Two loci on chromosome 5 are associated with serum IgE levels in Labrador retrievers

Update on the role of genetic factors, environmental factors and allergens in canine atopic dermatitis

BACKGROUND

Canine atopic dermatitis (cAD) is a common, complex and multifactorial disease involving, among others, genetic predisposition, environmental factors and allergic sensitisation.

OBJECTIVE

This review summarises the current evidence on the role of genetic and environmental factors and allergic sensitisation in the pathogenesis of cAD since the last review by ICADA in 2015.

MATERIALS AND METHODS

Online citation databases and proceedings from international meetings on genetic factors, environmental factors and allergens relevant to cAD that had been published between 2015 and 2022 were reviewed.

RESULTS

Despite intensive research efforts, the detailed genetic background predisposing to cAD and the effect of a wide range of environmental factors still need more clarification. Genome-wide association studies and investigations on genetic biomarkers, such as microRNAs, have provided some new information. Environmental factors appear to play a major role. Lifestyle, especially during puppyhood, appears to have an important impact on the developing immune system. Factors such as growing up in a rural environment, large size of family, contact with other animals, and a nonprocessed meat-based diet may reduce the risk for subsequent development of cAD. It appears that Toxocara canis infection may have a protective effect against Dermatophagoides farinae-induced cAD. House dust mites (D. farinae and D. pteronyssinus) remain the most common allergen group to which atopic dogs react. Currently, the major allergens related to D. farinae in dogs include Der f 2, Der f 15, Der f 18 and Zen 1.

CONCLUSIONS AND CLINICAL RELEVANCE

Canine atopic dermatitis remains a complex, genetically heterogeneous disease that is influenced by multiple environmental factors. Further, well-designed studies are necessary to shed more light on the role of genetics, environmental factors and major allergens in the pathogenesis of cAD.

A review of cutaneous hypersensitivity reactions in dogs: A diagnostician's guide to allergy

Allergic dermatoses are common in people and domestic animals. Resultant lesions are routinely biopsied and submitted for histological examination to confirm a diagnosis or rule out diseases with overlapping or atypical clinical features. Diagnostic pathologists and clinicians are often faced with the difficult task of determining whether an allergic reaction pattern is present on both the microscopic and macroscopic levels and correlating histopathologic findings with clinical and historical data to achieve a precise clinical diagnosis. The bulk of the current veterinary literature on allergic dermatoses focuses on atopic dermatitis in dogs, distantly followed by cats, horses, and other animals. The objectives of this review are to demonstrate the key histopathologic and clinical diagnostic features of the various allergy-mediated reaction patterns, and to provide diagnosticians with a practical guide for clinicopathological correlations. Current concepts in the pathophysiology of immediate hypersensitivity reactions, with a focus on atopic dermatitis, are discussed. Points of potential histopathologic overlap between the "classic" allergic reaction pattern and less common inflammatory, predominately eosinophilic, conditions that may mimic this pattern will be discussed with the goal of highlighting the critical need for collaboration between pathologists and clinicians in furthering patient care.

Altered plasma cytokines in dogs with atopic dermatitis

BACKGROUND

Canine (Canis lupus familiaris) atopic dermatitis (AD) shares similar clinical signs to human AD. The abnormal immune response of AD is orchestrated by T lymphocytes, and may include variable involvement of cytokines, regulatory T (Treg) cells, eosinophils, mast cells and other immune components. Helper T (Th)2 cytokines often predominate initially, followed by Th1 cytokines in more chronic phases.

HYPOTHESIS/OBJECTIVES

Pro-inflammatory and Treg cytokines have been shown to play a role in human AD, yet their importance is not clear in canine AD. Hence, this study aimed to measure the concentrations of cytokines/chemokines not traditionally associated with Th1/Th2 response.

ANIMALS

Canine AD patients (n = 27), compared to control dogs (n = 11).

METHODS AND MATERIALS

A total of 19 plasma cytokines were assayed using canine specific multiplex immuno-assays.

RESULTS

The plasma concentrations of CXC Motif Chemokine Ligand 8 (CXCL8), interleukin (IL)-7 and IL-15 cytokines were elevated in canine AD patients, compared to control dogs. In addition, stem-cell factor (SCF) concentrations were reduced in the plasma of canine AD patients compared to control dogs. Distinct cytokine profiles were found in dogs belonging to the Staffordshire breeds, a group with increased risk of AD. In particular, granulocyte-macrophage colony-stimulating factor (GM-CSF) had significantly elevated concentrations.

