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Suárez-Herrera N, Garanto A, Collin RWJ. Understanding and Rescuing the Splicing Defect Caused by the Frequent ABCA4 Variant c.4253+43G>A Underlying Stargardt Disease. Nucleic Acid Ther 2024; 34:73-82. [PMID: 38466963 DOI: 10.1089/nat.2023.0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Pathogenic variants in ABCA4 are the underlying molecular cause of Stargardt disease (STGD1), an autosomal recessive macular dystrophy characterized by a progressive loss of central vision. Among intronic ABCA4 variants, c.4253+43G>A is frequently detected in STGD1 cases and is classified as a hypomorphic allele, generally associated with late-onset cases. This variant was previously reported to alter splicing regulatory sequences, but the splicing outcome is not fully understood yet. In this study, we attempted to better understand its effect on splicing and to rescue the aberrant splicing via antisense oligonucleotides (AONs). Wild-type and c.4253+43G>A variant-harboring maxigene vectors revealed additional skipping events, which were not previously detected upon transfection in HEK293T cells. To restore exon inclusion, we designed a set of 27 AONs targeting either splicing silencer motifs or the variant region and screened these in maxigene-transfected HEK293T cells. Candidate AONs able to promote exon inclusion were selected for further testing in patient-derived photoreceptor precursor cells. Surprisingly, no robust splicing modulation was observed in this model system. Overall, this research helped to adequately characterize the splicing alteration caused by the c.4253+43G>A variant, although future development of AON-mediated exon inclusion therapy for ABCA4 is needed.
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Affiliation(s)
- Nuria Suárez-Herrera
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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Suárez-Herrera N, Riswick IB, Vázquez-Domínguez I, Duijkers L, Karjosukarso DW, Piccolo D, Bauwens M, De Baere E, Cheetham ME, Garanto A, Collin RWJ. Proof-of-concept for multiple AON delivery by a single U7snRNA vector to restore splicing defects in ABCA4. Mol Ther 2024; 32:837-851. [PMID: 38243599 PMCID: PMC10928313 DOI: 10.1016/j.ymthe.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/13/2023] [Accepted: 01/12/2024] [Indexed: 01/21/2024] Open
Abstract
The high allelic heterogeneity in Stargardt disease (STGD1) complicates the design of intervention strategies. A significant proportion of pathogenic intronic ABCA4 variants alters the pre-mRNA splicing process. Antisense oligonucleotides (AONs) are an attractive yet mutation-specific therapeutic strategy to restore these splicing defects. In this study, we experimentally assessed the potential of a splicing modulation therapy to target multiple intronic ABCA4 variants. AONs were inserted into U7snRNA gene cassettes and tested in midigene-based splice assays. Five potent antisense sequences were selected to generate a multiple U7snRNA cassette construct, and this combination vector showed substantial rescue of all of the splicing defects. Therefore, the combination cassette was used for viral synthesis and assessment in patient-derived photoreceptor precursor cells (PPCs). Simultaneous delivery of several modified U7snRNAs through a single AAV, however, did not show substantial splicing correction, probably due to suboptimal transduction efficiency in PPCs and/or a heterogeneous viral population containing incomplete AAV genomes. Overall, these data demonstrate the potential of the U7snRNA system to rescue multiple splicing defects, but also suggest that AAV-associated challenges are still a limiting step, underscoring the need for further optimization before implementing this strategy as a potential treatment for STGD1.
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Affiliation(s)
- Nuria Suárez-Herrera
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | - Iris B Riswick
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | - Irene Vázquez-Domínguez
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | - Lonneke Duijkers
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | - Dyah W Karjosukarso
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | | | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | | | - Alejandro Garanto
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands; Radboud University Medical Center, Amalia Children's Hospital, Department of Pediatrics, Nijmegen 6252GA, the Netherlands
| | - Rob W J Collin
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands.
