A novel mutation in TTC8 is associated with progressive retinal atrophy in the golden retriever
© Downs et al.; licensee BioMed Central Ltd. 2014
Received: 27 November 2013
Accepted: 14 January 2014
Published: 16 April 2014
Generalized progressive retinal atrophy (PRA) is a group of inherited eye diseases characterised by progressive retinal degeneration that ultimately leads to blindness in dogs. To date, more than 20 different mutations causing canine-PRA have been described and several breeds including the Golden Retriever are affected by more than one form of PRA. Genetically distinct forms of PRA may have different clinical characteristics such as rate of progression and age of onset. However, in many instances the phenotype of different forms of PRA cannot be distinguished at the basic clinical level achieved during routine ophthalmoscopic examination. Mutations in two distinct genes have been reported to cause PRA in Golden Retrievers (prcd-PRA and GR_PRA1), but for approximately 39% of cases in this breed the causal mutation remains unknown.
A genome-wide association study of 10 PRA cases and 16 controls identified an association on chromosome 8 not previously associated with PRA (praw = 1.30×10-6 and corrected with 100,000 permutations, pgenome = 0.148). Using haplotype analysis we defined a 737 kb critical region containing 6 genes. Two of the genes (TTC8 and SPATA7) have been associated with Retinitis Pigmentosa (RP) in humans. Using targeted next generation sequencing a single nucleotide deletion was identified in exon 8 of the TTC8 gene of affected Golden Retrievers. The frame shift mutation was predicted to cause a premature termination codon. In a larger cohort, this mutation, TTC8 c.669delA, segregates correctly in 22 out of 29 cases tested (75.9%). Of the PRA controls none are homozygous for the mutation, only 3.5% carry the mutation and 96.5% are homozygous wildtype.
Our results show that PRA is genetically heterogeneous in one of the world’s numerically largest breeds, the Golden Retriever, and is caused by multiple, distinct mutations. Here we discuss the mutation that causes a form of PRA, that we have termed PRA2, that accounts for approximately 30% of PRA cases in the breed. The genetic explanation for approximately 9% of cases remains to be identified. PRA2 is a naturally occurring animal model for Retinitis Pigmentosa, and potentially Bardet-Biedl Syndrome.
Progressive retinal atrophy (PRA) is a group of inherited eye disorders that occur in many different dog breeds. Each form of PRA shows a simple pattern of mendelian inheritance, and is due to a mutation in one gene. However, over 20 different PRA-causing mutations have now been identified in a number of different genes. Some breeds, including Golden Retrievers (GR), may have more than one genetic form of PRA.
Canine PRA is considered to be the equivalent of Retinitis Pigmentosa (RP), which is a group of inherited human eye diseases.
This paper has identified a gene called TTC8 that is associated with PRA in GR. Interestingly the human TTC8 gene has previously been associated with RP. There is a one DNA base deletion in the gene which results in a shorter than normal protein to be made by the faulty version of the gene.
All the cases in this study were genetically screened for the other two known mutations for PRA in GR, and none were homozygous (two copies) for either of those mutations.
The gene was first identified by whole genome scanning 10 cases and 16 controls. A single mutation was identified in the gene by DNA sequencing, and it was confirmed by screening a larger number of dogs.
In animals inherited and progressive retinal diseases are commonly referred to as progressive retinal atrophy (PRA), which is characterised by a progressive bilateral retinal degeneration resulting in loss of vision. In typical PRA rod photoreceptor responses are lost first followed by cone photoreceptor responses . Fundus changes observed in PRA are bilateral and symmetrical and include tapetal hyper-reflectivity in the early stages followed by vascular attenuation, pigmetary changes and atrophy of the optic nerve head in the later stages of disease . Numerous, genetically distinct, forms of PRA have been documented in more than 100 dog breeds and while they exhibit similar clinical signs, the aetiology, age of onset and rate of progression may vary both between and within breeds. While a particular mutation (and corresponding form of PRA) may be shared by multiple breeds, due to the population structure of the domestic dog most PRA-affected dogs within a single breed are expected to share the same mutation. At least 20 disease-causing mutations have so far been associated with PRA. Most of them are autosomal recessive diseases but there are examples of X-linked as well as dominant PRA-disorders in dogs (for review see ). However, the causative mutation for many forms of PRA remains undefined. PRA is considered the veterinary equivalent of Retinitis Pigmentosa (RP), which is the collective name for a group of inherited human retinal disorders that leads to progressive loss of vision in approximately 1 in 4000 people [4–6]. Rod photoreceptor cells are predominantly affected and therefore clinical symptoms typically include night blindness and loss of peripheral vision. With disease progression the cones also degenerate resulting in central vision loss and eventually complete blindness is possible. To date, more than 192 genes have been shown to cause a wide spectrum of human retinal disease, including RP . Mutations in these genes currently only account for approximately 30% of autosomal recessive RP cases . RP is also a major component of a number of systemic diseases including Bardet-Biedl Syndrome (BBS).
