Whole genome sequencing identified a 16 kilobase deletion on ECA13 associated with distichiasis in Friesian horses.

BACKGROUND: Distichiasis, an ocular disorder in which aberrant cilia (eyelashes) grow from the opening of the Meibomian glands of the eyelid, has been reported in Friesian horses. These misplaced cilia can cause discomfort, chronic keratitis, and corneal ulceration, potentially impacting vision due to corneal fibrosis, or, if secondary infection occurs, may lead to loss of the eye. Friesian horses represent the vast majority of reported cases of equine distichiasis, and as the breed is known to be affected with inherited monogenic disorders, this condition was hypothesized to be a simply inherited Mendelian trait. RESULTS: A genome wide association study (GWAS) was performed using the Axiom 670 k Equine Genotyping array (MNEc670k) utilizing 14 cases and 38 controls phenotyped for distichiasis. An additive single locus mixed linear model (EMMAX) approach identified a 1.83 Mb locus on ECA5 and a 1.34 Mb locus on ECA13 that reached genome-wide significance (pcorrected = 0.016 and 0.032, respectively). Only the locus on ECA13 withstood replication testing (p = 1.6 × 10- 5, cases: n = 5 and controls: n = 37). A 371 kb run of homozygosity (ROH) on ECA13 was found in 13 of the 14 cases, providing evidence for a recessive mode of inheritance. Haplotype analysis (hapQTL) narrowed the region of association on ECA13 to 163 kb. Whole-genome sequencing data from 3 cases and 2 controls identified a 16 kb deletion within the ECA13 associated haplotype (ECA13:g.178714_195130del). Functional annotation data supports a tissue-specific regulatory role of this locus. This deletion was associated with distichiasis, as 18 of the 19 cases were homozygous (p = 4.8 × 10- 13). Genotyping the deletion in 955 horses from 54 different breeds identified the deletion in only 11 non-Friesians, all of which were carriers, suggesting that this could be causal for this Friesian disorder. CONCLUSIONS: This study identified a 16 kb deletion on ECA13 in an intergenic region that was associated with distichiasis in Friesian horses. Further functional analysis in relevant tissues from cases and controls will help to clarify the precise role of this deletion in normal and abnormal eyelash development and investigate the hypothesis of incomplete penetrance.

A missense mutation in damage-specific DNA binding protein 2 is a genetic risk factor for ocular squamous cell carcinoma in Belgian horses.

BACKGROUND: Belgian horses are commonly affected with ocular squamous cell carcinoma (SCC), the most common cancer of the equine eye. A missense mutation in damage-specific DNA binding protein 2 (DDB2 c.1013C>T, p.Thr338Met) has been established as a recessive genetic risk factor for ocular SCC in the Haflinger breed. A sample of Belgian horses with unknown SCC phenotype was shown to possess this variant at a similar frequency to the Haflinger breed. Retrospective studies indicate that chestnut coat colour may predispose to the development of SCC. OBJECTIVES: To determine if DDB2 c.1013C>T is a risk factor for ocular SCC in a strictly phenotyped sample of Belgian horses. To investigate associations between coat colour loci genotypes and ocular SCC. STUDY DESIGN: Retrospective and prospective case identification, genetic investigation. METHODS: Genomic DNA was isolated from blood, hair or formalin-fixed paraffin-embedded tissue from 25 Belgian horses with histologically confirmed ocular SCC and 18 unaffected Belgian horses. Association testing of 34 single nucleotide variants from 11 genomic loci and genotyping for DDB2 c.1013C>T and coat colour alleles were performed. Exons of DDB2 were sequenced in four cases and two controls. Associations were analysed by Chi-square or Fisher's exact tests and relative risk was calculated. RESULTS: Homozygosity for DDB2 c.1013C>T was significantly associated with ocular SCC (P = 7.4 × 10-7 ). Seventy-six per cent of affected horses were homozygous for the variant. Relative risk for homozygous horses developing SCC was 4.0 (P = 1.0 × 10-4 ). Sequencing DDB2 did not identify a variant more concordant with disease phenotype. An association between disease and coat colour loci was not identified. MAIN LIMITATIONS: Phenotyping was determined at a single timepoint. Each included horse genotyped as chestnut, so association with this MC1R variant could not be investigated. CONCLUSIONS: A missense variant, DDB2 c.1013C>T, p.Thr338Met, is a risk factor for ocular SCC in Belgian horses. A genetic risk test is commercially available.

