1. Multi-omics approach dissects cis-regulatory mechanisms underlying North Carolina macular dystrophy, a retinal enhanceropathy
- Author
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Van de Sompele, Stijn, Small, Kent W., Cicekdal, Munevver Burcu, Soriano, Víctor López, D’haene, Eva, Shaya, Fadi S., Agemy, Steven, Van der Snickt, Thijs, Rey, Alfredo Dueñas, Rosseel, Toon, Van Heetvelde, Mattias, Vergult, Sarah, Balikova, Irina, Bergen, Arthur A., Boon, Camiel J.F., De Zaeytijd, Julie, Inglehearn, Chris F., Kousal, Bohdan, Leroy, Bart P., Rivolta, Carlo, Vaclavik, Veronika, van den Ende, Jenneke, van Schooneveld, Mary J., Gómez-Skarmeta, José Luis, Tena, Juan J., Martinez-Morales, Juan R., Liskova, Petra, Vleminckx, Kris, De Baere, Elfride, Human Genetics, ANS - Complex Trait Genetics, ARD - Amsterdam Reproduction and Development, Ophthalmology, Ghent University, European Commission, Foundation Fighting Blindness, and Research Foundation - Flanders
- Subjects
Adult ,EXPRESSION ,DOMAINS ,PHOTORECEPTOR ,North Carolina macular dystrophy, NCMD ,non-coding single-nucleotide variants, SNVs ,PRDM13 ,Retina ,STRUCTURAL VARIANTS ,Xenopus laevis ,Genetics ,Medicine and Health Sciences ,Animals ,Humans ,Ccis-regulatory elements, CREswhole-genome sequencing ,North Carolina macular dystrophy ,Genetics (clinical) ,Corneal Dystrophies, Hereditary ,NCMD ,enhanceropathy ,Biology and Life Sciences ,TRANSGENESIS ,multi-omics ,GENE ,DUPLICATION ,UMI-4 ,Pedigree ,FAMILY ,GENOME ,cis-regulatory elements, CREs ,whole-genome sequencing ,cis-regulatory elements ,UMI-4C ,CREs ,non-coding single-nucleotide variants ,SNVs ,Human medicine ,human retina ,Tomography, Optical Coherence ,IRX1 - Abstract
North Carolina macular dystrophy (NCMD) is a rare autosomal-dominant disease affecting macular development. The disease is caused by non-coding single-nucleotide variants (SNVs) in two hotspot regions near PRDM13 and by duplications in two distinct chromosomal loci, overlapping DNase I hypersensitive sites near either PRDM13 or IRX1. To unravel the mechanisms by which these variants cause disease, we first established a genome-wide multi-omics retinal database, RegRet. Integration of UMI-4C profiles we generated on adult human retina then allowed fine-mapping of the interactions of the PRDM13 and IRX1 promoters and the identification of eighteen candidate cis-regulatory elements (cCREs), the activity of which was investigated by luciferase and Xenopus enhancer assays. Next, luciferase assays showed that the non-coding SNVs located in the two hotspot regions of PRDM13 affect cCRE activity, including two NCMD-associated non-coding SNVs that we identified herein. Interestingly, the cCRE containing one of these SNVs was shown to interact with the PRDM13 promoter, demonstrated in vivo activity in Xenopus, and is active at the developmental stage when progenitor cells of the central retina exit mitosis, suggesting that this region is a PRDM13 enhancer. Finally, mining of single-cell transcriptional data of embryonic and adult retina revealed the highest expression of PRDM13 and IRX1 when amacrine cells start to synapse with retinal ganglion cells, supporting the hypothesis that altered PRDM13 or IRX1 expression impairs interactions between these cells during retinogenesis. Overall, this study provides insight into the cis-regulatory mechanisms of NCMD and supports that this condition is a retinal enhanceropathy., This work was supported by grants from Ghent University Special Research Fund (BOF20/GOA/023) (E.D.B., K.V., B.P.L.); Ghent University Hospital Innovation Fund NucleUZ (E.D.B.); JED Foundation (E.D.B.); H2020 Marie Sklodowska-Curie Innovative Training Networks (ITN) StarT (grant No. 813490) (E.D.B., K.V., J.L.G.-S., J.J.T., J.R.M.-M.); EJP RD Solve-RET EJPRD19-234 (E.D.B., P.L.,B.K., C.R., J.L.G.-S., J.J.T., J.R.M.-M.), SNSF grant # 204285 (C.R.), and Foundation Fighting Blindness in Columbia, MD (grant #: BR-GE-1216-0715-CSH). S.V.d.S. (1145719N) is PhD fellow of the Research Foundation Flanders (FWO), E.D.B. (1802220N) and B.P.L. (1803816N) are FWO Senior Clinical Investigators; M.B.C., V.L.S., and A.D.R. are Early Starting Researcher of ITN StarT (grant # 813490). B.K., B.P.L., C.J.F.B., E.D.B., P.L., and V.V. are members of ERN-EYE (Framework Partnership Agreement No 739534-ERNEYE). K.W.S. received an unrestricted grant from The Molecular Insight Research Foundation.
- Published
- 2022
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