Biology subjects

Leeb, T.

Publications and source records attributed to Leeb, T..

12 recordsLinked to original sources

bioRxiv2026

Phloiokeratosis - a new ichthyosiform hyperkeratotic cornification disorder in dogs with SUV39H1 variants

The continuous renewal of healthy epidermis depends on the finely regulated proliferation of basal keratinocytes and subsequent differentiation as the newly formed cells move upwards through the different layers of the epidermis. Perturbations in keratinocyte differentiation may lead to cornification disorders. We investigated seven dogs of different breeds belonging to four independent families that showed striking multifocal tree bark-like skin lesions. Histopathologically, lesional skin was characterized by pronounced epidermal and infundibular hyperkeratosis with epidermal and sebaceous gland hyperplasia. We therefore tentatively termed the phenotype phloiokeratosis, derived from the Greek word phloios for tree bark and keratosis indicating abnormal keratinization. Whole genome sequencing of DNA from affected dogs revealed four independent variants in the SUV39H1 gene encoding the SUV39H1 histone lysine methyltransferase, an H3K9 methyltransferase, which is involved in epigenetic silencing of chromatin. Phloiokeratosis is inherited as an X-chromosomal semi-dominant trait. Four of the affected dogs in our study were heterozygous females and had lesion patterns reminiscent of Blaschko lines. In two of them, trio analyses experimentally confirmed de novo mutation events in the SUV39H1 gene. Previously, Suv39h1-/- knockout mice had been reported to have normal skin. So far, no human patients with SUV39H1 loss-of-function variants have been reported. The findings in SUV39H1 mutant dogs with phloiokeratosis for the first time link SUV39H1 deficiency to a heritable skin phenotype. Our study highlights the essential role of SUV39H1-mediated epigenetic silencing during normal keratinocyte differentiation and provides a unique model for further investigations. Author SummaryThe integrity of the skin depends on a balanced equilibrium of keratinocyte proliferation, differentiation, and sloughing of terminally differentiated cells into the environment requiring finely regulated changes in the global transcriptome of differentiating keratinocytes. We investigated seven dogs belonging to four different families with a new disorder of cornification characterized by tree bark-like outgrowths of the epidermis. Histopathological examinations confirmed that the outermost layer of the epidermis was thickened in affected dogs. The genetic analysis yielded four different SUV39H1 loss-of-function variants in the affected dogs from the four families. The SUV39H1 gene encodes an enzyme that is involved in the epigenetic silencing of chromatin. The newly characterized inherited skin disease in dogs is the first clinical phenotype that has been linked to SUV39H1 deficiency. Most likely, SUV39H1 deficiency leads to delayed epigenetic silencing and consequently delayed differentiation of keratinocytes. Dogs with this rare skin disease provide an improved understanding of the essential role of SUV39H1 in the epigenetic control of gene expression in skin.

genetics↗

bioRxiv2025

Reproducibility of the evaluation of genetic variant pathogenicity based on the animal variant classification guidelines

Until recently, due to the absence of standardized guidelines tailored for veterinary use, the evaluation of genetic variant pathogenicity for single-gene diseases was based on a personal interpretation of the presented evidence, which has led to ambiguous interpretation. With the publication of the animal variant classification guidelines (AVCG), a more objective approach became available. Variants are evaluated based on twenty-three criteria and labeled as pathogenic, likely pathogenic, variant of uncertain significance, likely benign or benign. While the accuracy was thoroughly tested in the original publication, the reproducibility of the various steps involved was only briefly checked, which is why the current study was performed. Each variant from a set of 150 published likely causal variants for single-gene diseases from three species (dog, cat, horse) was independently and blindly assessed by three different reviewers, each applying the same AVCG. An overall agreement of 93% for decisions on the scope, i.e. whether they fit the inclusion criteria to allow evaluation with AVCG, was found. More importantly, the reproducibility was 65% for the pathogenicity classification and this increased to 83% clinically relevant agreement. While a direct comparison of the reproducibility with human literature is not possible for the scope, the reproducibility on pathogenicity classification is in line with reports using the human American College for Medical Genetics and Genomics and Association for Molecular Pathology guidelines for human variants. Overall, based on the current study, the reproducibility of the guidelines in veterinary species is within current expectations.

genetics↗

bioRxiv2025

Evolutionary dynamics of a lethal recessive allele in reintroduced fragmented lynx populations