Canine diseases have already proved valuable natural models for the study of many varied human conditions such as cardiac conotruncal malformations , myotubular myopathy  and hereditary retinopathies such as Leber congenital amaurosis (LCA) and achromatopsia [11, 12]. Further to this, canine models for human eye diseases have proved invaluable in gene-therapy studies, most notably the canine model of LCA associated with RPE65 [13–17].
Most PRA cases in the Golden Retriever (GR) are clinically indistinguishable from PRA cases of other breeds. The mode of inheritance appears from pedigree information to be consistent with autosomal recessive and the age of diagnosis is most commonly at approximately 5 years of age . We previously identified a form of PRA, GR_PRA1, caused by a mutation in the SLC4A3 gene that accounts for the majority (61%) of cases of PRA in the GR breed . In the closely related Labrador Retriever (LR) breed, a mutation in the PRCD (progressive rod cone degeneration) gene can explain the majority of PRA cases . The PRCD-mutation has also been associated with PRA in a small number of PRA-affected GRs .
Here we report the identification of a single base deletion in the TTC8 gene, which is one of seven genes encoding a protein complex (BBSome) that has been proposed to promote ciliary membrane biogenesis and to be an important factor in the development of Bardet-Biedl Syndrome . The deletion causes a shift in the reading frame resulting in a subsequent premature termination codon. We present evidence that this putative loss-of-function mutation represents a third susceptibility locus for PRA, known hereafter as GR_PRA2, in Golden Retrievers.
PRCD and PRA1 screening
To exclude the possibility that the affected GRs were positive for the mutations already known to cause prcd-PRA or GR_PRA1, all 29 GR cases in our study were screened for the previously described, autosomal recessive PRCD  and GR_PRA1 mutations . None of the affected GRs were homozygous for either of these mutations. A single individual was heterozygous for the PRCD mutation and five were heterozygous for the GR_PRA1 mutation, while the remaining 23 were homozygous for the wildtype (normal) alleles at both loci.
Genome-wide association mapping
Haplotype and homozygosity analysis
All of the coding sequence of the SPATA7 and TTC8 retinal transcripts from a healthy dog of unknown age or breed were successfully sequenced, confirming that both genes are transcribed in the canine retina. The presence of the SPATA7 variant, c.A1378G, in the healthy retinal mRNA transcript was surprising. While there is a chance the tissue could have come from a dog that had not yet developed PRA, we think it unlikely. The location of this variant was only modestly conserved at the DNA level and poorly conserved at the amino acid level in 35 eutherian mammals (data not shown). In addition the c.A1378G variant was predicted to be benign by SIFT  and PolyPhen . Taken together these data suggested that the variant was unlikely to be pathogenic and it was therefore eliminated from further investigation.
The exonic variant detected by resequencing was a frame-shifting deletion of a single adenine in exon 8 (TTC8 c.669delA in transcript ENSCAFT00000050179, CFA8:63,129,154). The deletion was predicted to cause a premature stop codon (p.Lys223ArgfsX15), possibly resulting in the degredation of mRNA by nonsense-mediated decay or a truncated protein product (Figure 6). TTC8 c.669delA affects both isoforms of the protein.
