Quantitative and qualitative histopathological assessments may yield complementary and novel insights into myocardial tissue alterations in dogs with myxomatous mitral valve disease (MMVD) and dilated cardiomyopathy (DCM). This study aimed to compare myocardial histopathological features in multiple, region-matched cardiac specimens from dogs with MMVD, DCM, and cardiac-healthy controls using quantitative and qualitative histopathological methods. Dogs with MMVD (n=27), DCM (n=16), and cardiac healthy controls (n=32) were enrolled. Tissue proportions of cardiomyocytes, fibrosis, and fat, as well as the arterial lumen-to-area ratio (LAR), were quantitatively evaluated in each dog using a digital image analysis software, whereas the presence of endocardial thickening, fibrosis, fat, and attenuated wavy fibers was qualitatively assessed. Clinical MMVD dogs had higher proportions of fibrosis in the left ventricular (LV) lateral wall, the LV posterior papillary muscle, and left atrium compared to controls, and more MMVD dogs had thickened endocardium in the LA compared to controls (all P<0.05). Clinical DCM dogs had higher proportions of fibrosis in both atria compared to controls (P<0.05), and higher fibrosis in the interventricular septum compared to clinical MMVD dogs (P<0.05). Dogs with DCM and atrial fibrillation had higher proportions of atrial fibrosis compared to DCM dogs without atrial fibrillation (P<0.05). Neither the LAR nor the presence of attenuated wavy fibers differed between the groups in any region. In conclusion, myocardial histopathological alterations were predominantly left-sided in MMVD dogs and bilateral in DCM dogs. Histopathological characteristics in certain cardiac regions varied with disease type and severity, underscoring their potential role in disease pathogenesis.

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 inconsistencies. With the publication of the animal variant classification guidelines (AVCG), a more objective approach became available. Variants are evaluated by the International Society of Animal Genetics (ISAG)-endorsed Variant Pathogenicity Working Group (VPWG) based on 23 criteria and are subsequently 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 analysis 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 VPWG reviewers, each applying the same AVCG. An overall agreement of 93% for decisions on the scope, that is, whether they fit the inclusion criteria to allow evaluation with AVCG, was found. More importantly, the reproducibility of pathogenicity label assignment was 65% and the reproducibility of clinical relevance was 83%. The reproducibility of AVCG-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, the reproducibility of the AVCG classifications as used by the ISAG-endorsed VPWG supports the utility of these classifications in veterinary species.

The Animal Variant Classification Guidelines (AVCG) were developed to standardize and objectify the classification of putative disease-causing variants. These guidelines are sufficiently reproducible and are used to classify previously published and new disease-causing variants across species. Here, the guidelines are updated (AVCG.v2), based on a three-phase decision process. Overall, four new criteria and seven clarifying comments were added. The number of criteria has increased from 23 to 27, with three new criteria supporting pathogenicity and one new criterion supporting benign classification. Pharmacogenomic variants were determined to fall within the scope of the guidelines. These updated guidelines are being used by the Variant Pathogenicity Working Group (VPWG), part of the Animal Genetic Testing Standardization standing committee, which is a committee of elected members of the International Society for Animal Genetics (ISAG). Under the auspices of ISAG, the VPWG retrospectively classifies published putative disease-causing variants. The pathogenicity label for a variant will be presented in the variant tables of Online Mendelian Inheritance in Animals (OMIA; https://omia.org/). The AVCGv.2 criteria and recommendations were developed by the expertise of the animal genetics community and the ISAG Executive Committee through the Animal Genetics Testing Standardization Committee endorses and strongly encourages their use to evaluate the evidence supporting pathogenicity of putative disease-causing variants.

Circulating microRNAs (miRNAs) are potential biomarkers for numerous diseases. Characterization of the whole blood (WB) miRNA-transcriptome (miRNome) in cats is lacking, which limits the potential use of miRNAs as biomarkers for diseases such as feline cardiovascular disease. The aims of the present study were to profile and evaluate circulating miRNAs in feline WB by high-throughput sequencing of the total miRNome in WB from twelve domestic mixed breed (DOM) and Norwegian Forest (NFO) cats stringently diagnosed with or without preclinical hypertrophic cardiomyopathy (HCM). A total of 459 mature miRNAs were identified in feline WB, of which 40 were potential novel feline miRNAs. A majority, 85.3%, of the miRNAs showed sequence similarity with human miRNAs. An effect of breed was found, with up to thirteen WB miRNAs being differentially abundant between breeds. The majority of the significant breed-specific miRNAs in feline WB could be associated with regulation of haematopoietic cells. One miRNA, miR-204-5p, was potentially associated with preclinical HCM in NFO cats, but the results need to be confirmed in a larger and sex-unbiased cohort. In conclusion, here we used miRNome-sequencing to identify hundreds of circulating miRNAs in feline WB. Breed should be considered when evaluating the miRNome in feline WB.

