Multi-omics approach dissects cis-regulatory mechanisms underlying North Carolina macular dystrophy, a retinal enhanceropathy

Stijn Van de Sompele; Kent W Small; Munevver Burcu Cicekdal; Víctor López Soriano; Eva D'haene; Fadi S Shaya; Steven Agemy; Thijs Van der Snickt; Alfredo Dueñas Rey; Toon Rosseel; Mattias Van Heetvelde; Sarah Vergult; Irina Balikova; Arthur A Bergen; Camiel J F Boon; Julie De Zaeytijd; Chris F Inglehearn; Bohdan Kousal; Bart P Leroy; Carlo Rivolta; Veronika Vaclavik; Jenneke van den Ende; Mary J van Schooneveld; José Luis Gómez-Skarmeta; Juan J Tena; Juan R Martinez-Morales; Petra Liskova; Kris Vleminckx; Elfride De Baere

doi:10.1016/j.ajhg.2022.09.013

Multi-omics approach dissects cis-regulatory mechanisms underlying North Carolina macular dystrophy, a retinal enhanceropathy

Am J Hum Genet. 2022 Nov 3;109(11):2029-2048. doi: 10.1016/j.ajhg.2022.09.013. Epub 2022 Oct 14.

Authors

Stijn Van de Sompele¹, Kent W Small², Munevver Burcu Cicekdal³, Víctor López Soriano¹, Eva D'haene¹, Fadi S Shaya², Steven Agemy⁴, Thijs Van der Snickt¹, Alfredo Dueñas Rey¹, Toon Rosseel¹, Mattias Van Heetvelde¹, Sarah Vergult¹, Irina Balikova⁵, Arthur A Bergen⁶, Camiel J F Boon⁷, Julie De Zaeytijd⁸, Chris F Inglehearn⁹, Bohdan Kousal¹⁰, Bart P Leroy¹¹, Carlo Rivolta¹², Veronika Vaclavik¹³, Jenneke van den Ende¹⁴, Mary J van Schooneveld¹⁵, José Luis Gómez-Skarmeta¹⁶, Juan J Tena¹⁶, Juan R Martinez-Morales¹⁶, Petra Liskova¹⁷, Kris Vleminckx¹⁸, Elfride De Baere¹⁹

Affiliations

¹ Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
² Macula and Retina Institute, Los Angeles and Glendale, California, USA.
³ Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
⁴ Department of Ophthalmology, SUNY Downstate Medical Center University, Brooklyn, New York, USA.
⁵ Department of Ophthalmology, University Hospitals Leuven, Leuven, Belgium.
⁶ Department of Human Genetics, Amsterdam UMC, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands; Queen Emma Centre of Precision Medicine, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, The Netherlands.
⁷ Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands; Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands.
⁸ Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.
⁹ Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK.
¹⁰ Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic.
¹¹ Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium; Department of Head & Skin, Ghent University, Ghent, Belgium; Division of Ophthalmology & Center for Cellular & Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
¹² Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
¹³ University of Lausanne, Jules-Gonin Eye Hospital, Lausanne, Switzerland.
¹⁴ Center for Medical Genetics, Antwerp University Hospital, Antwerp, Belgium.
¹⁵ Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands; Bartiméus, Diagnostic Center for Complex Visual Disorders, Zeist, The Netherlands.
¹⁶ Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain.
¹⁷ Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic.
¹⁸ Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
¹⁹ Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium. Electronic address: [email protected].

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.

Keywords: IRX1; North Carolina macular dystrophy, NCMD; PRDM13; UMI-4C; cis-regulatory elements, CREs; enhanceropathy; human retina; multi-omics; non-coding single-nucleotide variants, SNVs; whole-genome sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adult
Animals
Corneal Dystrophies, Hereditary*
Humans
Pedigree
Retina / metabolism
Tomography, Optical Coherence*
Xenopus laevis / genetics

Supplementary concepts

Macular dystrophy, retinal, 1, North Carolina type