CONCLUSIONS AND CLINICAL RELEVANCE

Some of the plasma cytokine alterations in canine AD described here, particularly of IL-7, have not been reported previously. Monitoring these distinctive cytokine alterations could be useful for diagnosis and monitoring of canine AD in dogs.

Frequency and predisposing factors for canine otitis externa in the UK - a primary veterinary care epidemiological view

BACKGROUND

Otitis externa is a commonly diagnosed disorder in dogs and can carry a high welfare impact on affected animals. This study aimed to report the prevalence and explore the role of breed and aural conformation as predisposing factors for canine otitis externa in the UK. The study used a cohort design of dogs under UK primary veterinary care at clinics participating in the VetCompass Programme during 2016. Risk factor analysis used multivariable logistic regression modelling.

RESULTS

The study included a random sample of 22,333 dogs from an overall population of 905,554 dogs under veterinary care in 2016. The one-year period prevalence of otitis externa was 7.30% (95% confidence interval [CI]: 6.97 to 7.65). Breed and ear carriage were the highest ranked risk factors. Compared with crossbred dogs, sixteen breed types showed increased odds, including: Basset Hound (odds ratio [OR] 5.87), Chinese Shar Pei (OR 3.44), Labradoodle (OR 2.95), Beagle (OR 2.54) and Golden Retriever (OR 2.23). Four breeds showed protection (i.e. reduced odds) of otitis externa: Chihuahua (OR 0.20), Border Collie (OR 0.34), Yorkshire Terrier (OR 0.49) and Jack Russell Terrier (OR 0.52). Designer breed types overall had 1.63 times the odds (95% CI 1.31 to 2.03) compared with crossbred dogs. Compared with breeds with erect ear carriage, breeds with pendulous ear carriage had 1.76 times the odds (95% CI 1.48 to 2.10) and breeds with V-shaped drop ear carriage had 1.84 times the odds (95% CI 1.53 to 2.21) of otitis externa.

CONCLUSIONS

Breed itself and breed-associated ear carriage conformation are important predisposing factors for canine otitis externa. Greater awareness of these associations for both predisposed and protected breeds could support veterinary practitioners to promote cautious and low-harm approaches in their clinical advice on preventive care for otitis externa, especially in predisposed breeds.

Update on pathogenesis, diagnosis, and treatment of atopic dermatitis in dogs

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.

Identification of modifiable pre- and postnatal dietary and environmental exposures associated with owner-reported canine atopic dermatitis in Finland using a web-based questionnaire

A cross-sectional hypothesis generating study was performed to investigate modifiable exposures such as whether feeding pattern (a non-processed meat based diet, NPMD, or an ultra-processed carbohydrate based diet, UPCD), certain environmental factors and their timing of exposure might be associated with the development of canine atopic dermatitis (CAD). Also, genetic and demographic factors were tested for associations with CAD. The data was collected from the validated internet-based DogRisk food frequency questionnaire in Finland. A total of 2236 dogs were eligible for the study (the owners reported 406 cases and 1830 controls). Our main interest was to analyze modifiable early risk factors of CAD, focusing on nutritional and environmental factors. We tested four early life periods; prenatal, neonatal, early postnatal and late postnatal periods. Twenty-two variables were tested for associations with CAD using logistic regression analysis. From the final models we identified novel dietary associations with CAD: the NPMD during the prenatal and early postnatal periods had a significant negative association with the incidence of CAD in adult dogs (age above 1 year). Oppositely, UPCD was associated with a significantly higher risk for CAD incidence. Other variables that were associated with a significantly lower risk for CAD were maternal deworming during pregnancy, sunlight exposure during early postnatal period, normal body condition score during the early postnatal period, the puppy being born within the same family that it would stay in, and spending time on a dirt or grass surface from 2 to 6 months. Also, the genetic factors regarding maternal history of CAD, allergy-prone breeds and more than 50% white-colored coat all showed a significant positive association with CAD incidence in agreement with previous findings. Although no causality can be established, feeding NPMD early in life seemed to be protective against CAD, while UPCD could be considered a risk factor. Prospective intervention studies are needed to establish the causal effects of the protective role of NPMD on prevalence of CAD during the fetal and early postnatal life.