Conservation programs worldwide use reintroductions and translocations as management tools to support endangered species. Such efforts often face genetic challenges, as small populations and restricted gene flow can lead to inbreeding and loss of genetic diversity. Inbreeding depression is a well-known risk in small, isolated populations, where reduced genetic diversity can compromise fitness and threaten population persistence. While correlations between inbreeding and reduced fitness are well documented, so far, no causal variant for a fitness-relevant phenotype has been described in a wild population. Here, we combine long-term health and population data with genomic analyses to identify a recessive lethal allele responsible for extensive organ mineralization in young Eurasian lynx (Lynx lynx) from a reintroduced population in Switzerland. The causal variant is located in FGF23 and predicted to impair secretion of fibroblast growth factor 23, an important regulator of phosphate homeostasis. The deleterious allele was likely introduced from one of the lynx source populations and subsequently increased in frequency through founder effects and inbreeding. All three Swiss lynx populations show high inbreeding levels (FROH > 0.4), reflecting substantial loss of genetic diversity. Our findings uniquely demonstrate how demographic history, founder effects, genetic drift, and inbreeding interact to shape the fate of a recessive deleterious allele, highlighting the importance of multiscale monitoring in wildlife conservation.

evolutionary biology↗

bioRxiv2025

A missense variant in PAOX in American Staffordshire Terriers with juvenile-onset polyneuropathy

Hereditary polyneuropathies in dogs mirror many features of human Charcot-Marie-Tooth (CMT) disease and offer valuable spontaneous models for discovery of genes variants involved in this disorder. A juvenile-onset polyneuropathy (JOP) in American Staffordshire Terriers (ASTs) resembles CMT, with motor and sensory deficits, often accompanied by laryngeal paralysis. To identify the underlying genetic cause, we conducted a genome-wide association study (GWAS) with 24 affected and 53 control ASTs that identified a significant locus at the distal end of chromosome 28. Homozygosity mapping analysis further defined a critical interval spanning 11 protein-coding genes and whole-genome sequencing revealed a missense variant in the PAOX gene encoding polyamine oxidase (NC_049249.1:g.41474541G>A), leading to a glycine-to-arginine substitution at a highly conserved residue, XP_038435135.1:p.(Gly382Arg). Genotypes at this variant were homozygous alternate in 96% of the affected dogs (n=53) and either homozygous reference or heterozygous in 336 unaffected ASTs; the mutant allele was not detected in any of 2519 genomes of other dog breeds. In silico predictions consistently supported its pathogenicity, and structural modeling suggested altered substrate binding. Although PAOX expression was preserved, proteomic profiling in affected nerve tissue revealed reduced levels of myelin-associated proteins, as well as dysregulation of mitochondrial and proteasomal pathways. Our findings establish this PAOX missense variant as the likely cause of JOP in ASTs and highlight the breed as a valuable large-animal model for studying inherited peripheral neuropathies. These results expand the spectrum of genes implicated in polyneuropathies and provide a basis for genetic testing and informed breeding strategies in ASTs. Author summaryWe studied a hereditary peripheral nerve disorder in American Staffordshire Terriers characterized by exercise intolerance, coordination problems, general weakness and difficulty breathing due to laryngeal paralysis. These signs closely resemble a group of inherited diseases in people known as Charcot-Marie-Tooth disease. To understand the genetic basis of this condition in dogs, we analyzed the genomes of affected and healthy individuals. Our research led us to a single gene, PAOX, which carries a missense variant likely affecting the function of polyamine oxidase and ultimately disrupting how the nerve cells function and survive. Most affected dogs had two copies of the mutant allele, while it was absent or in only one copy in healthy dogs. Additional analyses suggested that the variant may interfere with the nerves ability to maintain their structure and function properly. The mutant allele does not appear to reduce the overall level of PAOX protein, but it may affect how the protein works. Our findings provide a new genetic test that can help breeders avoid producing affected puppies. They also highlight this condition in dogs as a valuable model for understanding similar diseases in humans.

genetics↗

bioRxiv2023

Single-cell profiling of bronchoalveolar cells reveals a Th17 signature in neutrophilic severe equine asthma

Severe equine asthma (SEA) shares clinical and pathological features with human neutrophilic asthma, serving as a rare natural model for this condition. To uncover the elusive immune mechanisms driving SEA, we performed single-cell mRNA sequencing (scRNA-seq) on cryopreserved bronchoalveolar cells from 11 Warmblood horses, five controls and six with SEA. We identified six major cell types, showing significant heterogeneity and novel subtypes. Notably, we observed monocyte-lymphocyte complexes and detected a robust Th17 signature in SEA, with CXCL13 upregulation in intermediate monocytes. Asthmatic horses exhibited expansion of the B cell population, Th17 polarization of the T cell populations, and dysregulation of genes associated with T cell function. Neutrophils demonstrated enhanced migratory capacity and heightened aptitude for neutrophil extracellular trap formation. These findings provide compelling evidence for a predominant Th17 immune response in neutrophilic SEA, driven by dysregulation of monocyte and T cell genes. The dysregulated genes identified through scRNA-seq have potential as biomarkers and therapeutic targets for SEA and provide insights into human neutrophilic asthma. One Sentence SummarySingle-cell mRNA sequencing identifies a predominant Th17-mediated immune response in severe equine asthma

immunology↗

bioRxiv2023

How clean is clean? In-vitro comparison of biofilm removal efficacy and cleaning characteristics of three debridement pads