BACKGROUND:Echocardiography is widely used to breed-screen cats for the presence of heart disease. Left-sided cardiac dimensions are non-linearly related to body weight (BW), but the association with signalment variables is incompletely evaluated. OBJECTIVE:To validate previously published prediction equations (PE) and 95% prediction intervals (PI) and study the effects of breed, age, sex, and neutering on BW-normalized aortic (Ao), left atrial (LA) and ventricular (LV) dimensions. ANIMALS:56 169 pure-bred adult cats. METHODS:Data from heart screens conducted between 1999 and 2023 were included. Body-weight-(BW)-based PE and 95% PIs were obtained by allometric scaling including only cats considered normal. The effects of signalment variables on BW-normalized cardiac dimensions were examined using group-wise comparisons and uni- and multivariable analyses. RESULTS:The PE and PI changed marginally from those previously reported. The BW-normalized measurements showed greater variation for LV systolic than diastolic measurements (p < 0.001), and LA showed greater variation than Ao measurements. All signalment variables had small but significant effects on BW-normalized variables (p < 0.001), where the effect of breed was most prominent. None of the breeds had a variable median measurement > 10% above or below the PE, or > 10% of cats outside the PI. Signalment main effects persisted after adjusting for examiner and year of examination. CONCLUSIONS AND CLINICAL RELEVANCE:Breed, age, sex, and neutering status had small and mostly clinically irrelevant effects on BW-normalized Ao, LA, and LV linear dimensions. The PE and PI intervals are valid in adult pure-bred cats across many breeds, different ages, sexes, and neutering status.

IntroductionThe correct labeling of a genetic variant as pathogenic is important as breeding decisions based on incorrect DNA tests can lead to the unwarranted exclusion of animals, potentially compromising the long-term health of a population. In human medicine, the American college of Medical Genetics (ACMG) guidelines provide a framework for variant classification. This study aims to apply these guidelines to six genetic variants associated with hypertrophic cardiomyopathy (HCM) in certain cat breeds and to propose a modified criterion for variant classification.MethodsGenetic samples were sourced from five cat breeds: Maine Coon, Sphynx, Ragdoll, Devon Rex, and British Short- and Longhair. Allele frequencies were determined, and in the subset with phenotypes available, odds ratios to determine the association with HCM were calculated. In silico evaluation followed with joint evidence and data from other publications assisting in the classification of each variant.ResultsTwo variants, MYBPC3:c.91G > C [A31P] and MYBPC3:c.2453C > T [R818W], were designated as pathogenic. One variant, MYH7:c.5647G > A [E1883K], was found likely pathogenic, while the remaining three were labeled as variants of unknown significance.DiscussionRoutine genetic testing is advised solely for the MYBPC3:c.91G > C [A31P] in the Maine Coon and MYBPC3:c.2453C > T [R818W] in the Ragdoll breed. The human ACMG guidelines serve as a suitable foundational tool to ascertain which variants to include; however, refining them for application in veterinary medicine might be beneficial.

Assessing the pathogenicity of a disease-associated genetic variant in animals accurately is vital, both on a population and individual scale. At the population level, breeding decisions based on invalid DNA tests can lead to the incorrect inclusion or exclusion of animals and compromise the long-term health of a population, and at the level of the individual animal, lead to incorrect treatment and even life-ending decisions. Criteria to determine pathogenicity are not standardized, i.e., no guidelines for animal variants are available. Here, we aimed to develop and validate guidelines to be used by the community for Mendelian disorders in domestic animals to classify variants in categories based on standardized criteria. These so-called animal variant classification guidelines (AVCG) were based on those developed for humans by The American College of Medical Genetics and Genomics (ACMG). In a direct comparison, 83% of the pathogenic variants were correctly classified with ACMG, while this increased to 92% with AVCG. We described methods to develop datasets for benchmarking the criteria and identified the most optimal in silico variant effect predictor tools. As the reproducibility was high, we classified 72 known disease-associated variants in cats and 40 other disease-associated variants in eight additional species.