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Williams BN, Draper A, Lang PF, Lewis TR, Smith AL, Mayerl SJ, Rougié M, Simon JM, Arshavsky VY, Greenwald SH, Gamm DM, Pinilla I, Philpot BD. Heterogeneity in the progression of retinal pathologies in mice harboring patient mimicking Impg2 mutations. Hum Mol Genet 2024; 33:448-464. [PMID: 37975905 PMCID: PMC10877459 DOI: 10.1093/hmg/ddad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023] Open
Abstract
Biallelic mutations in interphotoreceptor matrix proteoglycan 2 (IMPG2) in humans cause retinitis pigmentosa (RP) with early macular involvement, albeit the disease progression varies widely due to genetic heterogeneity and IMPG2 mutation type. There are currently no treatments for IMPG2-RP. To aid preclinical studies toward eventual treatments, there is a need to better understand the progression of disease pathology in appropriate animal models. Toward this goal, we developed mouse models with patient mimicking homozygous frameshift (T807Ter) or missense (Y250C) Impg2 mutations, as well as mice with a homozygous frameshift mutation (Q244Ter) designed to completely prevent IMPG2 protein expression, and characterized the trajectory of their retinal pathologies across postnatal development until late adulthood. We found that the Impg2T807Ter/T807Ter and Impg2Q244Ter/Q244Ter mice exhibited early onset gliosis, impaired photoreceptor outer segment maintenance, appearance of subretinal deposits near the optic disc, disruption of the outer retina, and neurosensorial detachment, whereas the Impg2Y250C/Y250C mice exhibited minimal retinal pathology. These results demonstrate the importance of mutation type in disease progression in IMPG2-RP and provide a toolkit and preclinical data for advancing therapeutic approaches.
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Affiliation(s)
- Brittany N Williams
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, United States
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States
- Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Adam Draper
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, United States
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Patrick F Lang
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, United States
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Tylor R Lewis
- Department of Ophthalmology, Duke University, Durham, NC 27705, United States
| | - Audrey L Smith
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, United States
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Steven J Mayerl
- Department of Ophthalmology and Visual Sciences, McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Marie Rougié
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, United States
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Jeremy M Simon
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, United States
- Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University, Durham, NC 27705, United States
| | | | - David M Gamm
- Department of Ophthalmology and Visual Sciences, McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Isabel Pinilla
- Department of Ophthalmology, Lozano Blesa University Hospital, Zaragoza 50009, Spain
- Aragón Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
- Department of Surgery, University of Zaragoza, Zaragoza 50009, Spain
| | - Benjamin D Philpot
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, United States
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, United States
- Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC 27599, United States
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Birtel J, Caswell R, De Silva SR, Herrmann P, Rehman S, Lotery AJ, Mahroo OA, Michaelides M, Webster AR, MacLaren RE, Charbel Issa P. IMPG2-Related Maculopathy. Am J Ophthalmol 2024; 258:32-42. [PMID: 37806544 DOI: 10.1016/j.ajo.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 10/01/2023] [Accepted: 10/01/2023] [Indexed: 10/10/2023]
Abstract
PURPOSE To investigate the phenotype, variability, and penetrance of IMPG2-related maculopathy. DESIGN Retrospective observational case series. METHODS Clinical evaluation, multimodal retinal imaging, genetic testing, and molecular modeling. RESULTS A total of 25 individuals with a mono-allelic IMPG2 variant were included, 5 of whom were relatives of patients with IMPG2-associated retinitis pigmentosa. A distinct maculopathy was present in 17 individuals (median age, 52 years; range, 20-72 years), and included foveal elevation with or without subretinal vitelliform material or focal atrophy of the retinal pigment epithelium. Best-corrected visual acuity (BCVA) was ≥20/50 in the better eye (n = 15), and 5 patients were asymptomatic. Longitudinal observation (n = 8, up to 19 years) demonstrated stable maculopathy (n = 3), partial/complete resorption (n = 4) or increase (n = 1) of the subretinal material, with overall stable vision (n = 6). No manifest maculopathy was observed in 8 individuals (median age, 58 years; range, 43-83 years; BCVA ≥20/25), all were identified through segregation analysis. All 8 individuals were asymptomatic, with minimal foveal changes observed on optical coherence tomography in 3 cases. A total of 18 different variants were detected, 11 of them truncating. Molecular modeling of 5 missense variants [c.727G>C, c.1124C>A, c.2816T>A, c.3047T>C, and c.3193G>A] supported the hypothesis that these have a loss-of-function effect. CONCLUSIONS Mono-allelic IMPG2 variants may result in haploinsufficiency manifesting as a maculopathy with variable penetrance and expressivity. Family members of patients with IMPG2-related retinitis pigmentosa may present with vitelliform lesions. The maculopathy often remains limited to the fovea and is usually associated with moderate visual impairment.
