Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa

Suzanne E de Bruijn; Alessia Fiorentino; Daniele Ottaviani; Stephanie Fanucchi; Uirá S Melo; Julio C Corral-Serrano; Timo Mulders; Michalis Georgiou; Carlo Rivolta; Nikolas Pontikos; Gavin Arno; Lisa Roberts; Jacquie Greenberg; Silvia Albert; Christian Gilissen; Marco Aben; George Rebello; Simon Mead; F Lucy Raymond; Jordi Corominas; Claire E L Smith; Hannie Kremer; Susan Downes; Graeme C Black; Andrew R Webster; Chris F Inglehearn; L Ingeborgh van den Born; Robert K Koenekoop; Michel Michaelides; Raj S Ramesar; Carel B Hoyng; Stefan Mundlos; Musa M Mhlanga; Frans P M Cremers; Michael E Cheetham; Susanne Roosing; Alison J Hardcastle

doi:10.1016/j.ajhg.2020.09.002

Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa

Am J Hum Genet. 2020 Nov 5;107(5):802-814. doi: 10.1016/j.ajhg.2020.09.002. Epub 2020 Oct 5.

Authors

Suzanne E de Bruijn¹, Alessia Fiorentino², Daniele Ottaviani³, Stephanie Fanucchi⁴, Uirá S Melo⁵, Julio C Corral-Serrano³, Timo Mulders⁶, Michalis Georgiou⁷, Carlo Rivolta⁸, Nikolas Pontikos², Gavin Arno⁹, Lisa Roberts¹⁰, Jacquie Greenberg¹⁰, Silvia Albert¹¹, Christian Gilissen¹¹, Marco Aben¹¹, George Rebello¹⁰, Simon Mead¹², F Lucy Raymond¹³, Jordi Corominas¹¹, Claire E L Smith¹⁴, Hannie Kremer¹⁵, Susan Downes¹⁶, Graeme C Black¹⁷, Andrew R Webster⁹, Chris F Inglehearn¹⁸, L Ingeborgh van den Born¹⁹, Robert K Koenekoop²⁰, Michel Michaelides⁹, Raj S Ramesar¹⁰, Carel B Hoyng⁶, Stefan Mundlos⁵, Musa M Mhlanga²¹, Frans P M Cremers¹, Michael E Cheetham², Susanne Roosing²², Alison J Hardcastle²

Affiliations

¹ 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.
² UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership.
³ UCL Institute of Ophthalmology, London, EC1V 9EL, UK.
⁴ 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.
⁵ Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany; Institute for Medical and Human Genetics, Charité - Universitätsmedizin, Berlin, 10117, Germany.
⁶ 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.
⁷ UCL Institute of Ophthalmology, London, EC1V 9EL, UK; Moorfields Eye Hospital, London, EC1V 2PD, UK.
⁸ 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.
⁹ 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.
¹⁰ 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.
¹¹ Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands.
¹² MRC Prion Unit at UCL, UCL Institute of Prion Disease, London, W1W 7FF, UK.
¹³ 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.
¹⁴ Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, LS2 9JT, UK.
¹⁵ 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.
¹⁶ 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.
¹⁷ UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester, M13 9WL, UK.
¹⁸ 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.
¹⁹ The Rotterdam Eye Hospital, Rotterdam, 3011 BH, the Netherlands.
²⁰ Department of Paediatric Surgery, Human Genetics and Ophthalmology, McGill University, Montréal, QC H4A 3J1, Canada.
²¹ 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.
²² 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. Electronic address: [email protected].

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.

Keywords: GDPD; Hi-C; RP17; dominant retinitis pigmentosa; ectopic expression; photoreceptor precursors cells; retinal organoids; stem cells; structural variants; topologically associated domains; whole-genome sequencing.

Publication types

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

MeSH terms

Adult
Amino Acid Sequence
Cell Differentiation
Cellular Reprogramming
Child
Chromosome Mapping
Chromosomes, Human, Pair 17 / chemistry*
Cohort Studies
Enhancer Elements, Genetic
Female
Fibroblasts / metabolism
Fibroblasts / pathology
Gene Expression
Genes, Dominant
Genome, Human
Humans
Induced Pluripotent Stem Cells / metabolism
Induced Pluripotent Stem Cells / pathology
Male
Nuclear Proteins / genetics*
Nuclear Proteins / metabolism
Organoids / metabolism
Organoids / pathology
Phosphoric Diester Hydrolases / genetics*
Phosphoric Diester Hydrolases / metabolism
Polymorphism, Genetic
Primary Cell Culture
Retinal Cone Photoreceptor Cells / metabolism*
Retinal Cone Photoreceptor Cells / pathology
Retinitis Pigmentosa / diagnosis
Retinitis Pigmentosa / genetics*
Retinitis Pigmentosa / metabolism
Retinitis Pigmentosa / pathology
Transcription Factors / genetics*
Transcription Factors / metabolism
Whole Genome Sequencing

Substances

Nuclear Proteins
Transcription Factors
Phosphoric Diester Hydrolases
glycerophosphodiester phosphodiesterase

Abstract

Publication types

MeSH terms

Substances

Grants and funding