 improves owner-assessed cognitive function over a 3-month period and may have broader, but more subtle effects on frailty, activity and happiness as reported by owners.
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Affiliation(s)
- Katherine E Simon
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Katharine Russell
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
- Southeast Veterinary Neurology, Miami, FL, USA
| | - Alejandra Mondino
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Chin-Chieh Yang
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Beth C Case
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Zachary Anderson
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Christine Whitley
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Emily Griffith
- Department of Statistics, College of Sciences, North Carolina State University, Raleigh, NC, USA
| | - Margaret E Gruen
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Natasha J Olby
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.
- Comparative Medicine Institute, NC State University, Raleigh, NC, USA.
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4
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Wallis LJ, Radford AD, Belshaw Z, Jackson J, Kubinyi E, German AJ, Westgarth C. Cross-sectional United Kingdom surveys demonstrate that owners and veterinary professionals differ in their perceptions of preventive and treatment healthcare needs in ageing dogs. Front Vet Sci 2024; 11:1358480. [PMID: 38638642 PMCID: PMC11024473 DOI: 10.3389/fvets.2024.1358480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/12/2024] [Indexed: 04/20/2024] Open
Abstract
Perceptions of dog owners and veterinary professionals (surgeons/nurses) can influence the preventive healthcare and treatment provided to dogs, especially at the senior life-stage, when chronic diseases become more common. This study compared perceptions of healthcare of dogs as they age between dog owners and veterinary professionals. Data from two online surveys (owners: N = 633, veterinary professionals: N = 305) examined perceived need for veterinary visits and vaccinations. In addition, 48 clinical signs were rated on perceived prevalence (whether owners' dogs had experienced them) and how urgently they should seek veterinary advice. Groups were compared using descriptive statistics and chi-square. Owners most often believed a 'healthy' senior dog (>7 years) should go to the vet once a year (47% owners vs. 25% veterinary professionals, p < 0.001), compared with veterinary professionals every 6 months (39 vs. 73%). A minority (14%) of owners would just take the dog 'if they got sick' but only 2% of veterinary professionals advised this, and 16% of owners of dogs of all ages had not had any contact with their veterinary practise in the previous year. Nearly all veterinary professionals (92%) believed that senior/geriatric dogs should receive yearly vaccinations. However, 28% of owners' dogs of all ages were not vaccinated in the previous year and, of these, 33% did not believe that older dogs need vaccinations. Only 10% of dogs considered 'old' by their owners had attended a senior wellness clinic or examination, despite 14% of practises offering them. The three most common clinical signs reported by owners were slowing down on walks (57%), dental tartar (53%) and being stiff on rising (50%). Owners perceived urgency to seek veterinary care was lower if they had experienced the clinical sign before. In the current study, dog owners and veterinary professionals differed in their opinions about the need for veterinary care, suggesting new educational initiatives, and more effective communication is required.
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Affiliation(s)
- Lisa J. Wallis
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Ethology, ELTE Eotvos Lorand University, Budapest, Hungary
| | - Alan D. Radford
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Zoe Belshaw
- EviVet Research Consultancy, Nottingham, United Kingdom
| | - Jodie Jackson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Eniko Kubinyi
- Department of Ethology, ELTE Eotvos Lorand University, Budapest, Hungary
- MTA-ELTE Lendület “Momentum” Companion Animal Research Group, ELTE Eotvos Lorand University, Budapest, Hungary
| | - Alexander J. German
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Carri Westgarth
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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Smith JG, Krichbaum S, Montgomery L, Cox E, Katz JS. A preliminary analysis of the effect of individual differences on cognitive performance in young companion dogs. Anim Cogn 2024; 27:30. [PMID: 38557907 PMCID: PMC10984887 DOI: 10.1007/s10071-024-01868-4] [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: 05/19/2023] [Revised: 03/04/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
Many factors influence cognitive performance in dogs, including breed, temperament, rearing history, and training. Studies in working dog populations have demonstrated age-related improvements in cognitive task performance across the first years of development. However, the effect of certain factors, such as age, sex, and temperament, on cognitive performance in puppies has yet to be evaluated in a more diverse population of companion dogs. In this study, companion dogs under 12 months of age were tested once on two tasks purported to measure aspects of executive function: the delayed-search task (DST) and the detour reversal task (DRT). Owners also filled out the Canine Behavioral Assessment and Research Questionnaire (C-BARQ) to evaluate how temperament influenced task performance. Contrary to prior research, performance did not improve with age on either task. However, the lack of age effects was likely the result of small sample sizes and individual differences across other factors influencing performance. Specifically, temperament differences as measured by the C-BARQ subscales for nonsocial fear and excitability predicted task performance on the DST, but the effect of temperament on task performance differed between males and females. Excitability also predicted performance on the DRT, but the effect depended on the age of the dog. In addition, no correlations were observed between task measures, indicating a lack of construct validity. Overall, these findings provide a preliminary analysis of factors that appear to influence cognitive task performance in young companion dogs and highlight suggestions for future research evaluating the impact of individual differences on cognitive performance.
