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Daich Varela M, Jeste M, de Guimaraes TAC, Mahroo OA, Arno G, Webster AR, Michaelides M. Clinical, Ophthalmic, and Genetic Characterization of RPGRIP1-Associated Leber Congenital Amaurosis/Early-Onset Severe Retinal Dystrophy. Am J Ophthalmol 2024; 266:255-263. [PMID: 38768745 DOI: 10.1016/j.ajo.2024.05.007] [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: 11/16/2023] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
PURPOSE To present the clinical characteristics, retinal features, natural history, and genetics of RPGRIP1-associated early-onset severe retinal dystrophy (EOSRD)/Leber congenital amaurosis (LCA). DESIGN Retrospective case series. METHODS Review of clinical notes, multimodal retinal imaging, and molecular diagnosis of 18 patients (17 families) with EOSRD/LCA and disease-causing variants in RPGRIP1. RESULTS The mean age of visual symptoms onset was 0.87 ± 1 year (birth to 3 years), and the mean age at baseline visit was 11.4 ± 10.2 years (1-39 years). At the baseline visit, 44% of patients were legally blind (range, 2-39 years), and there was no significant association found between age and best-corrected visual acuity (BCVA) in cross-sectional analysis. Retinal evaluation showed an abolished electroretinogram or a cone-rod dystrophy pattern, no or minimal pigment deposits, a hyperautofluorescent ring at the posterior pole, and a largely preserved central macular architecture, with retained outer nuclear layer and ellipsoid zone island into adulthood. Eleven variants (48%) were previously unreported, and 13 families (76%) had a double-null (DN) genotype. Twelve patients (67%) had follow-up assessments over a 15.7 ± 9.5-year period. The rate of BCVA decline was 0.02 logarithm of the minimum angle of resolution (1 letter)/year. CONCLUSIONS RPGRIP1 EOSRD/LCA often presents at birth or early infancy, with nystagmus, decreased visual acuity, hyperopia, and photophobia. Patients with a DN genotype may develop symptoms earlier and have worse vision. Multimodal imaging may show a hyperautofluorescent posterior pole ring and relatively preserved central macular architecture, suggesting that the condition is a promising candidate for gene supplementation.
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Affiliation(s)
- Malena Daich Varela
- Moorfields Eye Hospital (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom
| | - Mrunmayi Jeste
- St Thomas' Hospital (M.J., O.A.M), London, United Kingdom
| | - Thales A C de Guimaraes
- Moorfields Eye Hospital (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom
| | - Omar A Mahroo
- Moorfields Eye Hospital (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom; St Thomas' Hospital (M.J., O.A.M), London, United Kingdom
| | - Gavin Arno
- Moorfields Eye Hospital (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom
| | - Andrew R Webster
- Moorfields Eye Hospital (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom
| | - Michel Michaelides
- Moorfields Eye Hospital (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom.
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2
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Dueñas Rey A, Del Pozo Valero M, Bouckaert M, Wood KA, Van den Broeck F, Daich Varela M, Thomas HB, Van Heetvelde M, De Bruyne M, Van de Sompele S, Bauwens M, Lenaerts H, Mahieu Q, Josifova D, Rivolta C, O'Keefe RT, Ellingford J, Webster AR, Arno G, Ayuso C, De Zaeytijd J, Leroy BP, De Baere E, Coppieters F. Combining a prioritization strategy and functional studies nominates 5'UTR variants underlying inherited retinal disease. Genome Med 2024; 16:7. [PMID: 38184646 PMCID: PMC10771650 DOI: 10.1186/s13073-023-01277-1] [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: 06/16/2023] [Accepted: 12/15/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND 5' untranslated regions (5'UTRs) are essential modulators of protein translation. Predicting the impact of 5'UTR variants is challenging and rarely performed in routine diagnostics. Here, we present a combined approach of a comprehensive prioritization strategy and functional assays to evaluate 5'UTR variation in two large cohorts of patients with inherited retinal diseases (IRDs). METHODS We performed an isoform-level re-analysis of retinal RNA-seq data to identify the protein-coding transcripts of 378 IRD genes with highest expression in retina. We evaluated the coverage of their 5'UTRs by different whole exome sequencing (WES) kits. The selected 5'UTRs were analyzed in whole genome sequencing (WGS) and WES data from IRD sub-cohorts from the 100,000 Genomes Project (n = 2397 WGS) and an in-house database (n = 1682 WES), respectively. Identified variants were annotated for 5'UTR-relevant features and classified into seven categories based on their predicted functional