We screened all the 26 GR dogs (10 cases and 16 controls) that were included in the GWA study for the coding variant, TTC8 c.669delA, to confirm the association of this variant with PRA and compare it with the most highly associated SNP markers, Marker 1 and Marker 2. The variant showed significant allelic association with PRA (praw = 6.31 × 10-7, pgenome = 0.019) and was more strongly associated than both Marker 1 at 63.614 Mb (praw = 5.79 × 10-6, pgenome = 0.109) and Marker 2 at 71.732 Mb (praw = 1.30×10-6, pPgenome = 0.037). Eight out of ten PRA cases and none of the controls were homozygous for TTC8 669delA. Both of the two remaining cases were homozygous for the wildtype (normal) haplotype. Neither were either of these two cases homozygous for the minor allele at Marker 2; one was heterozygous and the other homozygous for the wildtype/major allele. While the variant showed incomplete association with PRA, it has a strong likelihood of a deleterious effect on the protein. In addition, the nucleotide and the amino acid affected by TTC8 c.669delA is conserved in 32 eutherian mammals (data not shown). This mutation is therefore highly likely to be the causal mutation for GR_PRA2. Analysis of the segregation of TTC8 c.669delA with PRA in a family of Swedish ancestry (Additional file 1: Figure S1) indicated that PRA2 is recessive and fully penetrant.
PRA2 genotypes and PRA clinical status for 2500 GRs
PRA clinical status
PRA obligate carrier
Frequency of TTC8 c.669delA in various countries
Country of ancestry
TTC8 c.669delA frequency
1 in # affected expected
1 in # carriers expected
To determine whether TTC8 c.669delA is associated with PRA in related breeds we screened a further 175 dogs from three closely related breeds that could realistically share polymorphisms with the GR; 48 Chesapeake Bay Retrievers (CBR), 59 Flat-Coat Retrievers (FCR) and 71 LRs, including 19 LRs and 2 CBRs that were clinically affected with PRA but that were clear of the prcd mutation. One LR with PRA was homozygous for the mutation (TTC8-/-). The remaining 70 LR, 45 CBR and 59 FCR dogs were homozygous wildtype (TTC8+/+).
One of the GRs with PRA in our cohort that was homozygous for TTC8 c.669delA was reported to have clinical signs in addition to PRA. These were described as “hormonal changes and thyroid problems” by the dog’s owner/veterinarian, the precise nature of which are unknown, and attempts to gather further information pertaining to the phenotype of this dog were unsuccessful.
A bitch, diagnosed with PRA at the age of 5.9 years was reported to be in good health. She was short for the breed, at 30 kg was overweight for her size and gained weight easily. She had undergone metabolism tests (details of which were not reported), and while not treated, the results were considered borderline abnormal. The owner also reported that the dog had never been able to catch a ball in the air, suggesting it had poor coordination.
A dog, diagnosed with PRA at 2.9 years, was reported to be in good health until his death at 9 years, from cancer. At 52 cm tall, he was considered small for the breed, but was not overweight. The owner reported two behavioural idiosyncrasies: he was aggressive towards certain people when in the home, but not outside, and he also appeared to have a poor sense of smell.
In Golden Retrievers, mutations in two genes (SLC4A3 and PRCD) causing PRA in the breed have been described [18, 19]. These mutations account for approximately 61% of cases of PRA . The PRCD mutation appears to be very rare in the breed . Indeed, we have not identified any dogs homozygous for the PRCD mutation, and less than 2% are carriers of the mutation. Using a GWA analysis approach, we have identified a third causal mutation for PRA in the GR, a novel mutation in the TTC8 gene. We found that while this mutation does not explain all remaining cases of PRA in our study, suggesting that there is at least one more genetically distinct form of PRA in this breed, it does appear to be fully penetrant and a common cause of PRA in the breed.
Sequencing of SPATA7 and TTC8 from healthy retinal mRNA served four purposes: 1. It confirmed the presence of both mRNA transcripts in the normal canine retina. 2. The presence of the SPATA7 c.A1378G variant in mRNA from a healthy dog allowed the elimination of this variant from further investigation. 3. It revealed that the intron-exon boundaries predicted by the CanFam2 annotation for TTC8 in the dog are incorrect for five exons. They are instead identical to the human and mouse boundaries (Figure 5). 4. It revealed an exon orthologous to human exon 2A, that is absent from the Ensembl canine (CanFam2) prediction (Figure 5). As is the case in humans and mice, canine TTC8 is alternatively spliced to produce two isoforms (TTC8 and TTC8 2A). The precise functional difference between the two isoforms is unknown, but it is thought TTC82A plays in important role in the function of the protein in the photoreceptor cell-containing outer nuclear layer of the retina .