Genetic investigation of equine recurrent uveitis in Appaloosa horses.

Equine recurrent uveitis (ERU) is characterized by intraocular inflammation that often leads to blindness in horses. Appaloosas are more likely than any other breed to develop insidious ERU, distinguished by low-grade chronic intraocular inflammation, suggesting a genetic predisposition. Appaloosas are known for their white coat spotting patterns caused by the leopard complex spotting allele (LP) and the modifier PATN1. A marker linked to LP on ECA1 and markers near MHC on ECA20 were previously associated with increased ERU risk. This study aims to further investigate these loci and identify additional genetic risk factors. A GWAS was performed using the Illumina Equine SNP70 BeadChip in 91 horses. Additive mixed model approaches were used to correct for relatedness. Although they do not reach a strict Bonferroni genome-wide significance threshold, two SNPs on ECA1 and one SNP each on ECA12 and ECA29 were among the highest ranking SNPs and thus warranted further analysis (P = 1.20 × 10-5 , P = 5.91 × 10-6 , P = 4.91 × 10-5 , P = 6.46 × 10-5 ). In a second cohort (n = 98), only an association with the LP allele on ECA1 was replicated (P = 5.33 × 10-5 ). Modeling disease risk with LP, age and additional depigmentation factors (PATN1 genotype and extent of roaning) supports an additive role for LP and suggests an additive role for PATN1. Genotyping for LP and PATN1 may help predict ERU risk (AUC = 0.83). The functional role of LP and PATN1 in ERU development requires further investigation. Testing samples across breeds with leopard complex spotting patterns and a denser set of markers is warranted to further refine the genetic components of ERU.

Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project.

The Functional Annotation of Animal Genomes (FAANG) project aims to identify genomic regulatory elements in both sexes across multiple stages of development in domesticated animals. This study represents the first stage of the FAANG project for the horse, Equus caballus. A biobank of 80 tissue samples, two cell lines and six body fluids was created from two adult Thoroughbred mares. Ante-mortem assessments included full physical examinations, lameness, ophthalmologic and neurologic evaluations. Complete blood counts and serum biochemistries were also performed. At necropsy, in addition to tissue samples, aliquots of serum, ethylenediaminetetraacetic acid (EDTA) plasma, heparinized plasma, cerebrospinal fluid, synovial fluid, urine and microbiome samples from all regions of the gastrointestinal and urogenital tracts were collected. Epidermal keratinocytes and dermal fibroblasts were cultured from skin samples. All tissues were grossly and histologically evaluated by a board-certified veterinary pathologist. The results of the clinical and pathological evaluations identified subclinical eosinophilic and lymphocytic infiltration throughout the length of the gastrointestinal tract as well as a mild clinical lameness in both animals. Each sample was cryo-preserved in multiple ways, and nuclei were extracted from selected tissues. These samples represent the first published systemically healthy equine-specific biobank with extensive clinical phenotyping ante- and post-mortem. The tissues in the biobank are intended for community-wide use in the functional annotation of the equine genome. The use of the biobank will improve the quality of the reference annotation and allow all equine researchers to elucidate unknown genomic and epigenomic causes of disease.

Genetic risk for squamous cell carcinoma of the nictitating membrane parallels that of the limbus in Haflinger horses.

