A putative silencer variant in a spontaneous canine model of retinitis pigmentosa

Abstract

Retinitis pigmentosa (RP) is the leading cause of blindness with nearly two million people affected worldwide. Many genes have been implicated in RP, yet in 30-80% of the RP patients the genetic cause remains unknown. A similar phenotype, progressive retinal atrophy (PRA), affects many dog breeds including the Miniature Schnauzer. We performed clinical, genetic and functional experiments to identify the genetic cause of PRA in the breed. The age of onset and pattern of disease progression suggested that at least two forms of PRA, types 1 and 2 respectively, affect the breed, which was confirmed by genome-wide association study that implicated two distinct genomic loci in chromosomes 15 and X, respectively. Whole-genome sequencing revealed a fully segregating recessive regulatory variant in type 1 PRA. The associated variant has a very recent origin based on haplotype analysis and lies within a regulatory site with the predicted binding site of HAND1::TCF3 transcription factor complex. Luciferase assays suggested that mutated regulatory sequence increases expression. Case-control retinal expression comparison of six best HAND1::TCF3 target genes were analyzed with quantitative reverse-transcriptase PCR assay and indicated overexpression of EDN2 and COL9A2 in the affected retina. Defects in both EDN2 and COL9A2 have been previously associated with retinal degeneration. In summary, our study describes two genetically different forms of PRA and identifies a fully penetrant variant in type 1 form with a possible regulatory effect. This would be among the first reports of a regulatory variant in retinal degeneration in any species, and establishes a new spontaneous dog model to improve our understanding of retinal biology and gene regulation while the affected breed will benefit from a reliable genetic testing.

Deciphering primate retinal aging at single-cell resolution

“…2 D). TCF3 is associated with retinitis pigmentosa by forming HAND1::TCF3 complex and regulating the expression of retinal degeneration-related genes (Kaukonen et al, 2020 ). HDAC2 is one of histone deacetylase, whose downregulation is implicated in the pathogenesis of glaucoma by epigenetic regulation of extracellular matrix (ECM) genes (Park et al, 2017 ).…”

Integrative mapping of the dog epigenome: reference annotation for comparative inter-tissue and cross-species studies

“…To date, efforts to catalog functional elements in the dog genome are actively being pursued by two initiatives: 1) BarkBase [ 23 ] and 2) the Dog Genome Annotation (DoGA) project [ 39 ]. While both execute large-scale integrative annotations, they currently lack datasets that systematically dissect dynamic epigenomic marks such as histone marks and DNA methylation.…”

“…In domestic dogs, DNA methylation studies have been performed yet still lack epigenome-scale resolution. So far, public resources of functionally annotated dog genomes (i.e., BarkBase and DoGA) do not include methylome data [ 23,39 ]. To profile global DNA methylome landscape of the dog, we performed genome-wide MBD-seq experiments on 11 somatic tissues.…”

A Missense Variant in the Bardet-Biedl Syndrome 2 Gene (BBS2) Leads to a Novel Syndromic Retinal Degeneration in the Shetland Sheepdog

“…The use of canine genome banks facilitates WGS analysis, enabling further variant filtration whereby, a single genome can be used as a case in one study and a control genome for other studies. Although the majority of canine PRA-associated variants found are located within coding regions of the genome, disease-causing variants in non-coding areas have been identified [8][9][10]. WGS, as opposed to a targeted sequencing approach (including whole exome sequencing; WES) enables the entire genome to be interrogated and provides a comprehensive dataset.…”