consequence. We developed a variant prioritization strategy by integrating population frequency, specific criteria for each category, and family and phenotypic data. A selection of candidate variants underwent functional validation using diverse approaches. RESULTS Isoform-level re-quantification of retinal gene expression revealed 76 IRD genes with a non-canonical retina-enriched isoform, of which 20 display a fully distinct 5'UTR compared to that of their canonical isoform. Depending on the probe design, 3-20% of IRD genes have 5'UTRs fully captured by WES. After analyzing these regions in both cohorts, we prioritized 11 (likely) pathogenic variants in 10 genes (ARL3, MERTK, NDP, NMNAT1, NPHP4, PAX6, PRPF31, PRPF4, RDH12, RD3), of which 7 were novel. Functional analyses further supported the pathogenicity of three variants. Mis-splicing was demonstrated for the PRPF31:c.-9+1G>T variant. The MERTK:c.-125G>A variant, overlapping a transcriptional start site, was shown to significantly reduce both luciferase mRNA levels and activity. The RDH12:c.-123C>T variant was found in cis with the hypomorphic RDH12:c.701G>A (p.Arg234His) variant in 11 patients. This 5'UTR variant, predicted to introduce an upstream open reading frame, was shown to result in reduced RDH12 protein but unaltered mRNA levels. CONCLUSIONS This study demonstrates the importance of 5'UTR variants implicated in IRDs and provides a systematic approach for 5'UTR annotation and validation that is applicable to other inherited diseases.
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Affiliation(s)
- Alfredo Dueñas Rey
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marta Del Pozo Valero
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Manon Bouckaert
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Katherine A Wood
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Filip Van den Broeck
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Malena Daich Varela
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Huw B Thomas
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Mattias Van Heetvelde
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Stijn Van de Sompele
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Hanne Lenaerts
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Quinten Mahieu
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | | | - Carlo Rivolta
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Raymond T O'Keefe
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Jamie Ellingford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
- Genomics England, London, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
- Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium.
- Department of Pharmaceutics, Ghent University, Ghent, Belgium.
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3
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Torii K, Nishina S, Morikawa H, Mizobuchi K, Takayama M, Tachibana N, Kurata K, Hikoya A, Sato M, Nakano T, Fukami M, Azuma N, Hayashi T, Saitsu H, Hotta Y. The Structural Abnormalities Are Deeply Involved in the Cause of RPGRIP1-Related Retinal Dystrophy in Japanese Patients. Int J Mol Sci 2023; 24:13678. [PMID: 37761981 PMCID: PMC10531429 DOI: 10.3390/ijms241813678] [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: 07/22/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
Leber congenital amaurosis (LCA) is the most severe form of inherited retinal dystrophy. RPGRIP1-related LCA accounts for 5-6% of LCA. We performed whole-exome sequencing and whole-genome sequencing (WGS) on 29 patients with clinically suspected LCA and examined ophthalmic findings in patients with biallelic pathogenic variants of RPGRIP1. In addition to five previously reported cases, we identified five cases from four families with compound heterozygous RPGRIP1 variants using WGS. Five patients had null variants comprising frameshift variants, an Alu insertion, and microdeletions. A previously reported 1339 bp deletion involving exon 18 was found in four cases, and the deletion was relatively prevalent in the Japanese population (allele frequency: 0.002). Microdeletions involving exon 1 were detected in four cases. In patients with RPGRIP1 variants, visual acuity remained low, ranging from light perception to 0.2, and showed no correlation with age. In optical coherence tomography images, the ellipsoid zone (EZ) length decreased with age in all but one case of unimpaired EZ. The retinal structure was relatively preserved in all cases; however, there were cases with great differences in visual function compared to their siblings and a 56-year-old patient who still had a faint EZ line. Structural abnormalities may be important genetic causes of RPGRIP1-related retinal dystrophy in Japanese patients, and WGS was useful for detecting them.