Squamous cell carcinoma (SCC) is the most common cancer affecting the equine eye, with a higher incidence documented in Haflinger horses. Recently, a missense variant in the gene damage specific DNA binding protein 2 (DDB2, p.Thr338Met) on ECA12 was identified as a risk factor for the development of limbal SCC in Haflinger horses. SCC also occurs on the nictitating membrane; therefore, investigating the role of this missense variant in nictitating membrane SCC is warranted. In this study, a common ancestor was identified among Haflinger horses affected with limbal SCC or with nictitating membrane SCC, thus supporting a recessive risk factor for the development of cancer at both ocular locations. Analysis of genotype data from Haflinger horses with and without nictitating membrane SCC revealed that the same region on ECA12 associated with limbal SCC was also associated with nictitating membrane SCC (P < 2.04 × 10-5 ). Fine mapping of this locus using 25 cases and 49 controls supported the hypothesis that DDB2:c.1013C>T, p.Thr338Met, is a risk factor for nictitating membrane SCC, as 88% of our cases were homozygous for this variant and no other polymorphism was more strongly associated (P = 4.13 × 10-14 ). These data indicate that the genetic risk is the same for the development of both limbal and nictitating membrane SCC in Haflinger horses and validates utilization of genetic testing of the DDB2 variant for both clinical management and the guidance of mating decisions.

Effects of 0.2% brimonidine and 0.2% brimonidine-0.5% timolol on intraocular pressure and pupil size in normal equine eyes.

BACKGROUND: Brimonidine is an α2 -adrenergic agonist that decreases aqueous humour production and may increase uveoscleral outflow. It has not been evaluated in normal or glaucomatous equine eyes. OBJECTIVES: To evaluate the efficacy and safety of brimonidine in lowering intraocular pressure (IOP), alone and in conjunction with timolol, as a treatment for equine glaucoma by comparing IOP in normal equine eyes treated with brimonidine and brimonidine-timolol, respectively, with IOP in control eyes. STUDY DESIGN: A balanced crossover design with 16 horses receiving one of two treatments, brimonidine and brimonidine-timolol, during each of two 10-day study phases, was used. Four horses were randomly assigned to each of four combinations of treated eye (right or left) and drug order within the two 10-day study phases (brimonidine first or brimonidine-timolol first). METHODS: Pupil size and conjunctival hyperaemia were assessed twice per day and IOP was measured three times per day using rebound tonometry in both eyes of 16 normal horses throughout two 10-day study periods (brimonidine and brimonidine-timolol) separated by an 18-day washout period. One eye of each horse was treated with brimonidine or brimonidine-timolol and the opposite eye was treated with balanced salt solution (BSS). RESULTS: There were no adverse effects and no significant changes in pupil size in normal equine eyes treated with brimonidine or brimonidine-timolol. Average IOP in normal equine eyes treated with brimonidine (25.6 mmHg) was statistically higher than in eyes treated with brimonidine-timolol (24.6 mmHg) or BSS (24.5 mmHg). However, IOP differences were of ≤1 mmHg and thus not clinically important. MAIN LIMITATIONS: Horses with normal eyes may not be as sensitive to the IOP-lowering effects of treatment as horses with glaucoma. CONCLUSIONS: Brimonidine and brimonidine-timolol are well tolerated in normal horses but do not decrease IOP.

Combined keratectomy, strontium-90 irradiation and permanent bulbar conjunctival grafts for corneolimbal squamous cell carcinomas in horses (1990-2002): 38 horses.

OBJECTIVE: The purpose of this study was to evaluate the effectiveness of postoperative beta-irradiation with strontium-90 as an adjunctive treatment to superficial keratectomy and permanent bulbar conjunctival graft for removal of equine corneolimbal squamous cell carcinoma (SCC), in decreasing recurrence rate. STUDY: The retrospective case study included 38 horses diagnosed and treated for SCC of the eye that involved the limbus and/or cornea. The patients were treated between 1990 and 2002, with strontium-90 irradiation immediately after corneal and conjunctival graft surgery. Recurrence was defined as the postoperative and postirradiation regrowth of SCC in the same site and globe that was previously treated. RESULTS: The Appaloosa was the most commonly represented breed and horses that had more than one base coat color represented the majority of the cases (53%). The coat colors of white, chestnut/sorrel and gray were the most commonly represented colors of the horses treated. Eight horses (21%) could not be assessed for tumor recurrence due to lack of two or more post-treatment examinations, and another horse was enucleated 6 days postoperatively due to progressive corneal ulceration. Twenty-four horses (63% of the entire study population; 83% of the followed cases) had a mean +/- SD of 1754 +/- 1319 days without tumor recurrence, ranging from 14 days to 5110 days. Five horses (13% of the entire study population; 17% of the assessed horses) had tumor recurrence at a mean +/- SD of 449 +/- 339 days with a range of 29 days to 900 days. For the five recurrences, treatment included local excision (n = 1), enucleation (n = 2), and additional strontium-90 therapy (n = 3). CONCLUSIONS: The combination of superficial keratectomy, beta-irradiation and permanent bulbar conjunctival grafts for limbal, corneal or corneolimbal SCC in horses is effective in at least 83% of the horses. Recurrence occurred in about 17% of the horses. Multiple biannual re-examinations are recommended to observe for tumor recurrence.

