Identification of a Duplication in the RP17 Locus in an Individual With Pathogenic CEP290 Variants: Implications for...

Area of Science:

• Ophthalmology
• Genetics
• Molecular Biology

Background:

• Cone dystrophy is a group of inherited retinal diseases affecting cone photoreceptors.
• Structural variants (SVs) in the RP17 locus have been linked to dominant retinitis pigmentosa.
• CEP290 variants are known causes of inherited retinal diseases, including Bardet-Biedl syndrome and Leber congenital amaurosis.

Purpose of the Study:

• To determine the pathogenicity of a novel RP17 locus duplication in a cone dystrophy patient with biallelic CEP290 variants.
• To investigate the functional impact of the identified variants on photoreceptor development and function.
• To differentiate the contribution of the RP17 duplication versus CEP290 variants to the patient's phenotype.

Main Methods:

• Breakpoint polymerase chain reaction (PCR) to assess duplication inheritance.
• Ophthalmic evaluations including fundus examination, multimodal retinal imaging, and electroretinography (ERG).
• Generation and differentiation of patient-derived induced pluripotent stem cells into photoreceptor precursor cells (PPCs) and retinal organoids (ROs).
• Reverse-transcription PCR (RT-PCR), long-read cDNA sequencing, and immunohistochemistry to assess CEP290 splicing and photoreceptor morphology.
• Quantitative RT-PCR to measure GDPD1 expression.

Main Results:

• The proband and father carried a 324-kb duplication in the RP17 locus; the father was unaffected, while the proband exhibited cone dystrophy features.
• Compound heterozygous CEP290 variants led to pseudoexon inclusion and exon skipping, causing altered ciliation and reduced opsin trafficking in retinal organoids.
• In silico modeling indicated the RP17 duplication did not disrupt chromatin looping, and GDPD1 expression was not upregulated, unlike pathogenic RP17-SVs.
• The proband's cone dystrophy phenotype was consistent with CEP290 variant pathogenicity.

Conclusions:

• The novel RP17 duplication is likely benign, with the cone dystrophy phenotype attributed to CEP290 variants.
• Functional studies and in silico modeling are crucial for accurate classification of RP17 SVs.
• These findings underscore the importance of comprehensive genetic and functional analyses to prevent misdiagnosis in inherited retinal diseases.