In order to further test the validity of the insertion mutation, we screened 2500 GRs for the mutation (Table 1). We found that 75.9% of the PRA cases (not caused by PRCD or GR_PRA1), 40% of the obligate PRA carriers and 100% of clinically unaffected dogs (which could be clear of the mutation or carry a single copy) have TTC8 genotypes that are concordant with their clinical status. All 22 dogs with known phenotypes and homozygous for the mutation i.e. TTC8-/-, have developed PRA, suggesting that the mutation is fully penetrant within the Golden Retrievers investigated. The inheritance observed in a family of eight dogs (three cases) is supportive of a recessive mode (Additional file 1: Figure S1). The presence of the variant in GR dogs from countries including the USA, UK, France, Denmark and Sweden suggests the variant may have arisen prior to the geographic dispersion of the breed. The mutant allele frequencies indicate that between 1 in 480 and 1 in 8000 GRs is likely to be affected with this form of PRA, although up to 1 in 12 are expected to carry the mutant gene. There is a group of dogs with genotypes discordant with their phenotypes, comprising 7 PRA-affected dogs that are not homozygous for TTC8 c.669delA and three obligate carriers that do not carry TTC8 c.669delA. It is formally possible that the mutation has a dominant mode of inheritance with incomplete penetrance, or complex trait or compound heterozygote effects, although we have no evidence to suggest this might be the case. Indeed, only 1/7 PRA-affected dogs that are not homozygous for TTC8 c.669delA is heterozygous and could therefore potentially be a compound heterozygote. A further three of these seven dogs are heterozygous at the GR_PRA1 (SLC4A3) locus, and PRA in these dogs could potentially be caused by compound heterozygosity in SLC4A3. However, the three remaining dogs are homozygous for the wildtype alleles at all three loci described to date i.e. SLC4A3, TTC8 or PRCD, suggesting a fourth locus must be causing PRA in these dogs. The observation that none of these seven dogs are heterozygous at more than one locus suggests that the additive effects of heterozygosity is unlikely to be the cause of PRA in these dogs. Given that three distinct loci have now been implicated in PRA in the breed, these data taken together suggest it is likely that still more loci are responsible for the discordant cases.
The absence of the mutant TTC8 allele from FCR and CBR dogs tested, including some dogs affected with PRA, indicates that the mutation is rare and probably mainly confined to the GR breed, although identification of a LR (with clinically apparent PRA) homozygous for the variant suggests it may be present in the LR breed as well. However, as only 1/19 LR PRA cases, all of which have previously tested clear for prcd, is caused by the TTC8 variant, it is clearly a minor cause of PRA in the breed.
The PRA cases in our study that were homozygous for the TTC8 variant had an average age of diagnosis of 4.51 years, while the discordant GR PRA cases i.e. TTC8+/+ and TTC8+/- had an average age at diagnosis of 6.46 years. This difference could be indicative of the segregation of a fourth form of PRA in the GR breed, with a slightly older age of onset than GR_PRA2, although the age at diagnosis may not necessarily accurately reflect the age of onset.
The identification of a frameshift deletion in TTC8 in GR dogs with PRA, that is likely to be a significant susceptibility locus for PRA in this breed, establishes PRA2 as a model for human RP, and potentially BBS. This form of PRA in the GR may prove to be a valuable model for further studies to enhance our understanding of visual pathways and gene therapy investigations.
The diagnosis of individual dogs was provided by veterinary ophthalmologists through the BVA/KC/ISDS (British Veterinary Association/Kennel Club/International Sheep Dog Society) Eye Scheme in the UK, the Swedish Kennel Club Eye Scheme in Sweden and independent veterinary ophthalmologists. Cases were defined as dogs diagnosed as affected with PRA i.e. displaying ophthalmoscopic signs of PRA including tapetal hyperreflectivity and vascular attenuation and controls as those free of inherited eye disease of any kind, and at least 7 years old at the time of examination for the GWA analysis or any age for subsequent investigations.
