Structural PPT1 variant implicated in non–syndromic retinal degeneration in dogs

Abstract

Purpose : Aberrant functioning of rod and/or cone photoreceptors can ultimately lead to retinal degeneration and eventual blindness. Dogs are affected by a disease grouping comparable to retinitis pigmentosa, termed progressive retinal atrophy (PRA). In Miniature Schnauzers (MS) photoreceptor dysplasia (pd) is a form of PRA caused by a 2 nt deletion in RPGRORF15. We now report on a second form of PRA in the breed.

Methods : We collected 51 DNA samples from MS affected with PRA (average age of diagnosis ~3.9 ±1 years) and not affected with RPGR deletion, and from 56 clinically normal controls of the same breed (average age ~6.6 ±2.8 years). GWAS and homozygosity mapping defined a critical interval in the first 4,796,806 bp of CFA15. Whole genome sequencing (WGS) of two affected cases, a carrier and a control was followed by SNP calling with GATK, and structural variant analysis with DELLY.

Results : WGS data analysis pinpointed a complex structural variant consisting of the duplication of exon 5 of the PPT1 gene along with a conversion and insertion (named PPT1dci). PPT1dci was confirmed homozygous in a cohort of 22 cases, and 12 more cases were homozygous for the CFA15 disease haplotype. The variant was also found homozygous in 6 non-affected dogs. We detected the wildtype and three aberrant PPT1 transcripts in isolated white blood cell mRNA extracted from a PRA case homozygous for PPT1_dci. The aberrant transcripts involved inclusion of the duplicated exon 5 and novel exons following the activation of cryptic splice sites.

Conclusions : PPT1 is associated with a form of neuronal ceroid lipofuscinosis (CLN1), a syndromic retinal degenerative disorder in man, mouse and dog. We propose PPT1_dci as causative for a non-syndromic form of PRA. The variant has an incomplete penetrance in MS, potentially related to the presence of the wild-type transcript. The PPT1 gene encodes for palmitoyl-protein thioesterase, a lysosomal hydrolase involved in opsin palmitoylation. The high opsin turnover in the retina, and the presence of wildtype transcripts in the mutant may explain why the disease phenotype is retina-specific. To our knowledge, this is the first case of isolated retinal degeneration associated with a PPT1 variant.

This abstract was presented at the 2019 ARVO Annual Meeting, held in Vancouver, Canada, April 28 - May 2, 2019.