Profiles of matrix metalloproteinase activity in equine tear fluid during corneal healing in 10 horses with ulcerative keratitis.

OBJECTIVE: Levels of tear film matrix metalloproteinases (MMPs) activity are significantly elevated in horses with ulcerative keratitis and contribute to the excessive breakdown of stromal collagen. Changes in the amount of proteolytic activity in horse tear film during corneal healing and stromal remodeling have not yet been reported, but we hypothesize they should decrease. In the present study we analyzed serial tear fluid from horses with ulcerative keratitis to identify any changes in MMP activity during corneal healing and stromal remodeling. PROCEDURES: Samples of tear fluid were obtained from both eyes of 10 horses with ulcerative keratitis on the day of admission (day 1) at the hospital and then at various time points until complete healing of the cornea. Tear film MMP2 and MMP9 activity was determined by quantitative gelatin zymography. In all cases medical treatment included topical applications of equine serum, antibiotics, atropine and systemic administration of anti-inflammatory drugs. Surgical procedures were performed in several cases on day 2 in addition to the medical treatment. RESULTS: The mean total MMP activity (+/- SD) measured in relative standard units (RSU) in the tear fluid of the ulcerated eye (2.44 +/- 1.44) of the 10 horses was significantly higher than the mean in the contralateral eye (0.81 +/- 0.68) (P = 0.006), on the day of admission at the VMTH. The mean MMP activity in these ulcerated eyes significantly decreased (-82.4%) between the first day of admission and the day when the ulcer had completely healed (P = 0.0002). The activity level in the healed eye (0.43 +/- 0.17) was not significantly different to the one in the contralateral eye (0.36 +/- 0.18) on the day of complete corneal healing (P = 0.374). The level of MMP activity in the contralateral eye also decreased from 0.81 +/- 0.68-0.36 +/- 0.18 but this decrease (56%) was not significant (P = 0.069). CONCLUSIONS: Ulcerative keratitis in horses is associated with initially high levels of tear film proteolytic activity that decrease as the ulcers heal. The success of medical and surgical treatment of the corneal ulcers is reflected by the enzyme activity in tears. In horses successful treatment does lead to a rapid reduction in tear film proteolytic activity that corresponded with the improvement in the clinical signs of corneal ulceration. Measurement of MMP activity in the tear film might represent a way to monitor the progression of corneal healing in horses with ulcerative keratitis.

Connective tissue growth factor in tear film of the horse: detection, identification and origin.