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Affiliation(s)
- Johannes Birtel
- From the Oxford Eye Hospital (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Nuffield Laboratory of Ophthalmology (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom; Department of Ophthalmology (J.B.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Department of Ophthalmology (J.B., P.H.), University of Bonn, Bonn, Germany
| | - Richard Caswell
- Exeter Genomics Laboratory (R.C.), Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Samantha R De Silva
- From the Oxford Eye Hospital (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Nuffield Laboratory of Ophthalmology (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust (S.R.D.S., O.A.M., M.M., A.R.W.), London, United Kingdom; UCL Institute of Ophthalmology (S.R.D.S., O.A.M., M.M., A.R.W.), University College London, London, United Kingdom
| | - Philipp Herrmann
- Department of Ophthalmology (J.B., P.H.), University of Bonn, Bonn, Germany
| | - Salwah Rehman
- From the Oxford Eye Hospital (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Nuffield Laboratory of Ophthalmology (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Andrew J Lotery
- Clinical Neurosciences (A.J.L.), Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Southampton Eye Unit (A.J.L.), University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Omar A Mahroo
- Moorfields Eye Hospital NHS Foundation Trust (S.R.D.S., O.A.M., M.M., A.R.W.), London, United Kingdom; UCL Institute of Ophthalmology (S.R.D.S., O.A.M., M.M., A.R.W.), University College London, London, United Kingdom
| | - Michel Michaelides
- Moorfields Eye Hospital NHS Foundation Trust (S.R.D.S., O.A.M., M.M., A.R.W.), London, United Kingdom; UCL Institute of Ophthalmology (S.R.D.S., O.A.M., M.M., A.R.W.), University College London, London, United Kingdom
| | - Andrew R Webster
- Moorfields Eye Hospital NHS Foundation Trust (S.R.D.S., O.A.M., M.M., A.R.W.), London, United Kingdom; UCL Institute of Ophthalmology (S.R.D.S., O.A.M., M.M., A.R.W.), University College London, London, United Kingdom
| | - Robert E MacLaren
- From the Oxford Eye Hospital (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Nuffield Laboratory of Ophthalmology (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Peter Charbel Issa
- From the Oxford Eye Hospital (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Nuffield Laboratory of Ophthalmology (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.