Assessing the pathogenicity of a disease-associated variant in animals accurately is vital, both on a population and individual scale. At the population level, breeding decisions based on invalid DNA tests can lead to the incorrect exclusion of animals and compromise the long- term health of a population, and at the level of the individual animal, lead to incorrect treatment and even life-ending decisions. Criteria to determine pathogenicity are not standardized, hence no guidelines for animal variants are available. Here, we developed and optimized the animal variant classification guidelines, based on those developed for humans by The American College of Medical Genetics and Genomics, and demonstrated a superior classification in animals. We described methods to develop datasets for benchmarking the criteria and identified the most optimal in silico variant effect predictor tools. As the reproducibility was high, we classified 72 known disease-associated variants in cats and 40 other disease-associated variants in eight additional species. ### Competing Interest Statement HA is an employee of Wisdom Panel Mars Petcare Science & Diagnostics, a company that offers canine and feline DNA testing as a commercial service. CDdC is an employee of Antagene, a DNA testing and genetic analysis company for dogs, cats, horses, and wildlife.

AbstractBackground and aimsThe heart is a metabolic organ rich in mitochondria. The failing heart reprograms to utilize different energy substrates, which increase its oxygen consumption. These adaptive changes contribute to increased oxidative stress. Hypertrophic cardiomyopathy (HCM) is a common heart condition, affecting approximately 15% of the general cat population. Feline HCM shares phenotypical and genotypical similarities with human HCM, but the disease mechanisms for both species are incompletely understood. Our goal was to characterize global changes in metabolome between healthy control cats and cats with different stages of HCM.MethodsSerum samples from 83 cats, the majority (70/83) of which were domestic shorthair and included 23 healthy control cats, 31 and 12 preclinical cats with American College of Veterinary Internal Medicine (ACVIM) stages B1 and B2, respectively, and 17 cats with history of clinical heart failure or arterial thromboembolism (ACVIM stage C), were collected for untargeted metabolomic analysis. Multiple linear regression adjusted for age, sex and body weight was applied to compare between control and across HCM groups.ResultsOur study identified 1253 metabolites, of which 983 metabolites had known identities. Statistical analysis identified 167 metabolites that were significantly different among groups (adjusted P < 0.1). About half of the differentially identified metabolites were lipids, including glycerophospholipids, sphingolipids and cholesterol. Serum concentrations of free fatty acids, 3‐hydroxy fatty acids and acylcarnitines were increased in HCM groups compared with control group. The levels of creatine phosphate and multiple Krebs cycle intermediates, including succinate, aconitate and α‐ketoglutarate, also accumulated in the circulation of HCM cats. In addition, serum levels of nicotinamide and tryptophan, precursors for de novo NAD+ biosynthesis, were reduced in HCM groups versus control group. Glutathione metabolism was altered. Serum levels of cystine, the oxidized form of cysteine and cysteine‐glutathione disulfide, were elevated in the HCM groups, indicative of heightened oxidative stress. Further, the level of ophthalmate, an endogenous glutathione analog and competitive inhibitor, was increased by more than twofold in HCM groups versus control group. Finally, several uremic toxins, including guanidino compounds and protein bound putrescine, accumulated in the circulation of HCM cats.ConclusionsOur study provided evidence of deranged energy metabolism, altered glutathione homeostasis and impaired renal uremic toxin excretion. Altered lipid metabolism suggested perturbed structure and function of cardiac sarcolemma membrane and lipid signalling.

BACKGROUND:Dilated cardiomyopathy (DCM) is a life-threatening heart disease and a common cause of heart failure due to systolic dysfunction and subsequent left or biventricular dilatation. A significant number of cases have a genetic etiology; however, as a complex disease, the exact genetic risk factors are largely unknown, and many patients remain without a molecular diagnosis.METHODS:We performed GWAS followed by whole-genome, transcriptome, and immunohistochemical analyses in a spontaneously occurring canine model of DCM. Canine gene discovery was followed up in three human DCM cohorts.RESULTS:Our results revealed two independent additive loci associated with the typical DCM phenotype comprising left ventricular systolic dysfunction and dilatation. We highlight two novel candidate genes, RNF207 and PRKAA2, known for their involvement in cardiac action potentials, energy homeostasis, and morphology. We further illustrate the distinct genetic etiologies underlying the typical DCM phenotype and ventricular premature contractions. Finally, we followed up on the canine discoveries in human DCM patients and discovered candidate variants in our two novel genes.CONCLUSIONS:Collectively, our study yields insight into the molecular pathophysiology of DCM and provides a large animal model for preclinical studies.

