Bayesian model and selection signature analyses reveal risk factors for canine atopic dermatitis

Transcriptomic profiling of dorsal root ganglia in atopic and healthy dogs: A comparative RNA sequencing study with implications in cutaneous itch research

BACKGROUND

Itch is a common clinical sign in skin disorders. While the neural pathways of itch transmission from the skin to the brain are well understood in rodents, the same pathways in dogs remain unclear. The knowledge gap hinders the development of effective treatments for canine itch-related disorders.

HYPOTHESIS/OBJECTIVES

This study aimed to investigate the differential gene expression in the dorsal root ganglia (DRGs) between healthy and atopic dogs to identify specific molecules potentially involved in itch signalling and neuroinflammation in canine atopic dermatitis (cAD).

ANIMALS

Two atopic and four healthy dogs.

MATERIALS AND METHODS

DRGs were collected from atopic and healthy dogs to compare their transcriptional profiles using RNA sequencing.

RESULTS

Principal component and heatmap analyses revealed two distinct clusters separating atopic from healthy dogs. Consistent with this observation, we identified 627 (543 upregulated and 84 downregulated) differentially expressed genes (DEGs) in atopic compared with healthy dogs. We further narrowed down our genes of interest to common DEGs in each atopic dog, which revealed 159 (132 upregulated and 27 downregulated) DEGs. Among these genes, when we focused on itch signalling-associated molecules, P2RY12, IL-2RG, TLR1 and POSTN were significantly upregulated, while MRGPRD and LPAR3 were both significantly downregulated in atopic dogs compared with those in healthy dogs. Pathway analysis showed a significant upregulation of CREB signalling in neurons, myelination signalling and neuroinflammation signalling pathways in atopic dogs.

CONCLUSIONS AND CLINICAL RELEVANCE

Our study suggested that dysregulation of neuroinflammatory pathways might play a role in the pathomechanism of cAD as in humans.

The DoGA consortium expression atlas of promoters and genes in 100 canine tissues

The dog, Canis lupus familiaris, is an important model for studying human diseases. Unlike many model organisms, the dog genome has a comparatively poor functional annotation, which hampers gene discovery for development, morphology, disease, and behavior. To fill this gap, we established a comprehensive tissue biobank for both the dog and wolf samples. The biobank consists of 5485 samples representing 132 tissues from 13 dogs, 12 dog embryos, and 24 wolves. In a subset of 100 tissues from nine dogs and 12 embryos, we characterized gene expression activity for each promoter, including alternative and novel, i.e., previously not annotated, promoter regions, using the 5' targeting RNA sequencing technology STRT2-seq. We identified over 100,000 promoter region candidates in the recent canine genome assembly, CanFam4, including over 45,000 highly reproducible sites with gene expression and respective tissue enrichment levels. We provide a promoter and gene expression atlas with interactive, open data resources, including a data coordination center and genome browser track hubs. We demonstrated the applicability of Dog Genome Annotation (DoGA) data and resources using multiple examples spanning canine embryonic development, morphology and behavior, and diseases across species.

Updated insights into the molecular pathogenesis of canine atopic dermatitis

Atopic dermatitis (AD) is a common and chronic inflammatory skin disease with frequent relapses. The genomics revolution has greatly contributed and revolutionised our knowledge of human AD; understanding the molecular skin fingerprint of AD and associated pathogenic immune pathways has led to preclinical assessments of several novel treatments. Initial studies using microarray analysis to analyse transcriptome (gene expression) changes provided relevant insight on the inflammatory and structural changes occurring at the time of acute or chronic AD skin lesions, or after immunomodulating treatments with drugs ciclosporin and dupilumab, a monoclonal antibody anti-IL4 receptor. The studies revealed that human AD is characterised by the activation of multiple cytokine pathways (predominance of T helper cell [Th]2 with some activation of Th1, Th17 and Th22) as well as dysregulated expression of barrier components in the skin. There are several reports on the expression of different single molecular targets (e.g. interleukin [IL]-13, CCL17 and periostin) in spontaneous canine AD (cAD). However, significant studies of the transcriptome have been limited to a single microarray study analysing chronic AD skin lesions in dogs. While revealing a large number of genes differentially expressed in cAD skin, the small sample size (n = 13 dogs) and the lack of changes in key epidermal barrier and inflammatory cytokine genes in the microarrays have inhibited discussion towards specific immunological changes. This review summarises the current literature regarding the molecular mechanisms of spontaneous cAD, including the recent data regarding RNA sequencing, and compares some pathogenic aspects to the previously published data from human AD.

