1
|
Bayesian model and selection signature analyses reveal risk factors for canine atopic dermatitis. Commun Biol 2022; 5:1348. [PMID: 36482174 PMCID: PMC9731970 DOI: 10.1038/s42003-022-04279-8] [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: 07/13/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Canine atopic dermatitis is an inflammatory skin disease with clinical similarities to human atopic dermatitis. Several dog breeds are at increased risk for developing this disease but previous genetic associations are poorly defined. To identify additional genetic risk factors for canine atopic dermatitis, we here apply a Bayesian mixture model adapted for mapping complex traits and a cross-population extended haplotype test to search for disease-associated loci and selective sweeps in four dog breeds at risk for atopic dermatitis. We define 15 associated loci and eight candidate regions under selection by comparing cases with controls. One associated locus is syntenic to the major genetic risk locus (Filaggrin locus) in human atopic dermatitis. One selection signal in common type Labrador retriever cases positions across the TBC1D1 gene (body weight) and one signal of selection in working type German shepherd controls overlaps the LRP1B gene (brain), near the KYNU gene (psoriasis). In conclusion, we identify candidate genes, including genes belonging to the same biological pathways across multiple loci, with potential relevance to the pathogenesis of canine atopic dermatitis. The results show genetic similarities between dog and human atopic dermatitis, and future across-species genetic comparisons are hereby further motivated.
Collapse
|
2
|
Zamani P, Mohammadi H, Mirhoseini SZ. Genome-wide association study and genomic heritabilities for blood protein levels in Lori-Bakhtiari sheep. Sci Rep 2021; 11:23771. [PMID: 34887490 PMCID: PMC8660901 DOI: 10.1038/s41598-021-03290-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/01/2021] [Indexed: 01/01/2023] Open
Abstract
Serum protein levels are related to physiological and pathological status of animals and could be affected by both genetic and environmental factors. This study aimed to evaluate genetic variation of serum protein profile in sheep. Blood samples were randomly collected from 96 Lori-Bakhtiari ewes, a heavy meat-type breed. Total protein, albumin, globulin, α1, α2, β and γ globulins and IgG levels were measured in blood serum. The samples were genotyped using the Illumina OvineSNP50 BeadChip. The studied traits adjusted for age, birth type, birth season and estimate of breeding value for body weight were considered as pseudo-phenotypes in genome-wide association analysis. In the GWAS model, the first five principal components were fitted as covariates to correct the biases due to possible population stratification. The Plink, R and GCTA software were used for genome-wide association analysis, construction of Q-Q and Manhattan plots and estimation of genetic variances, respectively. Noticeable genomic heritabilities ± SE were estimated for total and γ globulins (0.868 ± 0.262 and 0.831 ± 0.364, respectively), but other protein fractions had zero or close to zero estimates. Based on the Bonferroni adjusted p values, four QTLs located on 181.7 Mbp of OAR3, 107.7 Mbp of OAR4, 86.3 Mbp of OAR7 and 83.0 Mbp of OAR8 were significantly associated with α1, β, β and γ globulins, respectively. The results showed that the PKP2, IGF2R, SLC22A1 and SLC22A2 genes could be considered as candidate genes for blood serum proteins. The present study showed significant genetic variations of some blood protein fractions.
Collapse
Affiliation(s)
- P Zamani
- Department of Animal Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - H Mohammadi
- Department of Animal Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - S Z Mirhoseini
- Department of Animal Science, Faculty of Agriculture, University of Guilan, Rasht, Iran
| |
Collapse
|
3
|
Nuttall TJ, Marsella R, Rosenbaum MR, Gonzales AJ, Fadok VA. Update on pathogenesis, diagnosis, and treatment of atopic dermatitis in dogs. J Am Vet Med Assoc 2020; 254:1291-1300. [PMID: 31067173 DOI: 10.2460/javma.254.11.1291] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Improved understanding of the pathogenesis of atopic dermatitis in dogs has led to more effective treatment plans, including skin barrier repair and new targeted treatments for management of allergy-associated itch and inflammation. The intent of this review article is to provide an update on the etiologic rationale behind current recommendations that emphasize a multimodal approach for the management of atopic dermatitis in dogs. Increasing knowledge of this complex disease process will help direct future treatment options.
Collapse
|
4
|
Tengvall K, Bergvall K, Olsson M, Ardesjö-Lundgren B, Farias FHG, Kierczak M, Hedhammar Å, Lindblad-Toh K, Andersson G. Transcriptomes from German shepherd dogs reveal differences in immune activity between atopic dermatitis affected and control skin. Immunogenetics 2020; 72:315-323. [PMID: 32556497 PMCID: PMC7320941 DOI: 10.1007/s00251-020-01169-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/28/2020] [Indexed: 11/30/2022]
Abstract
Canine atopic dermatitis (CAD) is an inflammatory and pruritic allergic skin disease with both genetic and environmental risk factors described. We performed mRNA sequencing of non-lesional axillary skin biopsies from nine German shepherd dogs. Obtained RNA sequences were mapped to the dog genome (CanFam3.1) and a high-quality skin transcriptome was generated with 23,510 expressed gene transcripts. Differentially expressed genes (DEGs) were defined by comparing three controls to five treated CAD cases. Using a leave-one-out analysis, we identified seven DEGs: five known to encode proteins with functions related to an activated immune system (CD209, CLEC4G, LOC102156842 (lipopolysaccharide-binding protein-like), LOC480601 (regakine-1-like), LOC479668 (haptoglobin-like)), one (OBP) encoding an odorant-binding protein potentially connected to rhinitis, and the last (LOC607095) encoding a novel long non-coding RNA. Furthermore, high mRNA expression of inflammatory genes was found in axillary skin from an untreated mild CAD case compared with healthy skin. In conclusion, we define genes with different expression patterns in CAD case skin helping us understand post-treatment atopic skin. Further studies in larger sample sets are warranted to confirm and to transfer these results into clinical practice.