Abstract Background Abnormally high serum cardiac troponin I (cTnI) concentration, reflecting leakage from or necrosis of cardiomyocytes, is a negative prognosticator for death in dogs. Objectives To investigate in critically ill cats whether serum cTnI concentration is abnormally high, identify conditions associated with abnormally high cTnI concentrations, and evaluate cTnI as an independent prognosticator for death and a potential coprognosticator to the acute patient physiologic and laboratory evaluation (APPLE) score in cats. Animals One hundred nineteen cats admitted to intensive care units (ICU) and 13 healthy cats at 2 university teaching hospitals. Methods Prospective study. Clinical examinations were performed, APPLE scores calculated, and serum cTnI and serum amyloid A (SAA) measured within 24 hours after admission. Outcome was defined as death/euthanasia or survival to discharge, 28 and 90 days after ICU‐admission. Prognostic capacity of cTnI, APPLE scores and models combining cTnI and scores were evaluated by receiver‐operator‐characteristic analyses. Results Median (IQR) serum cTnI concentration was higher in ill (0.63 [0.18‐2.65] ng/mL) compared to healthy (0.015 [0.005‐0.041] ng/mL) cats (P < .001) and higher in subgroups with structural cardiac disease (2.05 [0.54‐16.59] ng/mL; P < .001) or SAA >5 mg/L (0.84 [0.23‐2.81] ng/mL; P = .009) than in cats without these characteristics (0.45 [0.12‐1.70] and 0.35 [0.015‐0.96] ng/mL). The in‐hospital case fatality rate was 29%. Neither serum cTnI concentration for all critically ill cats (area‐under‐the‐curve 0.567 [95% CI 0.454‐0.680], n = 119) or subgroups (0.625 [0.387‐0.863], n = 27; 0.506 [0.360‐0.652], n = 86), nor APPLE scores (fast 0.568 [0.453‐0.682], full 0.585 [0.470‐0.699], n = 100), were significant prognosticators for death. Conclusions and Clinical Importance Abnormally high serum cTnI concentration was common in critically ill cats. Unlike in dogs, cTnI did not confer prognostic information regarding death.

[This corrects the article DOI: 10.1371/journal.pgen.1009726.].

Hypertrophic cardiomyopathy (HCM) is a common and potentially fatal heart disease in many cat breeds. An intronic variant in TNNT2, c.95-108G>A, was recently reported as the cause of HCM in the Maine Coon. The aim of this study was to determine this variant's allele frequency in different populations and its possible association with HCM. Based on 160 Maine Coon samples collected in Belgium, Italy, Sweden and the USA, the variant's allele frequency was estimated to be 0.32. Analysis of the 99 Lives feline whole genome sequencing database showed that the TNNT2 variant also occurs in other breeds, as well as mixed-breed cats. Comparison of 31 affected and 58 healthy cats did not reveal significantly increased odds for HCM in homozygotes. Based on the combined evidence and in agreement with the standards and guidelines for the interpretation of sequence variants, this variant is currently classified as a variant of unknown significance and should not be used for breeding decisions regarding HCM.

Variation in the diagnostic interpretation of radiographs is a well-recognised problem in human and veterinary medicine. One common solution is to create a 'consensus' score based on a majority or unanimous decision from multiple observers. While consensus approaches are generally assumed to improve diagnostic repeatability, the extent to which consensus scores are themselves repeatable has rarely been examined. Here we use repeated assessments by three radiologists of 196 hip radiographs from 98 cats within a health-screening programme to examine intra-observer, inter-observer, majority-consensus and unanimous-consensus repeatability scores for feline hip dysplasia. In line with other studies, intra-observer and inter-observer repeatability was moderate (63-71%), and related to the reference assessment and time taken to reach a decision. Consensus scores did show reduced variation between assessments compared to individuals, but consensus repeatability was far from perfect. Only 75% of majority consensus scores were in agreement between assessments, and based on Bayesian multinomial modelling we estimate that unanimous consensus scores can have repeatabilities as low as 83%. These results clearly show that consensus scores in radiology can have large uncertainties, and that future studies in both human and veterinary medicine need to include consensus-uncertainty estimates if we are to properly interpret radiological diagnoses and the extent to which consensus scores improve diagnostic accuracy.

Feline cardiomyopathy (FCM) is an important contributor to feline morbidity and mortality. This explorative follow-up questionnaire study was aimed at investigating the long-term outcome in cats breed-screened for FCM (BS-FCM) in three Nordic countries. Records of cats with ≥1 BS-FCM between 2004–2015 were included. Of the 1113 included cats, 104/1113 (9.3%) had developed FCM at some time-point. Fifty-nine of the 104 (56.7%) FCM cats were diagnosed within the screening program (ScreenFCM), and 33/59 (55.9%) of these were diagnosed at the first BS-FCM. ScreenFCM cats or with an owner-reported FCM diagnosis at a later time-point had a higher risk of cardiac-related death compared to cats that never developed FCM. A shorter lifespan was found in ScreenFCM cats compared to those with normal screen results (p < 0.001). Times to all-cause mortality were shorter (p < 0.001) in cats that developed FCM at any time-point compared to those that did not. Non-cardiac morbidities were similar in all screen classification groups. The large proportion of cats that developed FCM at a later time-point underscores the need for repeated screenings later in life. Cats that developed FCM at any time-point had a shorter lifespan, with a similar proportion and in line with the nature of non-cardiac morbidities, compared to those without FCM.