BACKGROUND: Healing of corneal ulcers in horses is often associated with profound corneal stromal fibrosis and scar formation resulting in visual impairment. Connective tissue growth factor (CTGF) is a fibrogenic cytokine involved in wound healing and scarring. The purpose of this study was to determine whether CTGF was present in the tear fluid of normal horse eyes and the eyes of horses with corneal ulcers in order to evaluate the role of CTGF in corneal wound healing and corneal scar formation. METHODS: Tear fluid samples were collected from 65 eyes of 44 horses; 32 samples from normal eyes, 21 samples from eyes with corneal ulceration, and 12 samples from the unaffected contralateral eyes of horses with ulcers. CTGF levels in the tears were determined by enzyme immunoassay using goat IgG against human CTGF. Antigenetic similarity of human and horse CTGF was established in a bio-equivalence assay. The identity of horse CTGF was confirmed by western blot. Lacrimal and nictitating membrane glands were investigated by immunohistochemistry in the attempt to clarify the origin of tear fluid CTGF. RESULTS: CTGF was detected in tear film of 23 normal unaffected eyes (72%) and 8 normal contralateral eyes (67%), with the mean CTGF levels (+/- SEM) being 51.5+/-19.2 and 13.4+/-3.9 ng/ml respectively. CTGF was found in 8 eyes with corneal ulcers (38%) with the mean CTGF concentration of 26.3+/-14.8 ng/ml. Western blot identified the protein detected as CTGF. The identification of CTGF in lacrimal glands suggests a major role of these glands in the presence of CTGF in tears. CONCLUSIONS: CTGF is present in horse tear fluid and derives, at least partly, from the lacrimal gland. Equine CTGF has strong antigenic similarity with human CTGF. Corneal disease leads to a decrease of CTGF concentrations in tears. The possible role of CTGF in the healing process of ocular surface requires further investigation.

Changes in antibiotic resistance in equine bacterial ulcerative keratitis (1991-2000): 65 horses.

OBJECTIVE: To document changes in antibiotic resistance of organisms in cases of equine bacterial ulcerative keratitis over a 10-year time period. DESIGN: A retrospective study. PARTICIPANTS: Medical records of equine patients with bacterial ulcerative keratitis seen at the University of Florida's VMTH for the years 1991-2000 were reviewed. MATERIALS AND METHODS: All cases of equine bacterial ulcerative keratitis for the above mentioned years were examined. Bacterial isolates were identified and subjected to Kirby-Bauer disc diffusion method sensitivity tests. Antibiotics used in the sensitivity tests included bacitracin, ampicillin, gentamicin, chloramphenicol, polymyxin B, trimethoprim-sulfa, neomycin, kanamycin, carbenicillin, tobramycin and enrofloxacin. RESULTS: A total of 65 bacterial isolates were subjected to sensitivity testing. Of these isolates, Pseudomonas aeruginosa accounted for 14 of the bacterial isolates (22%), Streptococcus equi subspecies zooepidemicus accounted for 13 of the bacterial isolates (20%), and Staphylococcus aureus accounted for four of the isolates (6%). A statistically significant increase in resistance of Pseudomonas aeruginosa isolates to the antibiotics gentamicin and tobramycin was found between the isolates from 1992 to 1998 and those from 1999 to 2000. An increase in resistance of Streptococcus equi subspecies zooepidemicus to gentamicin was found between the isolates from 1993 to 1997 and those from 1998 to 2000. CONCLUSIONS: Streptococcus equi subspecies zooepidemicus and Pseudomonas aeruginosa were the most common organisms isolated from cases of equine bacterial keratitis referred to the University of Florida's VMTH for the years 1991-2000. There appears to be an increase in resistance of Streptococcus equi subspecies zooepidemicus to gentamicin over the past 10 years. In addition, there is a significant increase in resistance of Pseudomonas aeruginosa to both gentamicin and tobramycin over the same time period.

Causal status as a determinant of feature centrality.

One of the major problems in categorization research is the lack of systematic ways of constraining feature weights. We propose one method of operationalizing feature centrality, a causal status hypothesis which states that a cause feature is judged to be more central than its effect feature in categorization. In Experiment 1, participants learned a novel category with three characteristic features that were causally related into a single causal chain and judged the likelihood that new objects belong to the category. Likelihood ratings for items missing the most fundamental cause were lower than those for items missing the intermediate cause, which in turn were lower than those for items missing the terminal effect. The causal status effect was also obtained in goodness-of-exemplar judgments (Experiment 2) and in free-sorting tasks (Experiment 3), but it was weaker in similarity judgments than in categorization judgments (Experiment 4). Experiment 5 shows that the size of the causal status effect is moderated by plausibility of causal relations, and Experiment 6 shows that effect features can be useful in retrieving information about unknown causes. We discuss the scope of the causal status effect and its implications for categorization research.