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Zekavat SM, Jorshery SD, Rauscher FG, Horn K, Sekimitsu S, Koyama S, Nguyen TT, Costanzo MC, Jang D, Burtt NP, Kühnapfel A, Shweikh Y, Ye Y, Raghu V, Zhao H, Ghassemi M, Elze T, Segrè AV, Wiggs JL, Del Priore L, Scholz M, Wang JC, Natarajan P, Zebardast N. Phenome- and genome-wide analyses of retinal optical coherence tomography images identify links between ocular and systemic health. Sci Transl Med 2024; 16:eadg4517. [PMID: 38266105 DOI: 10.1126/scitranslmed.adg4517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/03/2024] [Indexed: 01/26/2024]
Abstract
The human retina is a multilayered tissue that offers a unique window into systemic health. Optical coherence tomography (OCT) is widely used in eye care and allows the noninvasive, rapid capture of retinal anatomy in exquisite detail. We conducted genotypic and phenotypic analyses of retinal layer thicknesses using macular OCT images from 44,823 UK Biobank participants. We performed OCT layer cross-phenotype association analyses (OCT-XWAS), associating retinal thicknesses with 1866 incident conditions (median 10-year follow-up) and 88 quantitative traits and blood biomarkers. We performed genome-wide association studies (GWASs), identifying inherited genetic markers that influence retinal layer thicknesses and replicated our associations among the LIFE-Adult Study (N = 6313). Last, we performed a comparative analysis of phenome- and genome-wide associations to identify putative causal links between retinal layer thicknesses and both ocular and systemic conditions. Independent associations with incident mortality were detected for thinner photoreceptor segments (PSs) and, separately, ganglion cell complex layers. Phenotypic associations were detected between thinner retinal layers and ocular, neuropsychiatric, cardiometabolic, and pulmonary conditions. A GWAS of retinal layer thicknesses yielded 259 unique loci. Consistency between epidemiologic and genetic associations suggested links between a thinner retinal nerve fiber layer with glaucoma, thinner PS with age-related macular degeneration, and poor cardiometabolic and pulmonary function with a thinner PS. In conclusion, we identified multiple inherited genetic loci and acquired systemic cardio-metabolic-pulmonary conditions associated with thinner retinal layers and identify retinal layers wherein thinning is predictive of future ocular and systemic conditions.
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Affiliation(s)
- Seyedeh Maryam Zekavat
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Saman Doroodgar Jorshery
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Computer Science/Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1, Canada
- Department of Computer Science and Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Cardiovascular Imaging Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Franziska G Rauscher
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Leipzig University, Leipzig 04107, Germany
- Leipzig Research Centre for Civilization Diseases (LIFE), Leipzig University, Leipzig 04103, Germany
| | - Katrin Horn
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Leipzig University, Leipzig 04107, Germany
| | | | - Satoshi Koyama
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Trang T Nguyen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Maria C Costanzo
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dongkeun Jang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Noël P Burtt
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andreas Kühnapfel
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Leipzig University, Leipzig 04107, Germany
| | - Yusrah Shweikh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Yixuan Ye
- Computational Biology and Bioinformatics Program, Yale School of Medicine, New Haven, CT 06511, USA
| | - Vineet Raghu
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Cardiovascular Imaging Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hongyu Zhao
- Computational Biology and Bioinformatics Program, Yale School of Medicine, New Haven, CT 06511, USA
- School of Public Health, Yale University, New Haven, CT 06510, USA
| | - Marzyeh Ghassemi
- Departments of Computer Science/Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1, Canada
- Department of Computer Science and Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tobias Elze
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Ayellet V Segrè
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Janey L Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lucian Del Priore
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT 06510, USA
| | - Markus Scholz
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Leipzig University, Leipzig 04107, Germany
- Leipzig Research Centre for Civilization Diseases (LIFE), Leipzig University, Leipzig 04103, Germany
| | - Jay C Wang
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT 06510, USA
- Northern California Retina Vitreous Associates, Mountain View, CA 94040, USA
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nazlee Zebardast
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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6
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Kaltak M, Corradi Z, Collin RWJ, Swildens J, Cremers FPM. Stargardt disease-associated missense and synonymous ABCA4 variants result in aberrant splicing. Hum Mol Genet 2023; 32:3078-3089. [PMID: 37555651 PMCID: PMC10586196 DOI: 10.1093/hmg/ddad129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023] Open
Abstract
Missense variants in ABCA4 constitute ~50% of causal variants in Stargardt disease (STGD1). Their pathogenicity is attributed to their direct effect on protein function, whilst their potential impact on pre-mRNA splicing disruption remains poorly understood. Interestingly, synonymous ABCA4 variants have previously been classified as 'severe' variants based on in silico analyses. Here, we systemically investigated the role of synonymous and missense variants in ABCA4 splicing by combining computational predictions and experimental assays. To identify variants of interest, we used SpliceAI to ascribe defective splice predictions on a dataset of 5579 biallelic STGD1 probands. We selected those variants with predicted delta scores for acceptor/donor gain > 0.20, and no previous reports on their effect on splicing. Fifteen ABCA4 variants were selected, 4 of which were predicted to create a new splice acceptor site and 11 to create a new splice donor site. In addition, three variants of interest with delta scores < 0.20 were included. The variants were introduced in wild-type midigenes that contained 4-12 kb of ABCA4 genomic sequence, which were subsequently expressed in HEK293T cells. By using RT-PCR and Sanger sequencing, we identified splice aberrations for 16 of 18 analyzed variants. SpliceAI correctly predicted the outcomes for 15 out of 18 variants, illustrating its reliability in predicting the impact of coding ABCA4 variants on splicing. Our findings highlight a causal role for coding ABCA4 variants in splicing aberrations, improving the severity assessment of missense and synonymous ABCA4 variants, and guiding to new treatment strategies for STGD1.
