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- Ekesten, Björn, et al.
(författare)
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Abnormal Appearance of the Area Centralis in Labrador Retrievers With an ABCA4 Loss-of-function Mutation
- 2022
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Ingår i: Translational Vision Science & Technology. - : Association for Research in Vision and Ophthalmology (ARVO). - 2164-2591. ; 11:2
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: To study retinal appearance and morphology in Labrador retrievers (LRs) heterozygous and homozygous for an ABCA4 loss-of-function mutation. Methods: Ophthalmic examination, including ophthalmoscopy and simple testing of vision, was performed in five ABCA4(wt/wt), four ABCA4(wt/InsC), and six ABCA4(InsC/InsC) LRs. Retinas were also examined with confocal scanning laser ophthalmoscopy (cSLO) and optical coherence tomography (OCT). Infrared and fundus autofluorescence (FAF) images were studied, and outer nuclear layer (ONL) and neuroretinal thickness were measured in the central and peripheral area centralis. Results: Clinical signs in young ABCA4(InsC/InsC) LRs were subtle, whereas ophthalmoscopic findings and signs of visual impairment were obvious in old ABCA4InsC/InsC LRs. Retinal appearance and vision testing was unremarkable in heterozygous LRs regardless of age. The cSLO/OCT showed abnormal morphology including ONL thinning, abnormal outer retinal layer segmentation, and focal loss of retinal pigment epithelium in the fovea equivalent in juvenile ABCA4(InsC/InsC) LRs. The abnormal appearance extended into the area centralis and visual streak in middle-aged ABCA4(InsC/InsC) and then spread more peripherally. A mild phenotype was seen on cSLO/OCT and FAF in middle-aged to old ABCA4(wt/InsC) LRs. Conclusions: Abnormal appearance and morphology in the fovea equivalent are present in juvenile ABCA4InsC/InsC. In the older affected LRs, the visual streak and then the peripheral retina also develop an abnormal appearance. Vision deteriorates slowly, but some vision is retained throughout life. Older heterozygotes may show a mild retinal phenotype but no obvious visual impairment. The ABCA4InsC/InsC LR is a potential model for ABCA4-mediated retinopathies/juvenile-onset Stargardt disease in a species with human-sized eyes. Translational Relevance: The ABCA4(InsC) mutation causes juvenile-onset abnormal appearance of the fovea equivalent in affected dogs that slowly spreads in the retina, while only a mild phenotype is seen in older carriers. This is the first non-primate, large animal model for ABCA4-related/STGD1 retinopathies in a species with a fovea equivalent.
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| 4. |
- Mäkeläinen, Suvi, et al.
(författare)
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An ABCA4 loss-of-function mutation causes a canine form of Stargardt disease
- 2019
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Ingår i: PLOS Genetics. - : Public Library of Science. - 1553-7390 .- 1553-7404. ; 15:3
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Tidskriftsartikel (refereegranskat)abstract
- Autosomal recessive retinal degenerative diseases cause visual impairment and blindness in both humans and dogs. Currently, no standard treatment is available, but pioneering gene therapy-based canine models have been instrumental for clinical trials in humans. To study a novel form of retinal degeneration in Labrador retriever dogs with clinical signs indicating cone and rod degeneration, we used whole-genome sequencing of an affected sib-pair and their unaffected parents. A frameshift insertion in the ATP binding cassette subfamily A member 4 (ABCA4) gene (c.4176insC), leading to a premature stop codon in exon 28 (p.F1393Lfs*1395), was identified. In contrast to unaffected dogs, no full-length ABCA4 protein was detected in the retina of an affected dog. The ABCA4 gene encodes a membrane transporter protein localized in the outer segments of rod and cone photoreceptors. In humans, the ABCA4 gene is associated with Stargardt disease (STGD), an autosomal recessive retinal degeneration leading to central visual impairment. A hallmark of STGD is the accumulation of lipofuscin deposits in the retinal pigment epithelium (RPE). The discovery of a canine homozygous ABCA4 loss-of-function mutation may advance the development of dog as a large animal model for human STGD.
