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Whole genome sequencing for USH2A-associated disease reveals several pathogenic deep-intronic variants that are amenable to splice correction. HGG ADVANCES 2023; 4:100181. [PMID: 36785559 PMCID: PMC9918427 DOI: 10.1016/j.xhgg.2023.100181] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
A significant number of individuals with a rare disorder such as Usher syndrome (USH) and (non-)syndromic autosomal recessive retinitis pigmentosa (arRP) remain genetically unexplained. Therefore, we assessed subjects suspected of USH2A-associated disease and no or mono-allelic USH2A variants using whole genome sequencing (WGS) followed by an improved pipeline for variant interpretation to provide a conclusive diagnosis. One hundred subjects were screened using WGS to identify causative variants in USH2A or other USH/arRP-associated genes. In addition to the existing variant interpretation pipeline, a particular focus was put on assessing splice-affecting properties of variants, both in silico and in vitro. Also structural variants were extensively addressed. For variants resulting in pseudoexon inclusion, we designed and evaluated antisense oligonucleotides (AONs) using minigene splice assays and patient-derived photoreceptor precursor cells. Biallelic variants were identified in 49 of 100 subjects, including novel splice-affecting variants and structural variants, in USH2A or arRP/USH-associated genes. Thirteen variants were shown to affect USH2A pre-mRNA splicing, including four deep-intronic USH2A variants resulting in pseudoexon inclusion, which could be corrected upon AON treatment. We have shown that WGS, combined with a thorough variant interpretation pipeline focused on assessing pre-mRNA splicing defects and structural variants, is a powerful method to provide subjects with a rare genetic condition, a (likely) conclusive genetic diagnosis. This is essential for the development of future personalized treatments and for patients to be eligible for such treatments.
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Dulla K, Slijkerman R, van Diepen HC, Albert S, Dona M, Beumer W, Turunen JJ, Chan HL, Schulkens IA, Vorthoren L, den Besten C, Buil L, Schmidt I, Miao J, Venselaar H, Zang J, Neuhauss SCF, Peters T, Broekman S, Pennings R, Kremer H, Platenburg G, Adamson P, de Vrieze E, van Wijk E. Antisense oligonucleotide-based treatment of retinitis pigmentosa caused by USH2A exon 13 mutations. Mol Ther 2021; 29:2441-2455. [PMID: 33895329 PMCID: PMC8353187 DOI: 10.1016/j.ymthe.2021.04.024] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 12/14/2022] Open
Abstract
Mutations in USH2A are among the most common causes of syndromic and non-syndromic retinitis pigmentosa (RP). The two most recurrent mutations in USH2A, c.2299delG and c.2276G > T, both reside in exon 13. Skipping exon 13 from the USH2A transcript presents a potential treatment modality in which the resulting transcript is predicted to encode a slightly shortened usherin protein. Morpholino-induced skipping of ush2a exon 13 in zebrafish ush2armc1 mutants resulted in the production of usherinΔexon 13 protein and a completely restored retinal function. Antisense oligonucleotides were investigated for their potential to selectively induce human USH2A exon 13 skipping. Lead candidate QR-421a induced a concentration-dependent exon 13 skipping in induced pluripotent stem cell (iPSC)-derived photoreceptor precursors from an Usher syndrome patient homozygous for the c.2299delG mutation. Mouse surrogate mQR-421a reached the retinal outer nuclear layer after a single intravitreal injection and induced a detectable level of exon skipping until at least 6 months post-injection. In conclusion, QR-421a-induced exon skipping proves to be a highly promising treatment option for RP caused by mutations in USH2A exon 13.
