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de Bruijn SE, Fiorentino A, Ottaviani D, Fanucchi S, Melo US, Corral-Serrano JC, Mulders T, Georgiou M, Rivolta C, Pontikos N, Arno G, Roberts L, Greenberg J, Albert S, Gilissen C, Aben M, Rebello G, Mead S, Raymond FL, Corominas J, Smith CEL, Kremer H, Downes S, Black GC, Webster AR, Inglehearn CF, van den Born LI, Koenekoop RK, Michaelides M, Ramesar RS, Hoyng CB, Mundlos S, Mhlanga MM, Cremers FPM, Cheetham ME, Roosing S, Hardcastle AJ. Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa. Am J Hum Genet 2020; 107:802-814. [PMID: 33022222 PMCID: PMC7675008 DOI: 10.1016/j.ajhg.2020.09.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/02/2020] [Indexed: 01/07/2023] Open
Abstract
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.
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Affiliation(s)
- Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Alessia Fiorentino
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership
| | | | - Stephanie Fanucchi
- Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Department of Integrative Biomedical Science, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Uirá S Melo
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany; Institute for Medical and Human Genetics, Charité - Universitätsmedizin, Berlin, 10117, Germany
| | | | - Timo Mulders
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Michalis Georgiou
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; Moorfields Eye Hospital, London, EC1V 2PD, UK
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK; Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, 4031, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, 4001, Switzerland
| | - Nikolas Pontikos
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership
| | - Gavin Arno
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Moorfields Eye Hospital, London, EC1V 2PD, UK
| | - Lisa Roberts
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Jacquie Greenberg
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Silvia Albert
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Marco Aben
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - George Rebello
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Simon Mead
- MRC Prion Unit at UCL, UCL Institute of Prion Disease, London, W1W 7FF, UK
| | - F Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals, Cambridge, CB2 0QQ, UK; Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 OXY, UK
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Claire E L Smith
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, LS2 9JT, UK
| | - Hannie Kremer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Susan Downes
- UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Oxford Eye Hospital, Oxford University Hospitals NHS Trust and Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, OX3 9DU, UK
| | - Graeme C Black
- UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester, M13 9WL, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Moorfields Eye Hospital, London, EC1V 2PD, UK
| | - Chris F Inglehearn
- UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Robert K Koenekoop
- Department of Paediatric Surgery, Human Genetics and Ophthalmology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Michel Michaelides
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Moorfields Eye Hospital, London, EC1V 2PD, UK
| | - Raj S Ramesar
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Carel B Hoyng
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany; Institute for Medical and Human Genetics, Charité - Universitätsmedizin, Berlin, 10117, Germany
| | - Musa M Mhlanga
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Department of Integrative Biomedical Science, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa; Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisbon, 1649-028, Portugal; Epigenomics & Single Cell Biophysics Group, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525 GA, the Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Michael E Cheetham
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands.
| | - Alison J Hardcastle
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership
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