Blood samples were collected into EDTA tubes and genomic DNA was either extracted manually from peripheral blood leukocytes using QIAamp DNA Blood Midi Kit (Qiagen, Hilden, Germany) or automatically on a QIAsymphony SP/AS instrument (Qiagen, Hilden, Germany). DNA was also extracted from whole blood using a Nucleon Genomic DNA Extraction Kit (Tepnel Life Sciences, Manchester, UK), according to the manufacturer’s instructions. For samples collected as buccal mouth swabs, DNA was extracted using a QIAamp® DNA Blood Midi Kit (Qiagen, West Sussex, UK). A canine retinal tissue sample from a dog of unknown breed and free of PRA was taken post mortem, with the owner’s consent. RNA was extracted using an RNeasy Protect Mini Kit (Qiagen, West Sussex, UK) according to the manufacturer’s instructions.
PRCD and PRA1 screening
We genotyped DNA from 29 PRA-affected GRs for the PRCD and PRA1 mutations. The former was performed using the TaqMan allelic discrimination technique (Applied Biosystems Inc., Foster City, CA) according to the manufacturer’s instructions. Primers (Forward: 5′-GGCCTTTCTCCTGCAGACT-3′; Reverse: 5′-CAGCTTCTCACGGTTGGAC-3′) and PrimeTime Dual-Labelled Probes (G-probe: 5′-FAM-AGCCATGTGCACCACCCTCT-BHQ-3′ and C-probe: 5′-HEX-TGAGCCATGTACACCACCCTCT-BHQ-3′; IDT, Glasgow, UK) were designed with Primer3 . PCR amplification and allelic discrimination plate read and analysis were carried out on a Techne Quantica Real Time Thermal Cycler with the Quansoft software (Bibby Scientific Limited, Staffordshire, UK). The PRA1 genotyping was performed by PCR amplification using fluorescent primers (Forward: 5′-6-FAM-AGAGCAACCTTGTAACCCGTA-3′ and Reverse: 5′-GGAAGAAGGCAATGAGAAAGG-3′; IDT, Glasgow, UK) and subsequent fragment length polymorphism detection using an ABI 3130xl DNA Analyzer and GeneMapper® Software (Applied Biosystems, Inc., [ABI], Foster City, CA).
Genome-wide association mapping
CanineHD BeadChips (Illumina) were used to obtain genotype calls for 173,662 SNPs using DNA from 10 GR PRA cases and 16 GR controls and GWA analysis was conducted using the software package PLINK . After removing SNPs with a minor allele frequency <5% and missing genotype calls >10% from the analysis, a final data set of 103,264 markers remained. Sample call rate was >99.7% for all samples. Identity-by-state (IBS) clustering and Cochran–Mantel–Haenszel (CMH) meta-analysis with PLINK were used to examine and adjust for population stratification. As a correction for multiple testing, we repeated the GWA analyses using the Max(T) permutation procedure in PLINK (100,000 permutations, denoted by pgenome). An additional analysis using Fast Mixed Model (FMM) to correct for population stratification was also undertaken . Haplotype phases were inferred using PHASE . Visual inspection of SNP genotypes and haplotypes across the region was performed to define a homozygous critical region.
Next generation sequencing
Genomic DNA (3 μg) from 10 GR dogs (five PRA-affected, two obligate carrier and three PRA-clear) was used to prepare DNA libraries for sequencing, using the SureSelectXT Custom MP4 Kit (Agilent Technologies). Each kit contained a custom capture library of 34,097 biotinylated RNA baits, 120 bp in length and designed based on the CanFam2 reference sequence using Agilent Technologies’ eArray tool . Baits were designed to give 2× coverage and exclude repeat-masked regions, resulting in coverage of 59.1% (2.25/3.81 Mb) of the targeted regions. Target enrichment was performed according to the manufacturer’s instructions. Initial shearing of genomic DNA using a Covaris S220 and quality assessment of the final library using a 2100 Bioanalyser was undertaken by The Eastern Sequence and Informatics Hub (EASIH, University of Cambridge). The quantity of the captured library was assessed by quantitative PCR using the KAPA Library Quantification Kit for the Illumina Genome Analyzer Platform (KAPA Biosystems), according to the manufacturer’s instructions.
