The cause of autosomal-dominant retinitis pigmentosa (adRP), which leads to loss of vision and blindness, was investigated in families lacking a molecular diagnosis. A refined locus for adRP on Chr17q22 (RP17) was delineated through genotyping and genome sequencing, leading to the identification of structural variants (SVs) that segregate with disease. Eight different complex SVs were characterized in 22 adRP-affected families with >300 affected individuals. All RP17 SVs had breakpoints within a genomic region spanning YPEL2 to LINC01476. To investigate the mechanism of disease, we reprogrammed fibroblasts from affected individuals and controls into induced pluripotent stem cells (iPSCs) and differentiated them into photoreceptor precursor cells (PPCs) or retinal organoids (ROs). Hi-C was performed on ROs, and differential expression of regional genes and a retinal enhancer RNA at this locus was assessed by qPCR. The epigenetic landscape of the region, and Hi-C RO data, showed that YPEL2 sits within its own topologically associating domain (TAD), rich in enhancers with binding sites for retinal transcription factors. The Hi-C map of RP17 ROs revealed creation of a neo-TAD with ectopic contacts between GDPD1 and retinal enhancers, and modeling of all RP17 SVs was consistent with neo-TADs leading to ectopic retinal-specific enhancer-GDPD1 accessibility. qPCR confirmed increased expression of GDPD1 and increased expression of the retinal enhancer that enters the neo-TAD. Altered TAD structure resulting in increased retinal expression of GDPD1 is the likely convergent mechanism of disease, consistent with a dominant gain of function. Our study highlights the importance of SVs as a genomic mechanism in unsolved Mendelian diseases.

常染色体显性遗传性视网膜色素变性（adRP）会导致视力丧失和失明，在缺乏分子诊断的家庭中进行了调查。通过基因分型和基因组测序，确定了 Chr17q22 (RP17) 上 adRP 的精细位点，从而鉴定出与疾病分离的结构变异 (SV)。在 22 个受 adRP 影响的家庭中，有超过 300 名受影响的个体，其中有 8 种不同的复杂 SV 被表征。所有 RP17 SV 在从YPEL2到LINC01476 的基因组区域内都有断点。为了研究疾病的机制，我们将受影响个体和对照的成纤维细胞重新编程为诱导多能干细胞（iPSC），并将其分化为光感受器前体细胞（PPC）或视网膜类器官（RO）。对 RO 进行 Hi-C，并通过 qPCR 评估该位点的区域基因和视网膜增强子 RNA 的差异表达。该区域的表观遗传景观和 Hi-C RO 数据表明， YPEL2位于其自己的拓扑关联结构域 (TAD) 内，富含具有视网膜转录因子结合位点的增强子。 RP17 RO 的 Hi-C 图揭示了GDPD1和视网膜增强子之间具有异位接触的新 TAD 的形成，并且所有 RP17 SV 的建模与新 TAD 一致，导致异位视网膜特异性增强剂 - GDPD1可及性。 qPCR 证实GDPD1表达增加，进入 neo-TAD 的视网膜增强子表达增加。 TAD 结构的改变导致视网膜GDPD1表达增加，这可能是疾病的趋同机制，与显着的功能获得一致。 我们的研究强调了 SV 作为基因组机制在未解决的孟德尔疾病中的重要性。