Use of principle component analysis to quantitatively score the equine metabolic syndrome phenotype in an Arabian horse population

Characterisation of phenotypic patterns in equine exercise-associated myopathies

BACKGROUND

Equine exercise-associated myopathies are prevalent, clinically heterogeneous, generally idiopathic disorders characterised by episodes of myofibre damage that occur in association with exercise. Episodes are intermittent and vary within and between affected horses and across breeds. The aetiopathogenesis is often unclear; there might be multiple causes. Poor phenotypic characterisation hinders genetic and other disease analyses.

OBJECTIVES

The aim of this study was to characterise phenotypic patterns across exercise-associated myopathies in horses.

STUDY DESIGN

Historical cross-sectional study, with subsequent masked case-control validation study.

METHODS

Historical clinical and histological features from muscle samples (n = 109) were used for k-means clustering and validated using principal components analysis and hierarchical clustering. For further validation, a blinded histological study (69 horses) was conducted comparing two phenotypic groups with selected controls and horses with histopathological features characterised by myofibrillar disruption.

RESULTS

We identified two distinct broad phenotypes: a non-classic exercise-associated myopathy syndrome (EAMS) subtype was associated with practitioner-described signs of apparent muscle pain (p < 0.001), reluctance to move (10.85, p = 0.001), abnormal gait (p < 0.001), ataxia (p = 0.001) and paresis (p = 0.001); while a non-specific classic RER subtype was not uniquely associated with any particular variables. No histological differences were identified between subtypes in the validation study, and no identifying histopathological features for other equine myopathies identified in either subtype.

MAIN LIMITATIONS

Lack of an independent validation population; small sample size of smaller identified subtypes; lack of positive control myofibrillar myopathy cases; case descriptions derived from multiple independent and unblinded practitioners.

CONCLUSIONS

This is the first study using computational clustering methods to identify phenotypic patterns in equine exercise-associated myopathies, and suggests that differences in patterns of presenting clinical signs support multiple disease subtypes, with EAMS a novel subtype not previously described. Routine muscle histopathology was not helpful in sub-categorising the phenotypes in our population.

Geometric morphometrics of face profile across horse breeds and within Arabian horses

Horse traits under selection are largely quantitative and affected by multiple genes. Horse face shape is an example of a continuous trait, which due to the reliance on observational assessments, is classified into; "dished", "straight", and "roman-nosed". This categorization is often inadequate to convey the full spectrum of the face shape variation especially for genetic studies. The first objective of the current study was to use geometric morphometric methods to quantitatively phenotype face shapes and examine its variation across horse breeds. The second objective was to analyze the face shape variation within Arabian horses since face shape is (1) favored, valued, and genetically selected in certain lineages (e.g. Egyptian), (2) is evaluated by registries and scored in shows, and (3) in its extreme forms pose health concerns. We digitized landmarks on lateral profile photos, particularly on the dorsal curvature of the rostrum, and subjected these landmarks to Generalized Procrustes Analysis to generate independent shape and size variables which were statistically compared across breeds and within Arabians. Horse breeds varied in nasal curvature, ranging from extremely concave to extremely convex, with over 70 % of horse breeds exhibiting intermediate concavity (i.e., straight profile). Interestingly, Arabian horses possessed the highest diversity in face profile and individuals clustered into three distinct shape sub-groups (one dished and two straight profile clusters). Our quantitative phenotyping method can be the basis of future genetic studies of facial profile within Arabian lineages as a favored traits and potentially manage its extreme forms as a likely genetic disease.

Visual Assessment of Adiposity in Elite Hunter Ponies

Obesity is a critical problem in the equine industry, with ponies being at particularly high risk of developing obesity-related conditions such as metabolic syndrome and laminitis. The purpose of this study was to estimate the level of adiposity in an elite level of competitive show ponies, and to determine if adiposity was related to performance based on their model score (judged on conformation and appearance). Two researchers visually evaluated the body condition score (BCS) and cresty neck score (CNS) of 377 ponies at a national hunter competition. Thirty five percent of the ponies in the competition were considered obese, with BCS scores of 7 or higher. Mean BCS of the ponies was 6.7 ± 0.6 with a range of 5.25 - 8.25 and mean CNS was 2.8 ± 0.6, with a range of 1.75 - 4.5. Medium ponies had higher BCS (P<0.0001) and higher CNS (P=0.015) than the large ponies. There was a tendency for a relationship between body condition score and the model score in all ponies (r = 0.08; P = 0.059), and this was stronger within the large ponies (r =0.20; P <0.01). These findings show that elite competition ponies are dangerously overweight and that adiposity may influence performance in a judged event. This is of grave concern to the horse industry and needs to be addressed.

Identification of a Four-Gene Signature for Diagnosing Paediatric Sepsis

Aim

Early diagnosis of paediatric sepsis is crucial for the proper treatment of children and reduction of hospitalization and mortality. Biomarkers are a convenient and effective method for diagnosing any disease. However, huge differences among the studies reporting biomarkers for diagnosing sepsis have limited their clinical application. Therefore, in this study, we aimed to evaluate the diagnostic value of key genes involved in paediatric sepsis based on the data of the Gene Expression Omnibus database.

Methods

We used the GSE119217 dataset to identify differentially expressed genes (DEGs) between patients with and without paediatric sepsis. The most relevant gene modules of paediatric sepsis were screened through the weighted gene coexpression network analysis (WGCNA). Common genes (CGs) were found between DEGs and WGCNA. Genes with a potential diagnostic value in paediatric sepsis were selected from the CGs using least absolute shrinkage and selection operator regression and support vector machine recursive feature elimination. The principal component analysis, receiver operating characteristic curves, and C-index were used to verify the diagnostic value of the identified genes in six other independent sepsis datasets. Subsequently, a meta-analysis of the selected genes was performed to evaluate the value of these genes as biomarkers in paediatric sepsis.