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Affiliation(s)
- Melita Kaltak
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- R&D Department, ProQR Therapeutics, Leiden, 2333 CK, The Netherlands
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Jim Swildens
- R&D Department, ProQR Therapeutics, Leiden, 2333 CK, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
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7
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Zhou H, Arechavala-Gomeza V, Garanto A. Experimental Model Systems Used in the Preclinical Development of Nucleic Acid Therapeutics. Nucleic Acid Ther 2023; 33:238-247. [PMID: 37145922 PMCID: PMC10457615 DOI: 10.1089/nat.2023.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/23/2023] [Indexed: 05/07/2023] Open
Abstract
Preclinical evaluation of nucleic acid therapeutics (NATs) in relevant experimental model systems is essential for NAT drug development. As part of COST Action "DARTER" (Delivery of Antisense RNA ThERapeutics), a network of researchers in the field of RNA therapeutics, we have conducted a survey on the experimental model systems routinely used by our members in preclinical NAT development. The questionnaire focused on both cellular and animal models. Our survey results suggest that skin fibroblast cultures derived from patients is the most commonly used cellular model, while induced pluripotent stem cell-derived models are also highly reported, highlighting the increasing potential of this technology. Splice-switching antisense oligonucleotide is the most frequently investigated RNA molecule, followed by small interfering RNA. Animal models are less prevalent but also widely used among groups in the network, with transgenic mouse models ranking the top. Concerning the research fields represented in our survey, the mostly studied disease area is neuromuscular disorders, followed by neurometabolic diseases and cancers. Brain, skeletal muscle, heart, and liver are the top four tissues of interest reported. We expect that this snapshot of the current preclinical models will facilitate decision making and the share of resources between academics and industry worldwide to facilitate the development of NATs.
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Affiliation(s)
- Haiyan Zhou
- Genetics and Genomic Medicine Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Center, London, United Kingdom
| | - Virginia Arechavala-Gomeza
- Nucleic Acid Therapeutics for Rare Disorders (NAT-RD), Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Alejandro Garanto
- Department of Pediatrics, Amalia Children's Hospital, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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8
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Gaiani N, Bourgeois-Brunel L, Rocha D, Boulling A. Analysis of the impact of DGAT1 p.M435L and p.K232A variants on pre-mRNA splicing in a full-length gene assay. Sci Rep 2023; 13:8999. [PMID: 37268760 DOI: 10.1038/s41598-023-36142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023] Open
Abstract
DGAT1 is playing a major role in fat metabolism and triacylglyceride synthesis. Only two DGAT1 loss-of-function variants altering milk production traits in cattle have been reported to date, namely p.M435L and p.K232A. The p.M435L variant is a rare alteration and has been associated with skipping of exon 16 which results in a non-functional truncated protein, and the p.K232A-containing haplotype has been associated with modifications of the splicing rate of several DGAT1 introns. In particular, the direct causality of the p.K232A variant in decreasing the splicing rate of the intron 7 junction was validated using a minigene assay in MAC-T cells. As both these DGAT1 variants were shown to be spliceogenic, we developed a full-length gene assay (FLGA) to re-analyse p.M435L and p.K232A variants in HEK293T and MAC-T cells. Qualitative RT-PCR analysis of cells transfected with the full-length DGAT1 expression construct carrying the p.M435L variant highlighted complete skipping of exon 16. The same analysis performed using the construct carrying the p.K232A variant showed moderate differences compared to the wild-type construct, suggesting a possible effect of this variant on the splicing of intron 7. Finally, quantitative RT-PCR analyses of cells transfected with the p.K232A-carrying construct did not show any significant modification on the splicing rate of introns 1, 2 and 7. In conclusion, the DGAT1 FLGA confirmed the p.M435L impact previously observed in vivo, but invalidated the hypothesis whereby the p.K232A variant strongly decreased the splicing rate of intron 7.