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Affiliation(s)
- Kaoruko Torii
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Sachiko Nishina
- Division of Ophthalmology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Hazuki Morikawa
- Division of Ophthalmology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Kei Mizobuchi
- Department of Ophthalmology, The Jikei University School of Medicine, 3-25-8 Nishi-shimbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Masakazu Takayama
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Nobutaka Tachibana
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Kentaro Kurata
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Akiko Hikoya
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Miho Sato
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Tadashi Nakano
- Department of Ophthalmology, The Jikei University School of Medicine, 3-25-8 Nishi-shimbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Noriyuki Azuma
- Division of Ophthalmology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Takaaki Hayashi
- Department of Ophthalmology, The Jikei University School of Medicine, 3-25-8 Nishi-shimbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Yoshihiro Hotta
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
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4
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Nabavizadeh N, Bressin A, Shboul M, Moreno Traspas R, Chia PH, Bonnard C, Szenker‐Ravi E, Sarıbaş B, Beillard E, Altunoglu U, Hojati Z, Drutman S, Freier S, El‐Khateeb M, Fathallah R, Casanova J, Soror W, Arafat A, Escande‐Beillard N, Mayer A, Reversade B. A progeroid syndrome caused by a deep intronic variant in TAPT1 is revealed by RNA/SI-NET sequencing. EMBO Mol Med 2023; 15:e16478. [PMID: 36652330 PMCID: PMC9906387 DOI: 10.15252/emmm.202216478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 01/19/2023] Open
Abstract
Exome sequencing has introduced a paradigm shift for the identification of germline variations responsible for Mendelian diseases. However, non-coding regions, which make up 98% of the genome, cannot be captured. The lack of functional annotation for intronic and intergenic variants makes RNA-seq a powerful companion diagnostic. Here, we illustrate this point by identifying six patients with a recessive Osteogenesis Imperfecta (OI) and neonatal progeria syndrome. By integrating homozygosity mapping and RNA-seq, we delineated a deep intronic TAPT1 mutation (c.1237-52 G>A) that segregated with the disease. Using SI-NET-seq, we document that TAPT1's nascent transcription was not affected in patients' fibroblasts, indicating instead that this variant leads to an alteration of pre-mRNA processing. Predicted to serve as an alternative splicing branchpoint, this mutation enhances TAPT1 exon 12 skipping, creating a protein-null allele. Additionally, our study reveals dysregulation of pathways involved in collagen and extracellular matrix biology in disease-relevant cells. Overall, our work highlights the power of transcriptomic approaches in deciphering the repercussions of non-coding variants, as well as in illuminating the molecular mechanisms of human diseases.
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Affiliation(s)
- Nasrinsadat Nabavizadeh
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
- Division of Genetics, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
| | | | - Mohammad Shboul
- Department of Medical Laboratory SciencesJordan University of Science and TechnologyIrbidJordan
| | - Ricardo Moreno Traspas
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
| | - Poh Hui Chia
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
| | - Carine Bonnard
- Model Development, A*STAR Skin Research Labs (A*SRL)Singapore CitySingapore
| | - Emmanuelle Szenker‐Ravi
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
| | - Burak Sarıbaş
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
| | | | - Umut Altunoglu
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
| | - Zohreh Hojati
- Division of Genetics, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
| | - Scott Drutman
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller BranchRockefeller UniversityNew YorkNYUSA
| | - Susanne Freier
- Max Planck Institute for Molecular GeneticsBerlinGermany
| | | | - Rajaa Fathallah
- National Center for Diabetes, Endocrinology and GeneticsAmmanJordan
| | - Jean‐Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller BranchRockefeller UniversityNew YorkNYUSA
- Laboratory of Human Genetics of Infectious Diseases, Necker BranchINSERM U1163, Necker Hospital for Sick ChildrenParisFrance
- Imagine InstituteUniversity of ParisParisFrance
- Howard Hughes Medical InstituteNew YorkNYUSA
- Pediatric Hematology and Immunology UnitNecker Hospital for Sick ChildrenParisFrance
| | - Wesam Soror
- National Center for Diabetes, Endocrinology and GeneticsAmmanJordan
| | - Alaa Arafat