AimThe aim of this study was to elucidate the effectiveness of soft debridement in cleaning wounds varying in size and type of exudate and in creating/maintaining a window of opportunity for the wound to be able to heal. MethodsThis study presents a standardised in-vitro comparison of three different debridement pads based on the defined composition of exudate and standardised cleaning protocol followed by an robotic cleaning arm. Three important cleaning characteristics (fluid holding capacity, cleaning efficacy/capacity) and the biofilm removal efficacy of wounds varying in size and composition and viscosity of exudate were assessed. ResultsAll three debridement pads tested showed the ability to clean small to large wounds with different types of exudate (serous/fibrinous) as well as to remove biofilm cells to some extent. Long and dense fibres are favourable when it comes to taking up and holding onto exudate while shorter fibres help to break open harder to clean wounds. ConclusionA balance between fluid holding capacity and cleaning efficacy/capacity is important in order to achieve the best overall results and successfully remove exudate as well as biofilm cells from small to large wounds with different types of exudate. This in turn has a potential influence on the microenvironment of the wound. Key pointsO_LIThe right balance between the parameters tested in this study is crucial for a successful biofilm removal. C_LIO_LIThe type of exudate (serous, fibrinous) has an influence on the cleaning efficacy/capacity of debridement pads. C_LIO_LISoft debridement is able to remove biofilm cells and devitalized tissue as well as dead cells, exudate, proteins etc. C_LIO_LIGood cleaning efficacies without the ability to take up and hold onto exudate, protein and cells are not sufficient for the successful removal of biofilm. C_LI

microbiology↗

bioRxiv2022

Long-read RNA Sequencing Improves the Annotation of the Equine Transcriptome

1A high-quality reference genome assembly, a biobank of diverse equine tissues from the Functional Annotation of the Animal Genome (FAANG) initiative, and incorporation of long-read sequencing technologies, have enabled efforts to build a comprehensive and tissue-specific equine transcriptome. The equine FAANG transcriptome reported here provides up to 45% improvement in transcriptome completeness across tissue types when compared to either RefSeq or Ensembl transcriptomes. This transcriptome also provides major improvements in the identification of alternatively spliced isoforms, novel noncoding genes, and 3 transcription termination site (TTS) annotations. The equine FAANG transcriptome will empower future functional studies of important equine traits while providing future opportunities to identify allele-specific expression and differentially expressed genes across tissues.

genomics↗

bioRxiv2021

Dog10K_Boxer_Tasha_1.0: A long-read assembly of the dog reference genome

The domestic dog has evolved to be an important biomedical model for studies regarding the genetic basis of disease, morphology and behavior. Genetic studies in the dog have relied on a draft reference genome of a purebred female boxer dog named "Tasha" initially published in 2005. Derived from a Sanger whole genome shotgun sequencing approach coupled with limited clone-based sequencing, the initial assembly and subsequent updates have served as the predominant resource for canine genetics for 15 years. While the initial assembly produced a good quality draft, as with all assemblies produced at the time it contained gaps, assembly errors and missing sequences, particularly in GC-rich regions, which are found at many promoters and in the first exons of protein coding genes. Here we present Dog10K_Boxer_Tasha_1.0, an improved chromosome-level highly contiguous genome assembly of Tasha created with long-read technologies, that increases sequence contiguity >100-fold, closes >23,000 gaps of the Canfam3.1 reference assembly and improves gene annotation by identifying >1200 new protein-coding transcripts. The assembly and annotation are available at NCBI under the accession GCF_000002285.5.

genomics↗

bioRxiv2020

Dog color patterns explained by modular promoters of ancient canid origin

Distinctive color patterns in dogs are an integral component of canine diversity. Color pattern differences are thought to have arisen from mutation and artificial selection during and after domestication from wolves 1,2 but important gaps remain in understanding how these patterns evolved and are genetically controlled 3,4. In other mammals, variation at the ASIP gene controls both the temporal and spatial distribution of yellow and black pigments 3,5-7. Here we identify independent regulatory modules for ventral and hair cycle ASIP expression, and we characterize their action and evolutionary origin. Structural variants define multiple alleles for each regulatory module and are combined in different ways to explain five distinctive dog color patterns. Phylogenetic analysis reveals that the haplotype combination for one of these patterns is shared with arctic white wolves and that its hair cycle-specific module likely originated from an extinct canid that diverged from grey wolves more than 2 million years before present. Natural selection for a lighter coat during the Pleistocene provided the genetic framework for widespread color variation in dogs and wolves.