Effect of hepatitis B virus (HBV) infection on the course of pregnancy and newborns' health status

Introduction

The effect of chronic hepatitis B virus (HBV) infection on pregnancy is not clear. Hepatitis B virus infection of newborns in the case of natural delivery occurs in 70-90% of cases. Risk factors of infection are the presence of serum HBeAg and HBV DNA level above 10⁷ IU/ml. Active and passive prevention protect more than 95% of neonates born to mothers infected with HBV. The aim of the study was to determine the course of pregnancy in HBV-infected women, the mode of delivery, efficacy of prophylaxis against HBV infection in newborns, and health condition of newborns within the first years of life.

Material and methods

The course of 104 pregnancies in 69 women infected with HBV was monitored. Hepatitis B virus viral load was determined by PCR using the AmpliPre/COBAS TaqMan HBV system. Neonatal HBV infection and the health condition at birth and during the first year of life were analyzed.

Results

All included pregnant women were HBeAg negative. No clinically significant disorders were observed during pregnancy. Viral load measured in the third trimester did not exceed 10⁷ IU/ml in any pregnant woman. Only 5 (8%) of them demonstrated levels above 10⁵ IU/ml. Two women (1.9%) experienced a miscarriage, which was considered as not associated with HBV infection. The majority (56%) of pregnancies ended with spontaneous labor. Complete prevention against HBV was applied in 79% of newborns. Hepatitis B virus infection was diagnosed in 3 children who received incomplete or no prophylaxis. Hepatitis B virus infection occurred in 3 (2.9%) children born naturally, who did not receive proper prevention after delivery. The Apgar score in children born to mothers infected with HBV did not differ significantly from that in neonates born to healthy women from the same population. Allergic disorders developed in 17 children who underwent HBV prophylaxis.

Conclusions

Low viral load in pregnant women infected with HBV and the absence of HBeAg reduce the probability of infection of newborns. Proper prevention carried out after delivery seems to be the most important method to prevent HBV infection in newborns.

cgmisc: enhanced genome-wide association analyses and visualization

High-throughput genotyping and sequencing technologies facilitate studies of complex genetic traits and provide new research opportunities. The increasing popularity of genome-wide association studies (GWAS) leads to the discovery of new associated loci and a better understanding of the genetic architecture underlying not only diseases, but also other monogenic and complex phenotypes. Several softwares are available for performing GWAS analyses, R environment being one of them.

RESULTS

We present cgmisc, an R package that enables enhanced data analysis and visualization of results from GWAS. The package contains several utilities and modules that complement and enhance the functionality of the existing software. It also provides several tools for advanced visualization of genomic data and utilizes the power of the R language to aid in preparation of publication-quality figures. Some of the package functions are specific for the domestic dog (Canis familiaris) data.

AVAILABILITY AND IMPLEMENTATION

The package is operating system-independent and is available from: https://github.com/cgmisc-team/cgmisc

CONTACT

marcin.kierczak@imbim.uu.se.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Pollen Allergies in Humans and their Dogs, Cats and Horses: Differences and Similarities

Both humans and their most important domestic animals harbor IgE and a similar IgE receptor repertoire and expression pattern. The same cell types are also involved in the triggering or regulation of allergies, such as mast cells, eosinophils or T-regulatory cells. Translational clinical studies in domestic animals could therefore help cure animal allergies and at the same time gather knowledge relevant to human patients. Dogs, cats and horses may spontaneously and to different extents develop immediate type symptoms to pollen allergens. The skin, nasal and bronchial reactions, as well as chronic skin lesions due to pollen are in principle comparable to human patients. Pollen of various species most often causes allergic rhinitis in human patients, whereas in dogs it elicits predominantly eczematous lesions (canine atopic dermatitis), in horses recurrent airway obstruction or hives as well as pruritic dermatitis, and in cats bronchial asthma and so-called cutaneous reactive patterns (eosinophilic granuloma complex, head and neck pruritus, symmetric self-induced alopecia). In human allergy-specific IgE detection, skin tests or other allergen provocation tests should be completed. In contrast, in animals IgE and dermal tests are regarded as equally important and may even replace each other. However, for practical and economic reasons intradermal tests are most commonly performed in a specialized practice. As in humans, in dogs, cats and horses allergen immunotherapy leads to significant improvement of the clinical symptoms. The collected evidence suggests that canines, felines and equines, with their spontaneous allergies, are attractive model patients for translational studies.