- National Center for Diabetes, Endocrinology and GeneticsAmmanJordan
| | - Nathalie Escande‐Beillard
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
- Institute of Molecular and Cell Biology, A*STARSingapore CitySingapore
| | - Andreas Mayer
- Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Bruno Reversade
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
- Institute of Molecular and Cell Biology, A*STARSingapore CitySingapore
- Department of PaediatricsNational University of SingaporeSingapore CitySingapore
- Smart‐Health Initiative, BESE, KAUSTThuwalKingdom of Saudi Arabia
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5
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Li Y, Huang D, Pei Y, Wu Y, Xu R, Quan F, Gao H, Zhang J, Hou H, Zhang K, Li J. CasSABER for Programmable In Situ Visualization of Low and Nonrepetitive Gene Loci. Anal Chem 2023; 95:2992-3001. [PMID: 36703533 DOI: 10.1021/acs.analchem.2c04867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Site-specific imaging of target genes using CRISPR probes is essential for understanding the molecular mechanisms of gene function and engineering tools to modulate its downstream pathways. Herein, we develop CRISPR/Cas9-mediated signal amplification by exchange reaction (CasSABER) for programmable in situ imaging of low and nonrepetitive regions of the target gene in the cell nucleus. The presynthesized primer-exchange reaction (PER) probe is able to hybridize multiple fluorophore-bearing imager strands to specifically light up dCas9/sgRNA target-bound gene loci, enabling in situ imaging of fixed cellular gene loci with high specificity and signal-to-noise ratio. In combination with a multiround branching strategy, we successfully detected nonrepetitive gene regions using a single sgRNA. As an intensity-codable and orthogonal probe system, CasSABER enables the adjustable amplification of local signals in fixed cells, resulting in the simultaneous visualization of multicopy and single-copy gene loci with similar fluorescence intensity. Owing to avoiding the complexity of controlling in situ mutistep enzymatic reactions, CasSABER shows good reliability, sensitivity, and ease of implementation, providing a rapid and cost-effective molecular toolkit for studying multigene interaction in fundamental research and gene diagnosis.
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Affiliation(s)
- Yanan Li
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Di Huang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Yiran Pei
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Yonghua Wu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Ru Xu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Fenglei Quan
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Hua Gao
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Junli Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Hongwei Hou
- China National Tobacco Quality Supervision & Test Center, Zhengzhou450001, China
- Beijing Institute of Life Science and Technology, Beijing100083, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing100084, China
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6
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Daich Varela M, Bellingham J, Motta F, Jurkute N, Ellingford JM, Quinodoz M, Oprych K, Niblock M, Janeschitz-Kriegl L, Kaminska K, Cancellieri F, Scholl HPN, Lenassi E, Schiff E, Knight H, Black G, Rivolta C, Cheetham ME, Michaelides M, Mahroo OA, Moore AT, Webster AR, Arno G. Multidisciplinary team directed analysis of whole genome sequencing reveals pathogenic non-coding variants in molecularly undiagnosed inherited retinal dystrophies. Hum Mol Genet 2022; 32:595-607. [PMID: 36084042 PMCID: PMC9896476 DOI: 10.1093/hmg/ddac227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/23/2022] [Accepted: 09/04/2022] [Indexed: 02/07/2023] Open
Abstract
The purpose of this paper is to identify likely pathogenic non-coding variants in inherited retinal dystrophy (IRD) genes, using genome sequencing (GS). Patients with IRD were recruited to the study and underwent comprehensive ophthalmological evaluation and GS. The results of GS were investigated through virtual gene panel analysis, and plausible pathogenic variants and clinical phenotype evaluated by the multidisciplinary team (MDT) discussion. For unsolved patients in whom a specific gene was suspected to harbor a missed pathogenic variant, targeted re-analysis of non-coding regions was performed on GS data. Candidate variants were functionally tested by messenger RNA analysis, minigene or luciferase reporter assays. Previously unreported, likely pathogenic, non-coding variants in 7 genes (PRPF31, NDP, IFT140, CRB1, USH2A, BBS10 and GUCY2D), were identified in 11 patients. These were shown to lead to mis-splicing (PRPF31, IFT140, CRB1 and USH2A) or altered transcription levels (BBS10 and GUCY2D). MDT-led, phenotype-driven, non-coding variant re-analysis of GS is effective in identifying the missing causative alleles.