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Affiliation(s)
- Jordan G Smith
- Department of Psychological Sciences, Auburn University, Auburn, AL, USA.
- Canine Performance Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, USA.
- Auburn University, 104 Greene Hall, Auburn, AL, 36849, USA.
| | - Sarah Krichbaum
- Canine Performance Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Lane Montgomery
- Department of Psychological Sciences, Auburn University, Auburn, AL, USA
| | - Emma Cox
- Department of Psychological Sciences, Auburn University, Auburn, AL, USA
| | - Jeffrey S Katz
- Department of Psychological Sciences, Auburn University, Auburn, AL, USA
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6
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Li R, Hui Y, Zhang X, Zhang S, Lv B, Ni Y, Li X, Liang X, Yang L, Lv H, Yin Z, Li H, Yang Y, Liu G, Li J, Xie G, Wu S, Wang Z. Ocular biomarkers of cognitive decline based on deep-learning retinal vessel segmentation. BMC Geriatr 2024; 24:28. [PMID: 38184539 PMCID: PMC10770952 DOI: 10.1186/s12877-023-04593-8] [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: 01/25/2023] [Accepted: 12/13/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND The current literature shows a strong relationship between retinal neuronal and vascular alterations in dementia. The purpose of the study was to use NFN+ deep learning models to analyze retinal vessel characteristics for cognitive impairment (CI) recognition. METHODS We included 908 participants from a community-based cohort followed for over 15 years (the prospective KaiLuan Study) who underwent brain magnetic resonance imaging (MRI) and fundus photography between 2021 and 2022. The cohort consisted of both cognitively healthy individuals (N = 417) and those with cognitive impairment (N = 491). We employed the NFN+ deep learning framework for retinal vessel segmentation and measurement. Associations between Retinal microvascular parameters (RMPs: central retinal arteriolar / venular equivalents, arteriole to venular ratio, fractal dimension) and CI were assessed by Pearson correlation. P < 0.05 was considered statistically significant. The correlation between the CI and RMPs were explored, then the correlation coefficients between CI and RMPs were analyzed. Random Forest nonlinear classification model was used to predict whether one having cognitive decline or not. The assessment criterion was the AUC value derived from the working characteristic curve. RESULTS The fractal dimension (FD) and global vein width were significantly correlated with the CI (P < 0.05). Age (0.193), BMI (0.154), global vein width (0.106), retinal vessel FD (0.099), and CRAE (0.098) were the variables in this model that were ranked in order of feature importance. The AUC values of the model were 0.799. CONCLUSIONS Establishment of a predictive model based on the extraction of vascular features from fundus images has a high recognizability and predictive power for cognitive function and can be used as a screening method for CI.
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Affiliation(s)
- Rui Li
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Ying Hui
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | | | - Shun Zhang
- Department of Psychiatry, Kailuan Mental Health Centre, Hebei province, Tangshan, China
| | - Bin Lv
- Ping An Healthcare Technology, Beijing, China
| | - Yuan Ni
- Ping An Healthcare Technology, Beijing, China
| | - Xiaoshuai Li
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Xiaoliang Liang
- Department of Psychiatry, Kailuan Mental Health Centre, Hebei province, Tangshan, China
| | - Ling Yang
- School of Public Health, North China University of Science and Technology, Hebei province, Tangshan, China
| | - Han Lv
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zhiyu Yin
- Longzhen Senior Care, Beijing, China
| | - Hongyang Li
- Department of Ophthalmology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yingping Yang
- Ministry of Education Key Laboratory of Environment and Health, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guangfeng Liu
- Department of Ophthalmology, Peking University International Hospital, Beijing, China
| | - Jing Li
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing, China.
| | - Guotong Xie
- Ping An Healthcare Technology, Beijing, China.
| | - Shouling Wu
- Department of Cardiology, Kailuan General Hospital, 57 Xinhua E Rd, Tangshan, China.
| | - Zhenchang Wang
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing, China.