Identification of genetic loci associated with primary angle-closure glaucoma in the basset hound

PURPOSE

Primary angle-closure glaucoma (PACG) in dogs is usually caused by the gradual collapse of the iridocorneal angle and cleft, eventually leading to aqueous humor (AH) outflow obstruction. The condition occurs in several breeds of dogs and the prognosis for affected animals is typically poor. We have identified several basset hound (BH) pedigrees, as well as unrelated cases with characteristic PACG that in many aspects recapitulates PACG in human patients. The goal of this study was to utilize the BH PACG model to characterize the genetics of PACG, and potentially discover genetic factors contributing to PACG in humans and animals.

METHODS

We conducted a genome-wide logistic regression test for association using 37 PACG cases and 41 unaffected controls. Population stratification and cryptic relatedness were assessed using a multidimensional scaling analysis. The expression of two candidate genes within the target tissues of the BH eye was assessed by immunohistochemistry.

RESULTS

We report significant associations at two novel loci, specifically BICF2P31912 in COL1A2 on chromosome 14 with a per-allele odds ratio (OR, 95% confidence interval [CI]) of 3.35 (1.73-6.51), P(genome)=3.6×10⁻⁴; and BICF2P893476 residing in proximity to RAB22A on chromosome 24 with a per-allele OR (95% CI) of 3.93 (1.78-8.66), P(genome)=4.9×10⁻⁴. COL1A2 and RAB22A demonstrated widespread expression throughout the eye and were prominently noted in the ciliary body (CB), trabecular meshwork (TM), and iris.

CONCLUSIONS

Our finding of two genetic associations supports the potential segregation of PACG risk-conferring variants in the BH. The genetic associations identified may contribute to mechanisms underlying the pathogenesis of PACG, which remain to be elucidated.

An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts

The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now covers 99.8% of the euchromatic portion of the genome. We also present multiple RNA-Sequencing data sets from 10 different canine tissues to catalog ∼175,000 expressed loci. While about 90% of the coding genes previously annotated by EnsEMBL have measurable expression in at least one sample, the number of transcript isoforms detected by our data expands the EnsEMBL annotations by a factor of four. Syntenic comparison with the human genome revealed an additional ∼3,000 loci that are characterized as protein coding in human and were also expressed in the dog, suggesting that those were previously not annotated in the EnsEMBL canine gene set. In addition to ∼20,700 high-confidence protein coding loci, we found ∼4,600 antisense transcripts overlapping exons of protein coding genes, ∼7,200 intergenic multi-exon transcripts without coding potential, likely candidates for long intergenic non-coding RNAs (lincRNAs) and ∼11,000 transcripts were reported by two different library construction methods but did not fit any of the above categories. Of the lincRNAs, about 6,000 have no annotated orthologs in human or mouse. Functional analysis of two novel transcripts with shRNA in a mouse kidney cell line altered cell morphology and motility. All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts.

A mutation in the SUV39H2 gene in Labrador Retrievers with hereditary nasal parakeratosis (HNPK) provides insights into the epigenetics of keratinocyte differentiation

Hereditary nasal parakeratosis (HNPK), an inherited monogenic autosomal recessive skin disorder, leads to crusts and fissures on the nasal planum of Labrador Retrievers. We performed a genome-wide association study (GWAS) using 13 HNPK cases and 23 controls. We obtained a single strong association signal on chromosome 2 (p(raw) = 4.4×10⁻¹⁴). The analysis of shared haplotypes among the 13 cases defined a critical interval of 1.6 Mb with 25 predicted genes. We re-sequenced the genome of one case at 38× coverage and detected 3 non-synonymous variants in the critical interval with respect to the reference genome assembly. We genotyped these variants in larger cohorts of dogs and only one was perfectly associated with the HNPK phenotype in a cohort of more than 500 dogs. This candidate causative variant is a missense variant in the SUV39H2 gene encoding a histone 3 lysine 9 (H3K9) methyltransferase, which mediates chromatin silencing. The variant c.972T>G is predicted to change an evolutionary conserved asparagine into a lysine in the catalytically active domain of the enzyme (p.N324K). We further studied the histopathological alterations in the epidermis in vivo. Our data suggest that the HNPK phenotype is not caused by hyperproliferation, but rather delayed terminal differentiation of keratinocytes. Thus, our data provide evidence that SUV39H2 is involved in the epigenetic regulation of keratinocyte differentiation ensuring proper stratification and tight sealing of the mammalian epidermis.