Results

A total of 41 CGs were selected from the GSE119217 dataset. A four-gene signature composed of ANXA3, CD177, GRAMD1C, and TIGD3 effectively distinguished patients with paediatric sepsis from those in the control group. The signature was verified using six other independent datasets. In addition, the meta-analysis results showed that the pooled sensitivity, specificity, and area under the curve values were 1.00, 0.98, and 1.00, respectively.

Conclusion

The four-gene signature can be used as new biomarkers to distinguish patients with paediatric sepsis from healthy individuals.

Pathogenic genetic variations of C. acnes are associated with clinically relevant orthopedic shoulder infections

Many surgeons continue to face the clinical dilemma of interpreting a positive aspiration or unexpected positive Cutibacterium acnes (C. acnes) culture. There are factors that complicate the interpretation of positive cultures including variations in both frequency of false positive cultures and virulence properties. As indices of virulence, hemolytic strains, from previously confirmed clinically infected shoulders, were compared with non-hemolytic isolates determined to be contaminants, by RNA-sequencing (RNA-Seq). Six C. acnes isolates from patients who underwent revision total shoulder arthroplasty (TSA) were identified based on previously described infection criteria. Three C. acnes isolates from each group underwent RNA-Seq. Differential gene expression analysis, principal component analysis (PCA), and heatmap analysis were used to determine the gene variation and patterning between the definite infection and probable contaminant isolates. Differential gene expression analysis identified genes that were differentially expressed between the isolates classified as definite infection and isolates classified as probable contaminants. PCA using a 500 gene subset of identified genes was able to find combinations of these genes that separated out the definite infection and probable contaminants isolates. The heatmap demonstrated similar gene expression in the three Definite Infections isolates, and significantly different expression when compared with the probable contaminant isolates. Clinical significance: C. acnes revision TSA isolates classified as definite infection and probable contaminant demonstrated a similar gene expression pattern to each respective group and different gene expression pattern when compared between groups. These findings indicate distinct differences in C. acnes strains associated with clinically relevant orthopedic TSA infections.

Metabogenomics reveals four candidate regions involved in the pathophysiology of Equine Metabolic Syndrome

An analogous condition to human metabolic syndrome, Equine Metabolic Syndrome (EMS) is defined by several clinical signs including obesity, hyperinsulinemia, and peripheral insulin dysregulation (ID). Affected horses may also exhibit hypertension, hyperlipemia and systemic inflammation. Measures of ID typically comprise the gold-standard for diagnosis in veterinary care. Yet, the dynamic nature of insulin homeostasis and complex procedures of typical assays make accurate quantification of ID and EMS challenging. This work aimed to investigate new strategies for identification of biochemical markers and correlated genes in EMS. To quantify EMS risk within this population, we utilized a composite score derived from nine common diagnostic variables. We applied a global liquid chromatography/mass spectroscopy approach (HPLC/MS) to whole plasma collected from 49 Arabian horses, resulting in 3392 high-confidence features and identification of putative metabolites in public databases. We performed a genome wide association analysis with genotypes from the 670k Affymetrix Equine SNP array utilizing EMS-correlated metabolites as phenotypes. We discovered four metabolite features significantly correlated with EMS score (P < 1.474 × 10^-5). GWAs for these features results (P = 6.787 × 10^-7, Bonferroni) identified four unique candidate regions (r² > 0.4) containing 63 genes. Significant genomic markers capture 43.52% of the variation in the original EMS score phenotype. The identified genomic loci provide insight into the pathways controlling variation in EMS and the origin of genetic predisposition to the condition. Rapid, feasible and accurate diagnostic tools derived from metabogenomics can be translated into measurable benefits in the timeline and quality of preventative management practices to preserve health in horses.

The cresty neck score is an independent predictor of insulin dysregulation in ponies

Generalized obesity, regional adiposity, hyperinsulinemia and hypertriglyceridemia are all potential indicators of equine metabolic syndrome (EMS). This study aimed to assess the relationship between morphometric measurements of body condition and metabolic hormone concentrations in ponies, with and without a neck crest or generalised obesity. Twenty-six ponies were assigned a body condition score (BCS) and cresty neck score (CNS). Height, girth, and neck measurements were taken. An oral glucose test (OGT; 0.75g dextrose/kg BW) was performed and blood samples collected prior to and 2 hours post dosing. Basal blood samples were analysed for blood glucose, serum insulin, triglyceride and leptin, and plasma HMW adiponectin concentrations. Post-prandial samples were analysed for serum insulin concentration. The ponies were grouped as having a) a normal to fleshy body status (BCS ≤7 and CNS ≤2; n = 10); b) having a high CNS, but without generalised obesity (BCS ≤7 and CNS ≥3; n = 11), or c) being obese (BCS ≥8 and CNS ≥1; n = 5). Responses to the OGT indicated that both normal and insulin-dysregulated ponies were included in the cohort. Post-prandial serum insulin was positively associated with CNS (P<0.035) and ponies with a CNS ≥ 3 had 5 times greater odds of being insulin-dysregulated. The high CNS group had a greater insulin response to the OGT than those in the normal/fleshy group (P = 0.006), whereas obese ponies did not differ from the other two groups. Basal HMW adiponectin was negatively correlated with post-prandial insulin concentrations (r = -0.5, P = 0.009), as well as being decreased in the group with a high CNS, compared to the obese group (P = 0.05). Cresty neck score was more predictive of insulin dysregulation than BCS, and this may be relevant to the diagnosis of EMS. Adiponectin may also be a measure of insulin dysregulation that is independent of body condition.