Molecular basis of feline beta-glucuronidase deficiency: an animal model of mucopolysaccharidosis VII.

A family of domestic cats was found that exhibited clinical and biochemical abnormalities consistent with mucopolysaccharidosis VII, an autosomal recessive lysosomal storage disorder caused by beta-glucuronidase deficiency. beta-Glucuronidase activity was undetectable in affected cat fibroblasts and restored by retroviral gene transfer of rat beta-glucuronidase cDNA. beta-Glucuronidase mRNA was normal in affected cat testis by Northern blot analysis. Normal feline beta-glucuronidase cDNA was cloned and characterized, and amplified from affected cat fibroblasts by reverse transcription coupled polymerase chain reaction. There was a G-to-A transition in the affected cat cDNA that predicted an E351K substitution, destroyed a BssSI site, and eliminated GUSB enzymatic activity in expression studies. Multiple species comparison and the crystal structure of human beta-glucuronidase indicated that E351 is a highly conserved residue most likely essential in maintenance of the enzyme's conformation. BssSI digestion of polymerase chain reaction products amplified from genomic DNA indicated that affected cats were homozygous and cats with half-normal beta-glucuronidase activity were heterozygous for the missense mutation. Carriers identified in this manner produced affected kittens in prospective breedings, and a feline MPS VII breeding colony has been established.

Alignment and category learning.

Recent research shows that similarity comparisons involve an alignment process in which features are placed into correspondence. In 6 studies, the authors showed that alignment is involved in category learning as well. Within a category, aligned matches (feature matches occurring on the same dimension) facilitate learning more than nonaligned matches do (matches on different dimensions), although nonaligned matches still facilitate learning relative to nonmatches. Analogously, feature matches that cross category boundaries hurt learning more if they occur on the same versus a different dimension, and cross-category feature matches on different dimensions hurt learning relative to nonmatching features. Representational assumptions of category learning models must be modified to account for the differences between aligned and nonaligned feature matches.

Structural alignment in induction and similarity.

According to a structural alignment view, representational commonalities contribute to the perception of similarity, whereas nonshared attributes related to commonalities are candidate inferences in induction. This view was tested in 5 experiments. Novel animal pairs varying in the number of attributes and relations they shared were used to assess the relationship between induction and similarity. In Experiments 1 and 2, the number of shared attributes and the presence of 2 kinds of causal relations between attributes varied. Shared attributes increased both similarity and inductive strength judgments. Shared causal relations, possessed by both animals, influenced perceived similarity, but binding causal relations, which connected a shared attribute to a candidate inference in the induction task, were important for inductive strength. In Experiments 3-5, these results were extended through use of a noncausal relation and familiar animal categories.

Induction and category coherence.

In studies of category formation, subjects rarely construct family resemblance categories. Instead, they divide objects into categories using a single dimension. This is a puzzling result given the widely accepted view that natural categories are organized in terms of a family resemblance principle. The observation that natural categories support inductive inferences is used here to test the hypothesis that family resemblance categories would be constructed if stimuli were first used to generate inductive inferences. In two experiments, subjects answered either induction questions, which made interproperty relationships more salient, or frequency questions, which required information only about individual properties, before they performed a sorting task. Subjects were likely to produce family resemblance sorts if they had first answered induction questions but not if they had answered frequency questions.

Memory-based automaticity in the discrimination of visual numerosity.

In the development of memory-based models of automaticity, it is crucial to specify the nature of the memory representation. Seven experiments with 94 students use a counting task to determine whether a feature (i.e., identity, color, or orientation) is explicitly represented in memory. It is assumed that the degree of transfer to a pattern differing on one feature is determined by that feature's importance in supporting skilled performance. Experiment 1 determined the practice necessary to obtain automaticity. In Experiments 2a, 3a, and 4a, which investigated the nature of the representation after extended practice, changing neither the identity nor color of elements had strong effects on transfer, but changing pattern orientation did impair memory retrieval, thus suggesting that for the counting task, pattern orientation is more important than element identity or color. Experiments 2b, 3b, and 4b replicated these results after limited practice.