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Affiliation(s)
- Nicolas Gaiani
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Dominique Rocha
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Arnaud Boulling
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
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9
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Zekavat SM, Jorshery SD, Shweikh Y, Horn K, Rauscher FG, Sekimitsu S, Kayoma S, Ye Y, Raghu V, Zhao H, Ghassemi M, Elze T, Segrè AV, Wiggs JL, Scholz M, Priore LD, Wang JC, Natarajan P, Zebardast N. Insights into human health from phenome- and genome-wide analyses of UK Biobank retinal optical coherence tomography phenotypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.16.23290063. [PMID: 37292770 PMCID: PMC10246137 DOI: 10.1101/2023.05.16.23290063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The human retina is a complex multi-layered tissue which offers a unique window into systemic health and disease. Optical coherence tomography (OCT) is widely used in eye care and allows the non-invasive, rapid capture of retinal measurements in exquisite detail. We conducted genome- and phenome-wide analyses of retinal layer thicknesses using macular OCT images from 44,823 UK Biobank participants. We performed phenome-wide association analyses, associating retinal thicknesses with 1,866 incident ICD-based conditions (median 10-year follow-up) and 88 quantitative traits and blood biomarkers. We performed genome-wide association analyses, identifying inherited genetic markers which influence the retina, and replicated our associations among 6,313 individuals from the LIFE-Adult Study. And lastly, we performed comparative association of phenome- and genome- wide associations to identify putative causal links between systemic conditions, retinal layer thicknesses, and ocular disease. Independent associations with incident mortality were detected for photoreceptor thinning and ganglion cell complex thinning. Significant phenotypic associations were detected between retinal layer thinning and ocular, neuropsychiatric, cardiometabolic and pulmonary conditions. Genome-wide association of retinal layer thicknesses yielded 259 loci. Consistency between epidemiologic and genetic associations suggested putative causal links between thinning of the retinal nerve fiber layer with glaucoma, photoreceptor segment with AMD, as well as poor cardiometabolic and pulmonary function with PS thinning, among other findings. In conclusion, retinal layer thinning predicts risk of future ocular and systemic disease. Furthermore, systemic cardio-metabolic-pulmonary conditions promote retinal thinning. Retinal imaging biomarkers, integrated into electronic health records, may inform risk prediction and potential therapeutic strategies.