Genomic analyses identify 15 susceptibility loci and reveal HDAC2, SOX2-OT, and IGF2BP2 in a naturally-occurring canine model of gastric cancer

Gastric cancer (GC) is the fifth most common human cancer worldwide, but the genetic etiology is largely unknown. We performed a Bayesian genome-wide association study and selection analyses in a naturally-occurring canine model of GC, the Belgian Tervuren and Sheepdog breeds, to elucidate underlying genetic risk factors. We identified 15 loci with over 90% predictive accuracy for the GC phenotype. Variant filtering revealed germline putative regulatory variants for the EPAS1 (HIF2A) and PTEN genes and a coding variant in CD101. Although closely related to Tervuren and Sheepdogs, Belgian Malinois rarely develop GC. Across-breed analyses uncovered protective haplotypes under selection in Malinois at SOX2-OT and IGF2BP2. Among Tervuren and Sheepdogs, HDAC2 putative regulatory variants were present at comparatively high frequency and were associated with GC. Here, we describe a complex genetic architecture governing GC in a dog model, including genes such as PDZRN3, that have not been associated with human GC.

Large-scale genomic analysis of the domestic dog informs biological discovery

Recent advances in genomics, coupled with a unique population structure and remarkable levels of variation, have propelled the domestic dog to new levels as a system for understanding fundamental principles in mammalian biology. Central to this advance are more than 350 recognized breeds, each a closed population that has undergone selection for unique features. Genetic variation in the domestic dog is particularly well characterized compared with other domestic mammals, with almost 3000 high-coverage genomes publicly available. Importantly, as the number of sequenced genomes increases, new avenues for analysis are becoming available. Herein, we discuss recent discoveries in canine genomics regarding behavior, morphology, and disease susceptibility. We explore the limitations of current data sets for variant interpretation, tradeoffs between sequencing strategies, and the burgeoning role of long-read genomes for capturing structural variants. In addition, we consider how large-scale collections of whole-genome sequence data drive rare variant discovery and assess the geographic distribution of canine diversity, which identifies Asia as a major source of missing variation. Finally, we review recent comparative genomic analyses that will facilitate annotation of the noncoding genome in dogs.

Canine Atopic Dermatitis: Prevalence, Impact, and Management Strategies

Atopic dermatitis (AD) is a common inflammatory and pruritic allergic skin disease in humans and dogs worldwide. The pathogenesis of AD is multifactorial, immunologically complex, and may involve genetic factors, epidermal barrier dysfunction, microbiome changes, immune dysregulation, and allergic sensitization. Across species, prevalence of AD is on the rise. At present, there is no cure for canine AD (CAD). The treatment for CAD is multifaceted and aimed at controlling the pruritus, associated inflammation, and infections, repairing the skin barrier function, and dietary management. This review presents data on prevalence, impact, and complex immunological interactions in AD with a focus on subsequent management of the disease in the canine population. A multimodal approach for management of CAD to address varying clinical signs and responses to therapies is discussed.

Molecular and Physiological Functions of PACAP in Sweat Secretion

Sweat plays a critical role in human body, including thermoregulation and the maintenance of the skin environment and health. Hyperhidrosis and anhidrosis are caused by abnormalities in sweat secretion, resulting in severe skin conditions (pruritus and erythema). Bioactive peptide and pituitary adenylate cyclase-activating polypeptide (PACAP) was isolated and identified to activate adenylate cyclase in pituitary cells. Recently, it was reported that PACAP increases sweat secretion via PAC1R in mice and promotes the translocation of AQP5 to the cell membrane through increasing intracellular [Ca²⁺] via PAC1R in NCL-SG3 cells. However, intracellular signaling mechanisms by PACAP are poorly clarified. Here, we used PAC1R knockout (KO) mice and wild-type (WT) mice to observe changes in AQP5 localization and gene expression in sweat glands by PACAP treatment. Immunohistochemistry revealed that PACAP promoted the translocation of AQP5 to the lumen side in the eccrine gland via PAC1R. Furthermore, PACAP up-regulated the expression of genes (Ptgs2, Kcnn2, Cacna1s) involved in sweat secretion in WT mice. Moreover, PACAP treatment was found to down-regulate the Chrna1 gene expression in PAC1R KO mice. These genes were found to be involved in multiple pathways related to sweating. Our data provide a solid basis for future research initiatives in order to develop new therapies to treat sweating disorders.