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Provoost L. Cognitive Changes Associated with Aging and Physical Disease in Dogs and Cats. Vet Clin North Am Small Anim Pract 2024; 54:101-119. [PMID: 37722947 DOI: 10.1016/j.cvsm.2023.08.002] [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] [Indexed: 09/20/2023]
Abstract
Behavior changes may indicate primary physical disease or primary behavioral disorders in veterinary patients. It is imperative to recognize that secondary behavioral problems can develop due to medical causes. The incidence of systemic disease increases with age and behavior manifestations can be similar to those expected with cognitive dysfunction syndrome. In this article, we review basic concepts of cognition, aging, and cognitive dysfunction syndrome. Additionally, we provide information regarding factors that influence cognition, and the role medical conditions have on the behavior of aging pets.
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Affiliation(s)
- Lena Provoost
- Clinical Sciences & Advanced Medicine, University of Pennsylvania, 3900 Delancey Street, Philadelphia, PA 19104, USA.
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Francis JM, Mowat FM, Ludwig A, Hicks JM, Pumphrey SA. Quantifying refractive error in companion dogs with and without nuclear sclerosis: 229 eyes from 118 dogs. Vet Ophthalmol 2024; 27:70-78. [PMID: 37986551 PMCID: PMC10842750 DOI: 10.1111/vop.13163] [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: 03/29/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023]
Abstract
OBJECTIVE To evaluate the relationship between nuclear sclerosis (NS) and refractive error in companion dogs. ANIMALS STUDIED One hundred and eighteen companion dogs. PROCEDURES Dogs were examined and found to be free of significant ocular abnormalities aside from NS. NS was graded from 0 (absent) to 3 (severe) using a scale developed by the investigators. Manual refraction was performed. The effect of NS grade on refractive error was measured using a linear mixed effects analysis adjusted for age. The proportion of eyes with >1.5 D myopia in each NS grade was evaluated using a chi-square test. Visual impairment score (VIS) was obtained for a subset of dogs and compared against age, refractive error, and NS grade. RESULTS Age was strongly correlated with NS grade (p < .0001). Age-adjusted analysis of NS grade relative to refraction showed a mild but not statistically significant increase in myopia with increasing NS grade, with eyes with grade 3 NS averaging 0.58-0.88 D greater myopia than eyes without NS. However, the myopia of >1.5 D was documented in 4/58 (6.9%) eyes with grade 0 NS, 12/91 (13.2%) eyes with grade 1 NS, 13/57 (22.8%) eyes with grade 2 NS, and 7/23 (30.4%) eyes with grade 3 NS. Risk of myopia >1.5 D was significantly associated with increasing NS grade (p = .02). VIS was associated weakly with refractive error, moderately with age, and significantly with NS grade. CONCLUSIONS NS is associated with visual deficits in some dogs but is only weakly associated with myopia. More work is needed to characterize vision in aging dogs.
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Affiliation(s)
- Jenelle M Francis
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, USA
| | - Freya M Mowat
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Allison Ludwig
- Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jacqueline M Hicks
- Department of Biostatistics, School of Public Health, Boston University, Boston, Massachusetts, USA
- Dr. Francis's current address is Animal Eye Clinic, Matthews, North Carolina, USA
| | - Stephanie A Pumphrey
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, USA
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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: 28] [Impact Index Per Article: 14.0] [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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Morrill K, Chen F, Karlsson E. Comparative neurogenetics of dog behavior complements efforts towards human neuropsychiatric genetics. Hum Genet 2023; 142:1231-1246. [PMID: 37578529 DOI: 10.1007/s00439-023-02580-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/02/2023] [Indexed: 08/15/2023]
Abstract
Domestic dogs display a wide array of heritable behaviors that have intermediate genetic complexity thanks to a long history of human-influenced selection. Comparative genetics in dogs could address the scarcity of non-human neurogenetic systems relevant to human neuropsychiatric disorders, which are characterized by mental, emotional, and behavioral symptoms and involve vastly complex genetic and non-genetic risk factors. Our review describes the diverse behavioral "phenome" of domestic dogs, past and ongoing sources of behavioral selection, and the state of canine behavioral genetics. We highlight two naturally disordered behavioral domains that illustrate how dogs may prove useful as a comparative, forward neurogenetic system: canine age-related cognitive dysfunction, which can be examined more rapidly given the attenuated lifespan of dogs, and compulsive disorders, which may have genetic roots in purpose-bred behaviors. Growing community science initiatives aimed at the companion dog population will be well suited to investigating such complex behavioral phenotypes and offer a comparative resource that parallels human genomic initiatives in scale and dimensionality.