Collapse
Affiliation(s)
- K Tengvall
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - K Bergvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - M Olsson
- Division of Rheumatology, Department Medicine, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
| | - B Ardesjö-Lundgren
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - F H G Farias
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - M Kierczak
- Department of Cell and Molecular Biology, Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Å Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - K Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - G Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
5
|
Identification of differentially expressed microRNAs in the skin of experimentally sensitized naturally affected atopic beagles by next-generation sequencing. Immunogenetics 2020; 72:241-250. [PMID: 32219493 DOI: 10.1007/s00251-020-01162-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
Canine atopic dermatitis (AD) is a very common inflammatory skin disease, but limited data are available on the genetic characterization (somatic mutations, microarrays, and genome-wide association study (GWAS)) of skin lesions in affected dogs. microRNAs are good biomarkers in inflammatory and neoplastic diseases in people. The aim of this study was to evaluate microRNA expression in the skin of atopic beagles, before and after exposure to Dermatophagoides farinae. Four atopic and four unrelated age-matched healthy beagle dogs were enrolled. Total RNA was extracted from flash-frozen skin biopsies of healthy and atopic dogs. For the atopic dogs, skin biopsies were taken from non-lesional (day 0) and lesional skin (day 28 of weekly environmental challenge with Dermatophagoides farinae). Small RNA libraries were constructed and sequenced. The microRNA sequences were aligned to CanFam3.1 genome. Differential expressed microRNAs were selected on the basis of fold-change and statistical significance (fold-change ≥ 1.5 and p ≤ 0.05 as thresholds. A total of 277 microRNAs were sequenced. One hundred and twenty-one differentially regulated microRNAs were identified between non-lesional and healthy skin. Among these, two were increased amount and 119 were decreased amount. A total of 45 differentially regulated microRNAs between lesional and healthy skin were identified, 44 were decreased amount and one was increased amount. Finally, only two increased amount microRNAs were present in lesional skin when compared with that of non-lesional skin. This is the first study in which dysregulation of microRNAs has been associated with lesional and non-lesional canine AD. Larger studies are needed to understand the role of microRNA in canine AD.
Collapse
|
6
|
Ardesjö-Lundgren B, Tengvall K, Bergvall K, Farias FHG, Wang L, Hedhammar Å, Lindblad-Toh K, Andersson G. Comparison of cellular location and expression of Plakophilin-2 in epidermal cells from nonlesional atopic skin and healthy skin in German shepherd dogs. Vet Dermatol 2017; 28:377-e88. [PMID: 28386956 PMCID: PMC5516137 DOI: 10.1111/vde.12441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2016] [Indexed: 12/25/2022]
Abstract
Background Canine atopic dermatitis (CAD) is an inflammatory and pruritic allergic skin disease caused by interactions between genetic and environmental factors. Previously, a genome‐wide significant risk locus on canine chromosome 27 for CAD was identified in German shepherd dogs (GSDs) and Plakophilin‐2 (PKP2) was defined as the top candidate gene. PKP2 constitutes a crucial component of desmosomes and also is important in signalling, metabolic and transcriptional activities. Objectives The main objective was to evaluate the role of PKP2 in CAD by investigating PKP2 expression and desmosome structure in nonlesional skin from CAD‐affected (carrying the top GWAS SNP risk allele) and healthy GSDs. We also aimed at defining the cell types in the skin that express PKP2 and its intracellular location. Animals/Methods Skin biopsies were collected from nine CAD‐affected and five control GSDs. The biopsies were frozen for immunofluorescence and fixed for electron microscopy immunolabelling and morphology. Results We observed the novel finding of PKP2 expression in dendritic cells and T cells in dog skin. Moreover, we detected that PKP2 was more evenly expressed within keratinocytes compared to its desmosomal binding‐partner plakoglobin. PKP2 protein was located in the nucleus and on keratin filaments attached to desmosomes. No difference in PKP2 abundance between CAD cases and controls was observed. Conclusion Plakophilin‐2 protein in dog skin is expressed in both epithelial and immune cells; based on its subcellular location its functional role is implicated in both nuclear and structural processes.
Collapse
Affiliation(s)
- Brita Ardesjö-Lundgren
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, Box 582, SE-75123, Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-75007, Uppsala, Sweden
| | - Katarina Tengvall
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, Box 582, SE-75123, Uppsala, Sweden.,Neuroimmunology Unit, Centrum for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Kerstin Bergvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, SE-75007, Uppsala, Sweden
| | - Fabiana H G Farias
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, Box 582, SE-75123, Uppsala, Sweden
| | - Liya Wang
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Box 7011, SE-75007, Uppsala, Sweden
| | - Åke Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, SE-75007, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, Box 582, SE-75123, Uppsala, Sweden.,Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-75007, Uppsala, Sweden
| |
Collapse
|