North Carolina Macular Dystrophy: Phenotypic Variability and Computational Analysis of Disease-Associated Noncoding Variants

Abstract

North Carolina macular dystrophy (NCMD) is an autosomal dominant, congenital disorder affecting the central retina. Here, we report clinical and genetic findings in three families segregating NCMD and use epigenomic datasets from human tissues to gain insights into the effect of NCMD-implicated variants. METHODS.Clinical assessment and genetic testing were performed. Publicly available transcriptomic and epigenomic datasets were analyzed and the activity-by-contact method for scoring enhancer elements and linking them to target genes was used. RESULTS.A previously described, heterozygous, noncoding variant upstream of the PRDM13 gene was detected in all six affected study participants (chr6:100,040,987G>C [GRCh37/hg19]). Interfamilial and intrafamilial variability were observed; the visual acuity ranged from 0.0 to 1.6 LogMAR and fundoscopic findings ranged from visually insignificant, confluent, drusen-like macular deposits to coloboma-like macular lesions. Variable degrees of peripheral retinal spots (which were easily detected on widefield retinal imaging) were observed in all study subjects. Notably, a 6-year-old patient developed choroidal neovascularization and required treatment with intravitreal bevacizumab injections. Computational analysis of the five single nucleotide variants that have been implicated in NCMD revealed that these noncoding changes lie within two putative enhancer elements; these elements are predicted to interact with PRDM13 in the developing human retina. PRDM13 was found to be expressed in the fetal retina, with greatest expression in the amacrine precursor cell population. CONCLUSIONS.We provide further evidence supporting the role of PRDM13 dysregulation in the pathogenesis of NCMD and highlight the usefulness of widefield retinal imaging in individuals suspected to have this condition.

Multi-omics profiling, in vitro and in vivo enhancer assays dissect the cis-regulatory mechanisms underlying North Carolina macular dystrophy, a retinal enhanceropathy

“…Indeed, using the activity-by-contact (ABC) method based on Hi-C data from human embryonic stem cells, Green et al (2021) demonstrated that both hotspots encompass cCREs. 80 Interestingly, 70% of the macula-specific CREs that were identified in this study correspond with the seven candidate CREs that we identified in the PRDM13 locus (Suppl. Figure 12).…”

“…Indeed, using the activity-by-contact (ABC) method based on Hi-C data from human embryonic stem cells, Green et al (2021) demonstrated that both hotspots encompass cCREs. 85 Interestingly, 70% of the macula-specific CREs that were identified in this study correspond with the eight candidate CREs that we identified in the PRDM13 locus (Figure S11). It should also be noted that the quality of UMI-4C profiles, reflected by the number of UMIs, is dependent on both the genomic region the viewpoint is located in and the efficiency of the nested PCR reactions.…”

“…Both mutational hotspots have been identified as cCREs active at day 103 of embryonic development, i.e. the moment when retinal progenitor cells of the macula exit mitosis and differentiate towards photoreceptor fate, 85, 90 and the luciferase assays show an effect of the SNVs they contain on reporter gene expression. Therefore, disruption of PRDM13 expression during a critical step of maculogenesis can be assumed.…”

“…Comparison of the seven cCREs we identified in the PRDM13 locus using UMI-4C profiling integrated into our retina-specific multi-omics database RegRet (black bars) with the ten macula-specific CREs identified by Green et al (2021) using the activity-by-contact (ABC) method (grey bars). 80 …”

“…43 With regard to retina-specific chromatin interactions, Hi-C data from human retinal organoids was added. 47 To provide insight into retinal development, DNase-seq data from embryonic retinal tissue at five stages (74,85,89,103, and 125 days) were included. 46 Apart from the retina-specific datasets, multiple non-retinal tracks were added: UCNEs and ultraconserved gene regulatory blocks (UGRBs), 9 H3K27ac, H3K4me1, and H3K4me3 marks in seven cell lines (ENCODE Regulation), DNase I hypersensitive site peak clusters in 95 cell lines (ENCODE Regulation), ORegAnno elements, 78 ENCODE cCREs, RefSeq functional elements, GeneHancer regulatory elements and gene interactions, GeneCards gene transcription start sites, and Micro-C chromatin structure in H1-hESC.…”