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Affiliation(s)
- Kathleen Morrill
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Morningside Graduate School of Biomedical Sciences UMass Chan Medical School, Worcester, MA, USA.
| | - Frances Chen
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elinor Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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11
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Bray EE, Raichlen DA, Forsyth KK, Promislow DEL, Alexander GE, MacLean EL. Associations between physical activity and cognitive dysfunction in older companion dogs: results from the Dog Aging Project. GeroScience 2023; 45:645-661. [PMID: 36129565 PMCID: PMC9886770 DOI: 10.1007/s11357-022-00655-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 09/02/2022] [Indexed: 02/03/2023] Open
Abstract
Canine cognitive dysfunction (CCD) is a form of dementia that shares many similarities with Alzheimer's disease. Given that physical activity is believed to reduce risk of Alzheimer's disease in humans, we explored the association between physical activity and cognitive health in a cohort of companion dogs, aged 6-18 years. We hypothesized that higher levels of physical activity would be associated with lower (i.e., better) scores on a cognitive dysfunction rating instrument and lower prevalence of dementia, and that this association would be robust when controlling for age, comorbidities, and other potential confounders. Our sample included 11,574 companion dogs enrolled through the Dog Aging Project, of whom 287 had scores over the clinical threshold for CCD. In this observational, cross-sectional study, we used owner-reported questionnaire data to quantify dog cognitive health (via a validated scale), physical activity levels, health conditions, training history, and dietary supplements. We fit regression models with measures of cognitive health as the outcome, and physical activity-with several important covariates-as predictors. We found a significant negative relationship between physical activity and current severity of cognitive dysfunction symptoms (estimate = - 0.10, 95% CI: - 0.11 to - 0.08, p < 0.001), extent of symptom worsening over a 6-month interval (estimate = - 0.07, 95% CI: - 0.09 to - 0.05, p < 0.001), and whether a dog reached a clinical level of CCD (odds ratio = 0.53, 95% CI: 0.45 to 0.63, p < 0.001). Physical activity was robustly associated with better cognitive outcomes in dogs. Our findings illustrate the value of companion dogs as a model for investigating relationships between physical activity and cognitive aging, including aspects of dementia that may have translational potential for Alzheimer's disease. While the current study represents an important first step in identifying a relationship between physical activity and cognitive function, it cannot determine causality. Future studies are needed to rule out reverse causation by following the same dogs prospectively over time, and to evaluate causality by administering physical activity interventions.
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Affiliation(s)
- Emily E Bray
- Arizona Canine Cognition Center, School of Anthropology, University of Arizona, Tucson, AZ, USA.
- Canine Companions for Independence, National Headquarters, Santa Rosa, CA, USA.
| | - David A Raichlen
- Human and Evolutionary Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Kiersten K Forsyth
- College of Veterinary Medicine & Biomedical Sciences, M University, Texas A &, College Station, TX, USA
| | - Daniel E L Promislow
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Gene E Alexander
- Department of Psychology, University of Arizona, Tucson, AZ, USA
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA
- Arizona Alzheimer's Consortium, Phoenix, AZ, USA
- Department of Psychiatry, University of Arizona, Tucson, AZ, USA
- Neuroscience Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, USA
- Physiological Sciences Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, USA
| | - Evan L MacLean
- Arizona Canine Cognition Center, School of Anthropology, University of Arizona, Tucson, AZ, USA
- Department of Psychology, University of Arizona, Tucson, AZ, USA
- Cognitive Science Program, University of Arizona, Tucson, AZ, USA
- College of Veterinary Medicine, University of Arizona, Tucson, AZ, USA
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