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| 5. |
- Mäkeläinen, Suvi
(författare)
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Canine inherited retinal degenerations: a model for visual impairment in humans
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Inherited retinal degenerations (IRDs) form a clinically and genetically heterogeneous group of diseases, leading to visual impairment or blindness in both humans and dogs. The prevalence of IRDs is estimated at 1 in 2,000 in humans. In dogs, the exact prevalence is unknown, but close to 100 different breeds have been reported to be affected, many by more than one type of IRD. The identification of the underlying genetic variants is critical, as the results can be used to develop genetic tests, which allow breeders to make informed breeding decisions while preserving genetic variation.In Labrador retrievers, a novel form of IRD was recently identified, with clinical signs indicating cone-rod photoreceptor degeneration. In this thesis, a whole-genome sequencing approach was used to identify a frameshift insertion leading to a premature stop codon in the canine ABCA4 gene. In humans, mutations in the ABCA4 gene are the major cause of Stargardt disease (STGD), an autosomal recessive retinal degeneration leading to central visual impairment. Transcript and protein level investigations showed that the canine ABCA4 insertion is a loss-of-function mutation responsible for the novel canine IRD, and leads to a phenotype similar to STGD in humans.Golden retrievers are affected by at least four different forms of IRD, one of which is associated with a deletion in the TTC8 gene. Mutations in this gene in humans are involved in the Bardet-Biedl syndrome (BBS) with heterogeneous clinical signs. We were able to show that the canine deletion is a loss-of-function mutation resulting in a syndromic IRD similar to BBS.Lastly, while the human retinal transcriptome has been extensively studied, less is known about the gene expression patterns in the canine retina. Using short- and longread cDNA sequencing we characterized the canine retinal transcriptome, results that in the future can be used to identify and validate causative genetic variants for canine IRDs. The results of this thesis contribute to the understanding of two important IRDs affecting the health and welfare of both dogs and humans. In addition, the thesis highlights the importance of a well-characterized retinal transcriptome for successful identification of disease-causing alleles.
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| 6. |
- Mäkeläinen, Suvi, et al.
(författare)
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Deletion in the Bardet-Biedl Syndrome Gene TTC8 Results in a Syndromic Retinal Degeneration in Dogs
- 2020
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Ingår i: Genes. - : MDPI. - 2073-4425. ; 11:9
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Tidskriftsartikel (refereegranskat)abstract
- In golden retriever dogs, a 1 bp deletion in the canineTTC8gene has been shown to cause progressive retinal atrophy (PRA), the canine equivalent of retinitis pigmentosa. In humans,TTC8is also implicated in Bardet-Biedl syndrome (BBS). To investigate if the affected dogs only exhibit a non-syndromic PRA or develop a syndromic ciliopathy similar to human BBS, we recruited 10 affected dogs to the study. The progression of PRA for two of the dogs was followed for 2 years, and a rigorous clinical characterization allowed a careful comparison with primary and secondary characteristics of human BBS. In addition to PRA, the dogs showed a spectrum of clinical and morphological signs similar to primary and secondary characteristics of human BBS patients, such as obesity, renal anomalies, sperm defects, and anosmia. We used Oxford Nanopore long-read cDNA sequencing to characterize retinal full-lengthTTC8transcripts in affected and non-affected dogs, the results of which suggest that three isoforms are transcribed in the retina, and the 1 bp deletion is a loss-of-function mutation, resulting in a canine form of Bardet-Biedl syndrome with heterogeneous clinical signs.
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| 8. |
- Roy, Ananya, et al.
(författare)
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Using evolutionary constraint to define novel candidate driver genes in medulloblastoma
- 2023
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 120:33
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Tidskriftsartikel (refereegranskat)abstract
- Current knowledge of cancer genomics remains biased against noncoding mutations. To systematically search for regulatory noncoding mutations, we assessed mutations in conserved positions in the genome under the assumption that these are more likely to be functional than mutations in positions with low conservation. To this end, we use whole-genome sequencing data from the International Cancer Genome Consortium and combined it with evolutionary constraint inferred from 240 mammals, to identify genes enriched in noncoding constraint mutations (NCCMs), mutations likely to be regulatory in nature. We compare medulloblastoma (MB), which is malignant, to pilocytic astrocytoma (PA), a primarily benign tumor, and find highly different NCCM frequencies between the two, in agreement with the fact that malignant cancers tend to have more mutations. In PA, a high NCCM frequency only affects the BRAF locus, which is the most commonly mutated gene in PA. In contrast, in MB, >500 genes have high levels of NCCMs. Intriguingly, several loci with NCCMs in MB are associated with different ages of onset, such as the HOXB cluster in young MB patients. In adult patients, NCCMs occurred in, e.g., the WASF-2/ AHDC1/FGR locus. One of these NCCMs led to increased expression of the SRC kinase FGR and augmented responsiveness of MB cells to dasatinib, a SRC kinase inhibitor. Our analysis thus points to different molecular pathways in different patient groups. These newly identified putative candidate driver mutations may aid in patient stratification in MB and could be valuable for future selection of personalized treatment options.
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| 9. |
- Wang, Chao, et al.
(författare)
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A novel canine reference genome resolves genomic architecture and uncovers transcript complexity
- 2021
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Ingår i: Communications Biology. - : Springer Nature. - 2399-3642. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- 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. Here, the authors report an improved de novo reference genome for the domestic dog based on a female German Shepherd named Mischka. The new genome increases contiguity 55-fold over the previous dog assembly and uncovers functional elements that were not previously identifiable.
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