Paired-end sequencing resulting in 51-bp reads was conducted in a single lane on an Illumina Hiseq 2000, by the High Throughput Group (HTG) at the Welcome Trust Centre for Human Genetics (University of Oxford, UK). Sequence reads were aligned with the canine reference sequence (CanFam 2) using BWA , variant (SNP and indel) calls were made using GATK  and the aligned reads were visualised using the Integrative Genomics Viewer (IGV) . Variants considered candidates for further investigation were those that occurred in splice sites or resulted in non-synonymous changes to a protein, and that were homozygous in PRA cases, heterozygous in obligate carriers and heterozygous or homozygous for the wildtype allele in controls.
The exon-intron boundaries of canine TTC8 and SPATA7 were defined by producing ClustalW  alignments using the Ensembl predicted canine transcripts (TTC8: ENSCAFG00000017478; SPATA7: ENSCAFG00000017354) and available known mouse (TTC8: ENSMUSG00000021013; SPATA7: ENSMUSG00000021007) and human (TTC8: ENSG00000165533; SPATA7: ENSG00000042317) Ensembl transcripts. Primer3  was used to design primers in the exons for the amplification of cDNA as well as to design primers in introns seven and eight for the amplification and sequencing of TTC8 exon 8 in genomic DNA (Additional file 2: Table S1). SPATA7 and TTC8 mRNA sequence was amplified by reverse-transcriptase PCR using SuperScript®II Reverse Transcriptase (Invitrogen) according to the manufacturer’s instructions. To further investigate the remaining variant (TTC8 c.669delA) in a larger dataset exon 8 of TTC8 was amplified by polymerase chain reaction (PCR) using HotStarTaq Plus DNA Polymerase (Qiagen) in genomic DNA from the 26 GRs that were included in the GWA study. PCR products were purified using Multiscreen HTS-PCR filter plates (Millipore). Amplification products were sequenced on an ABI 3130xl DNA Analyzer using BigDye Terminator v3.1 (Applied Biosystems) and sequence traces were assembled, analyzed and compared using the Staden Package . The variant was analysed for association with PRA and compared with the most associated SNP markers, BICF2P582923 and BICF2G630416812, using the software package PLINK .
The suggestive causative mutation for PRA2 in exon 8, TTC8 c.669delA, was screened in 2500 GRs by PCR amplification using fluorescent primers (Forward: 5′-6-FAM- TGCCCTTTCCACAGAGCAC-3′ and Reverse: 5′- CCATGTCTAAGCCCTTCACAA-3′; IDT, Glasgow, UK) and subsequent fragment length polymorphism detection using an ABI 3130xl DNA Analyzer and GeneMapper® Software (Applied Biosystems, Inc., [ABI], Foster City, CA). The panel of 2500 GRs of any age (including the 26 DNA samples already sequenced), was made up of 29 PRA cases, 5 obligate carriers, 459 clear dogs and 2007 dogs with unknown PRA clinical status. Included in this cohort of 2500 dogs were 88 dogs of breeding age (between one and eight years of age), unrelated at the parent level (from 88 different dams and 88 different sires) and of UK ancestry. Also included were 87 dogs of French ancestry, 736 dogs of Swedish ancestry, 132 dogs of Danish ancestry and 179 dogs of US ancestry, collected specifically for allele frequency estimations. In addition, samples from 175 dogs representing three breeds that are closely related to the GR breed were also included in the mutation screening: LR (n = 71), CBR (n = 45) and FCR (n = 59).
Additional PRA2 phenotyping
Two dogs with PRA that were homozygous for TTC8 c.669delA were selected for additional phenotyping. The owners of these dogs were asked to complete a questionnaire assessing the overall health of their dog as well as the presence of systemic clinical signs known to be associated with BBS. These included kidney, reproductive, olfactory and behavioural/social abnormalities, obesity and diabetes mellitus.
Chesapeake bay retrievers
The authors would like to thank the owners who donated DNA samples from their dogs to this project. The authors also thank Dr Sue Pearce-Kelling from Optigen, LLC, Dr Anne Thomas from Antagene and Dr Kerstin Lindblad-Toh from the Broad Institute for DNA samples.
Supported by funding from the Kennel Club Charitable Trust, the Pet Plan Charitable Trust and donations from dog owners. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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