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Affiliation(s)
- Seyedeh Maryam Zekavat
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Saman Doroodgar Jorshery
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Computer Science/Medicine, University of Toronto, Toronto, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
- Department of Computer Science and Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Cardiovascular Imaging Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yusrah Shweikh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Katrin Horn
- Institute for Medical Informatics, Statistics and Epidemiology University of Leipzig, Germany and Leipzig Research Centre for Civilization Diseases (LIFE), Leipzig University, Leipzig, Germany
| | - Franziska G. Rauscher
- Institute for Medical Informatics, Statistics and Epidemiology University of Leipzig, Germany and Leipzig Research Centre for Civilization Diseases (LIFE), Leipzig University, Leipzig, Germany
| | | | - Satoshi Kayoma
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yixuan Ye
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Vineet Raghu
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Imaging Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hongyu Zhao
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- School of Public Health, Yale University, New Haven, CT, USA
| | - Marzyeh Ghassemi
- Departments of Computer Science/Medicine, University of Toronto, Toronto, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
- Department of Computer Science and Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tobias Elze
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Ayellet V. Segrè
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Janey L. Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology University of Leipzig, Germany and Leipzig Research Centre for Civilization Diseases (LIFE), Leipzig University, Leipzig, Germany
| | - Lucian Del Priore
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT, USA
| | - Jay C. Wang
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT, USA
- Northern California Retina Vitreous Associates, Mountain View, CA
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nazlee Zebardast
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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10
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Zhou S, Zhu G, Xu Y, Gao R, Zhang M, Zeng Q, Su W, Wang R. Mendelian randomization study on the causal effect of chickenpox on dementia. J Med Virol 2023; 95:e28420. [PMID: 36546403 DOI: 10.1002/jmv.28420] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/04/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
Some viruses, such as varicella zoster virus, are associated with severe dementia. The present study aims to identify the causal link between chickenpox and dementia. To date, the largest publicly available genome-wide association study (GWAS) for chickenpox (710 cases and 211 856 controls from European individuals) and for dementia (5933 cases and 212 859 controls from European individuals) were used to performed this two-sample Mendelian randomization (MR) study. We found no significant pleiotropy or heterogeneity in all seven selected chickenpox genetic instrumental variants in dementia GWAS. Of seven chickenpox genetic variants, two are located in the intergenic region and five are located in intron. We found that as chickenpox genetically increased, dementia risk increased based on an inverse-variance weighted analysis (β = 0.070, 95% confidence interval [CI] for β: 0.014-0.126; odds ratio [OR] = 1.073, 95% CI for OR: 1.015-1.134; p = 0.014) and weighted median (β = 0.071, 95% CI for β: 0.002-0.141; OR = 1.074, 95% CI for OR: 1.002-1.152; p = 0.045). Reverse MR analysis showed no causal effect of dementia on chickenpox. Our analysis suggests a causal effect of genetically increased chickenpox on dementia risk. Thus, chickenpox may be a potential risk factor for dementia.
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Affiliation(s)
- Shan Zhou
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Gaizhi Zhu
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Yaqi Xu
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Ran Gao
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Min Zhang
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Qi Zeng
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Wenting Su
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Renxi Wang
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
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11
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The Predicted Splicing Variant c.11+5G>A in RPE65 Leads to a Reduction in mRNA Expression in a Cell-Specific Manner. Cells 2022; 11:cells11223640. [PMID: 36429068 PMCID: PMC9688607 DOI: 10.3390/cells11223640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/01/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
Pathogenic variants in RPE65 lead to retinal diseases, causing a vision impairment. In this work, we investigated the pathomechanism behind the frequent RPE65 variant, c.11+5G>A. Previous in silico predictions classified this change as a splice variant. Our prediction using novel software's suggested a 124-nt exon elongation containing a premature stop codon. This elongation was validated using midigenes-based approaches. Similar results were observed in patient-derived induced pluripotent stem cells (iPSC) and photoreceptor precursor cells. However, the splicing defect in all cases was detected at low levels and thereby does not fully explain the recessive condition of the resulting disease. Long-read sequencing discarded other rearrangements or variants that could explain the diseases. Subsequently, a more relevant model was employed: iPSC-derived retinal pigment epithelium (RPE) cells. In patient-derived iPSC-RPE cells, the expression of RPE65 was strongly reduced even after inhibiting a nonsense-mediated decay, contradicting the predicted splicing defect. Additional experiments demonstrated a cell-specific gene expression reduction due to the presence of the c.11+5G>A variant. This decrease also leads to the lack of the RPE65 protein, and differences in size and pigmentation between the patient and control iPSC-RPE. Altogether, our data suggest that the c.11+5G>A variant causes a cell-specific defect in the expression of RPE65 rather than the anticipated splicing defect which was predicted in silico.
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