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Affiliation(s)
- Kalyan Dulla
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Ralph Slijkerman
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | | | - Silvia Albert
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Margo Dona
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Wouter Beumer
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Janne J Turunen
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Hee Lam Chan
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Iris A Schulkens
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Lars Vorthoren
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | | | - Levi Buil
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Iris Schmidt
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Jiayi Miao
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Hanka Venselaar
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Jingjing Zang
- University of Zürich, Institute of Molecular Life Sciences, 8057 Zürich, Switzerland
| | - Stephan C F Neuhauss
- University of Zürich, Institute of Molecular Life Sciences, 8057 Zürich, Switzerland
| | - Theo Peters
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Sanne Broekman
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Ronald Pennings
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Hannie Kremer
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | | | - Peter Adamson
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands; UCL, Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
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de Vrieze E, Cañas Martín J, Peijnenborg J, Martens A, Oostrik J, van den Heuvel S, Neveling K, Pennings R, Kremer H, van Wijk E. AON-based degradation of c.151C>T mutant COCH transcripts associated with dominantly inherited hearing impairment DFNA9. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 24:274-283. [PMID: 33815940 PMCID: PMC7985667 DOI: 10.1016/j.omtn.2021.02.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/24/2021] [Indexed: 01/22/2023]
Abstract
The c.151C>T founder mutation in COCH is a frequent cause of late-onset, dominantly inherited hearing impairment and vestibular dysfunction (DFNA9) in the Dutch/Belgian population. The initial clinical symptoms only manifest between the 3rd and 5th decade of life, which leaves ample time for therapeutic intervention. The dominant inheritance pattern and established non-haploinsufficiency disease mechanism indicate that suppressing translation of mutant COCH transcripts has high therapeutic potential. Single-molecule real-time (SMRT) sequencing resulted in the identification of 11 variants with a low population frequency (<10%) that are specific to the c.151C>T mutant COCH allele. Proof of concept was obtained that gapmer antisense oligonucleotides (AONs), directed against the c.151C>T mutation or mutant allele-specific intronic variants, are able to induce mutant COCH transcript degradation when delivered to transgenic cells expressing COCH minigenes. The most potent AON, directed against the c.151C>T mutation, was able to induce a 60% decrease in mutant COCH transcripts without affecting wild-type COCH transcript levels. Allele specificity decreased when increasing concentrations of AON were delivered to the cells. With the proven safety of AONs in humans, and rapid advancements in inner ear drug delivery, our in vitro studies indicate that AONs offer a promising treatment modality for DFNA9.
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Affiliation(s)
- Erik de Vrieze
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Corresponding author: Erik de Vrieze, Department of Otorhinolaryngology, Radboud University Medical Center, P.O. Box 9101, 6525 GA Nijmegen (Route 855), the Netherlands.
| | - Jorge Cañas Martín
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Jolien Peijnenborg
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Aniek Martens
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Jaap Oostrik
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Simone van den Heuvel
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Ronald Pennings
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
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Garanto A, Duijkers L, Tomkiewicz TZ, Collin RWJ. Antisense Oligonucleotide Screening to Optimize the Rescue of the Splicing Defect Caused by the Recurrent Deep-Intronic ABCA4 Variant c.4539+2001G>A in Stargardt Disease. Genes (Basel) 2019; 10:genes10060452. [PMID: 31197102 PMCID: PMC6628380 DOI: 10.3390/genes10060452] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/04/2019] [Accepted: 06/11/2019] [Indexed: 12/17/2022] Open
Abstract
Deep-sequencing of the ABCA4 locus has revealed that ~10% of autosomal recessive Stargardt disease (STGD1) cases are caused by deep-intronic mutations. One of the most recurrent deep-intronic variants in the Belgian and Dutch STGD1 population is the c.4539+2001G>A mutation. This variant introduces a 345-nt pseudoexon to the ABCA4 mRNA transcript in a retina-specific manner. Antisense oligonucleotides (AONs) are short sequences of RNA that can modulate splicing. In this work, we designed 26 different AONs to perform a thorough screening to identify the most effective AONs to correct splicing defects associated with c.4539+2001G>A. All AONs were tested in patient-derived induced pluripotent stem cells (iPSCs) that were differentiated to photoreceptor precursor cells (PPCs). AON efficacy was assessed through RNA analysis and was based on correction efficacy, and AONs were grouped and their properties assessed. We (a) identified nine AONs with significant correction efficacies (>50%), (b) confirmed that a single nucleotide mismatch was sufficient to significantly decrease AON efficacy, and (c) found potential correlations between efficacy and some of the parameters analyzed. Overall, our results show that AON-based splicing modulation holds great potential for treating Stargardt disease caused by splicing defects in ABCA4.
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Affiliation(s)
- Alejandro Garanto
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
| | - Lonneke Duijkers
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
| | - Tomasz Z Tomkiewicz
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
| | - Rob W J Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
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