The genomics revolution: will canine atopic dermatitis be predictable and preventable?

BACKGROUND

Heritability studies suggest that atopic dermatitis (AD) involves multiple genes and interactions with environmental factors. Advances in genomics have given us powerful techniques to study the genetics of AD.

OBJECTIVE

To review the application of these techniques to canine AD.

RESULTS

Candidate genes can be studied using quantitative PCR and genomic techniques, but these are hypothesis-dependent techniques and may miss novel genes. Hypothesis-free techniques avoid this limitation. Microarrays quantify expression of large numbers of genes, although false-positive associations are common. In the future, expression profiling could be used to produce a complete tissue transcriptome. Genome-wide linkage studies can detect AD-associated loci if enough affected dogs and unaffected relatives are recruited. Genome-wide association studies can be used to discover AD-associated single nucleotide polymorphisms without relying on related dogs. Genomic studies in dogs have implicated numerous genes in the pathogenesis of AD, including those involved in innate and adaptive immunity, inflammation, cell cycle, apoptosis, skin barrier formation and transcription regulation. These findings, however, have been inconsistent, and problems include low case numbers, inappropriate controls, inconsistent diagnosis, incomplete genome coverage, low-penetrance mutations and environmental factors.

CONCLUSIONS

Canine AD has a complex genotype that varies between breeds and gene pools. Breeding programmes to eliminate AD are therefore unlikely to succeed, but this complexity could explain variations in clinical phenotype and response to treatment. Genotyping of affected dogs will identify novel target molecules and enable better targeting of treatment and management options. However, we must avoid misuse of genomic data.

A COL11A2 mutation in Labrador retrievers with mild disproportionate dwarfism

We describe a mild form of disproportionate dwarfism in Labrador Retrievers, which is not associated with any obvious health problems such as secondary arthrosis. We designate this phenotype as skeletal dysplasia 2 (SD2). It is inherited as a monogenic autosomal recessive trait with incomplete penetrance primarily in working lines of the Labrador Retriever breed. Using 23 cases and 37 controls we mapped the causative mutation by genome-wide association and homozygosity mapping to a 4.44 Mb interval on chromosome 12. We re-sequenced the genome of one affected dog at 30x coverage and detected 92 non-synonymous variants in the critical interval. Only two of these variants, located in the lymphotoxin A (LTA) and collagen alpha-2(XI) chain gene (COL11A2), respectively, were perfectly associated with the trait. Previously described COL11A2 variants in humans or mice lead to skeletal dysplasias and/or deafness. The dog variant associated with disproportionate dwarfism, COL11A2:c.143G>C or p.R48P, probably has only a minor effect on collagen XI function, which might explain the comparatively mild phenotype seen in our study. The identification of this candidate causative mutation thus widens the known phenotypic spectrum of COL11A2 mutations. We speculate that non-pathogenic COL11A2 variants might even contribute to the heritable variation in height.

Total IgE and allergen-specific IgE and IgG antibody levels in sera of atopic dermatitis affected and non-affected Labrador- and Golden retrievers

Canine atopic dermatitis (CAD) is an allergic skin disease associated with IgE and IgG antibodies (Ab) to environmental allergens. The aim of this study was to determine which other factors influence serum Ab levels in CAD-affected and non-affected dogs as this has only been poorly investigated in dogs so far. Total and allergen-specific IgE levels and Dermatophagoides farinae (DF)-specific IgG1 and IgG4 were measured by ELISA in sera of 145 CAD-affected and 271 non-affected Labrador- and Golden retrievers. A multivariable logistic regression analysis including the factors age, breed, gender, castration, clinical CAD status and allergen-specific immunotherapy (ASIT) was performed. Golden retrievers had more frequently total (OR=1.87, 95% CI=1.26-2.87, p<0.01) and specific IgE levels above the threshold value than Labrador retrievers, suggesting that genetic factors influence IgE levels in dogs. Castration was generally associated with low Ab levels (OR=0.43-0.65, p<0.05). Surprisingly, dogs with CAD did not have increased odds for high IgE against any of the allergens tested. ASIT with DF was associated with high DF-specific IgG1 (OR=4.32, 95% CI 1.46-12.8, p<0.01) but was not associated with DF-specific IgG4 or decreased IgE levels. Further studies are needed to understand the role of allergen-specific IgE in CAD and of IgG1 in ASIT.