genetics↗

bioRxiv2019

PBMC Treatment Significantly Changes Gene Expression Regulation in Horses

Expression quantitative trait loci (eQTLs) are context dependent, and therefore change between tissues, cell types, and after cell treatment. In addition, SNP positions and RNAseq counts must be updated after assembly of new reference genome sequences. Therefore, we remapped eQTLs with Matrix eQTL using the previously generated and publicly available data from four contexts of peripheral blood mononuclear cells (PBMCs) from European Warmblood horses to the EquCab3.0 reference genome, and used a linear mixed model in R to identify eQTLs with significantly different gene expression regulation in treated PBMCs when compared to no treatment (baseline). We found no evidence that SNPs associated with significant changes in gene expression between MCK and a treatment in PBMCs caused strong opposing regulatory effects. We identified canonical pathways with a significant number of genes in PBMCs with altered gene expression regulation when treated with lipopolysaccharides (LPS) and hay-dust extract (HDE). Significant pathways included RhoA signaling in LPS, as well as histamine degradation, cholesterol biosynthesis, Fc{gamma}RIIB signaling, and others in HDE. Our results support previous research indicating that pathways altered between baseline and treatment of PBMCs in horses with LPS or HDE affect inflammatory responses through RhoA, B-cell signaling, IL-4 and IFN-{gamma}, and histamine.

genomics↗

bioRxiv2018

Christmas disease in a Hovawart family resembling human hemophilia B Leyden is caused by a single nucleotide deletion in a highly conserved transcription factor binding site of the F9 gene promoter

Hemophilia B is a classical monogenic X-chromosomal recessively transmitted bleeding disorder caused by genetic variants within the coagulation factor IX gene (F9). Although hemophilia B has been described in 28 dog breeds and four mixed-breed dogs hitherto, it has not yet been reported in the Hovawart. Here we describe the identification of a Hovawart family transmitting typical signs of an X-linked bleeding disorder. Five males had been reported to suffer from recurrent hemorrhagic episodes, four of them had to be euthanized finally and one died due to severe blood loss. A blood sample of one of these males with only 2% of the normal concentration of plasma factor IX (FIX) together with samples of seven relatives including the mother and grandmother were provided for further analysis. Next generation sequencing of DNA of the mother and grandmother revealed a single nucleotide deletion in the F9 promoter (NC_006621.3:g.109,501,492delC; CanFam3.1). Genotyping of the deletion in 1,298 dog specimens (81 different breeds) including 720 Hovawarts revealed that the mutant allele was only present in the aforementioned Hovawart family. The deletion is located 73 bp upstream of the F9 start codon in the highly conserved overlapping DNA binding sites of hepatocyte nuclear factor 4 (HNF4) and androgen receptor (AR). The deletion only abolishes binding of HNF4 as demonstrated by electrophoretic mobility shift assay (EMSA) using purified recombinant human HNF4 and a transient overexpression lysate of human AR with double-stranded DNA probes encompassing the mutant promoter region. Luciferase reporter assays using wild type and mutated promoter fragment constructs transfected into Hep G2 cells showed a 65.3% reduction in expression from the mutant promoter. The data presented here provide evidence that the deletion identified in the Hovawart family caused a rare type of hemophilia B resembling human hemophilia B Leyden.\n\nAuthor summaryHemophilia B is the rarer form of classical hemophilias resulting from the absence or residual activity of blood clotting factor IX. Due to its X-linked recessive inheritance normally only males are affected. In a disease subtype, termed hemophilia B Leyden, factor IX activities increase during puberty resulting in spontaneous improvement of bleeding symptoms or even clinical recovery. This surprising development-related alteration is caused by nucleotide variants in important developmental and hormone-responsive regulatory regions of the factor IX gene promoter interfering with transcription factor binding. Although hemophilia B has been reported in several dog breeds, subtypes resembling human hemophilia B Leyden were unknown hitherto. In addition, the single nucleotide deletion reported here in Hovawarts in the overlapping binding sites of transcription factor HNF4 and androgen receptor only affecting HNF4 binding, was unexpected. Although it is advisable to genotype females in the future to prevent a further spread of this subtype of the disorder, our findings also open up the possibility not to euthanize affected males inevitably but to treat until puberty if necessary.

genetics↗

bioRxiv2017

Development of a high-density, 2M SNP genotyping array and 670k SNP imputation array for the domestic horse

BackgroundTo date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.\n\nResultsUsing whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of [~]5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of [~]2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of [~]670 thousand SNPs (MNEc670k), was designed for genotype imputation.\n\nConclusionsHere, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

genomics↗