Abstract Circulating microRNAs (miRNAs) are potential biomarkers for numerous diseases. Characterization of the whole blood (WB) miRNA-transcriptome (miRNome) in cats is lacking, which limits the potential use of miRNAs as biomarkers for i.e. feline heart disease. The aims of the present study were to identify and evaluate circulating miRNAs in feline WB by high-throughput sequencing of the total miRNome in WB from twelve cats, representing domestic mixed breed (DOM) and Norwegian Forest (NFO) cats with or without preclinical hypertrophic cardiomyopathy (HCM). A total of 459 mature miRNAs were identified in feline WB, of which 40 were identified as potential novel miRNAs for cat. A majority, 85.3%, of the miRNAs showed sequence similarity with human miRNAs. An effect of breed was found, with up to thirteen miRNAs being differentially expressed between breeds. One miRNA, miR-204-5p, was potentially associated with preclinical HCM in NFO cats, but needs to be confirmed in a larger and sex-unbiased cohort. Most of the identified miRNAs in feline WB can be associated with regulation of haematopoietic cells. In conclusion, miRNome-sequencing can identify hundreds of circulating miRNAs in feline WB and breed should be considered when evaluating the miRNome in feline WB, especially in cohorts including preclinical patients.

Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a ~10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs–the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specific NEBL gene in a dachshund population and show that two of the NEBL candidate variants have regulatory potential in heart-derived cell lines and are associated with reduced NEBL isoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity.

Here we present a new high-quality canine reference genome with gap number reduced 41-fold, from 23,836 to 585. Analysis of existing and novel data, RNA-seq, miRNA-seq and ATAC-seq, revealed a large proportion of these harboured previously hidden elements, including genes, promoters and miRNAs. Short-read dark regions were detected, and genomic regions completed, including the DLA, TCR and 366 cancer genes. 10x sequencing of 27 dogs uncovered a total of 22.1 million SNPs, Indels and larger structural variants (SVs). 1.4% overlap with protein coding genes and could provide a source of normal or aberrant phenotypic modifications.

We present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted over CanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. A catalogue of canine “dark” regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1.4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.

Background Pesticide residue contamination of surface water in agricultural areas can have adverse effects on the ecosystem. We have performed an integrated chemical and bioanalytical profiling of surface water samples from Swedish agricultural areas, aiming to assess toxic activity due to presence of pesticides. A total of 157 water samples were collected from six geographical sites with extensive agricultural activity. The samples were chemically analyzed for 129 commonly used pesticides and transformation products. Furthermore, the toxicity was investigated using in vitro bioassays in the water samples following liquid–liquid extraction. Endpoints included oxidative stress response (Nrf2 activity), estrogen receptor (ER) activity, and aryl hydrocarbon receptor (AhR) activity. The bioassays were performed with a final enrichment factor of 5 for the water samples. All bioassays were conducted at non-cytotoxic conditions. Results A total of 51 pesticides and transformation products were detected in the water samples. Most of the compounds were herbicides, followed by fungicides, insecticides and transformation products. The highest total pesticide concentration in an individual sample was 39 µg/L, and the highest median total concentration at a sample site was 1.1 µg/L. The largest number of pesticides was 31 in a single sample. We found that 3% of the water samples induced oxidative stress response, 23% of the samples activated the estrogen receptor, and 77% of the samples activated the aryl hydrocarbon receptor. Using Spearman correlation coefficients, a statistically significant correlation was observed between AhR and ER activities, and AhR activity was strongly correlated with oxidative stress in samples with a high AhR activity. Statistically significant relationships were observed between bioactivities and individual pesticides, although the relationships are probably not causal, due to the low concentrations of pesticides. Co-occurrence of non-identified chemical pollutants and naturally occurring toxic compounds may be responsible for the induced bioactivities. Conclusions This study demonstrated that integrated chemical analysis and bioanalysis can be performed in water samples following liquid/liquid extraction with a final enrichment factor of 5. AhR and ER activities were induced in water samples from agricultural areas. The activities were presumably not caused by the occurrence of pesticides, but induced by other anthropogenic and natural chemicals.