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Affiliation(s)
- Malena Daich Varela
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | | | - Fabiana Motta
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Department of Ophthalmology, Universidade Federal de Sao Paulo, Sao Paulo 04021001, Brazil
| | - Neringa Jurkute
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Jamie M Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | | | - Lucas Janeschitz-Kriegl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Eva Lenassi
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | | | | | - Graeme Black
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | - Michel Michaelides
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Omar A Mahroo
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Anthony T Moore
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK,University of California, San Francisco, CA 94607, USA
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Gavin Arno
- To whom correspondence should be addressed at: UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1 9EL, UK. Tel: +44 2076086971;
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7
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Lee J, Jeong H, Won D, Shin S, Lee ST, Choi JR, Byeon SH, Kuht HJ, Thomas MG, Han J. Noncanonical Splice Site and Deep Intronic FRMD7 Variants Activate Cryptic Exons in X-linked Infantile Nystagmus. Transl Vis Sci Technol 2022; 11:25. [PMID: 35762937 PMCID: PMC9251792 DOI: 10.1167/tvst.11.6.25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Purpose We aim to report noncoding pathogenic variants in patients with FRMD7-related infantile nystagmus (FIN). Methods Genome sequencing (n = 2 families) and reanalysis of targeted panel next generation sequencing (n = 2 families) was performed in genetically unsolved cases of suspected FIN. Previous sequence analysis showed no pathogenic coding variants in genes associated with infantile nystagmus. SpliceAI, SpliceRover, and Alamut consensus programs were used to annotate noncoding variants. Minigene splicing assay was performed to confirm aberrant splicing. In silico analysis of exonic splicing enhancer and silencer was also performed. Results FRMD7 intronic variants were identified based on genome sequencing and targeted next-generation sequencing analysis. These included c.285-12A>G (pedigree 1), c.284+63T>A (pedigrees 2 and 3), and c. 383-1368A>G (pedigree 4). All variants were absent in gnomAD, and the both c.285-12A>G and c.284+63T>A variants were predicted to enhance new splicing acceptor gains with SpliceAI, SpliceRover, and Alamut consensus approaches. However, the c.383-1368 A>G variant only had a significant impact score on the SpliceRover program. The c.383-1368A>G variant was predicted to promote pseudoexon inclusion by binding of exonic splicing enhancer. Aberrant exonizations were validated through minigene constructs, and all variants were segregated in the families. Conclusions Deep learning–based annotation of noncoding variants facilitates the discovery of hidden genetic variations in patients with FIN. This study provides evidence of effectiveness of combined deep learning–based splicing tools to identify hidden pathogenic variants in previously unsolved patients with infantile nystagmus. Translational Relevance These results demonstrate robust analysis using two deep learning splicing predictions and in vitro functional study can lead to finding hidden genetic variations in unsolved patients.
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Affiliation(s)
- Junwon Lee
- Institute of Vision Research, Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Han Jeong
- Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, South Korea.,Institute of Vision Research, Department of Ophthalmology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Dongju Won
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea.,Dxome Co., Ltd. Seongnam-si, Gyeonggi-do, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea.,Dxome Co., Ltd. Seongnam-si, Gyeonggi-do, South Korea
| | - Suk Ho Byeon
- Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, South Korea.,Institute of Vision Research, Department of Ophthalmology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Helen J Kuht
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, RKCSB, PO Box 65, Leicester LE2 7LX, UK
| | - Mervyn G Thomas
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, RKCSB, PO Box 65, Leicester LE2 7LX, UK
| | - Jinu Han
- Institute of Vision Research, Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
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8
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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9
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Beryozkin A, Aweidah H, Carrero Valenzuela RD, Berman M, Iguzquiza O, Cremers FPM, Khan MI, Swaroop A, Amer R, Khateb S, Ben-Yosef T, Sharon D, Banin E. Retinal Degeneration Associated With RPGRIP1: A Review of Natural History, Mutation Spectrum, and Genotype-Phenotype Correlation in 228 Patients. Front Cell Dev Biol 2021; 9:746781. [PMID: 34722527 PMCID: PMC8551679 DOI: 10.3389/fcell.2021.746781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/15/2021] [Indexed: 12/03/2022] Open
Abstract
Purpose:RPGRIP1 encodes a ciliary protein expressed in the photoreceptor connecting cilium. Mutations in this gene cause ∼5% of Leber congenital amaurosis (LCA) worldwide, but are also associated with cone–rod dystrophy (CRD) and retinitis pigmentosa (RP) phenotypes. Our purpose was to clinically characterize RPGRIP1 patients from our cohort, collect clinical data of additional RPGRIP1 patients reported previously in the literature, identify common clinical features, and seek genotype–phenotype correlations. Methods: Clinical data were collected from 16 patients of our cohort and 212 previously reported RPGRIP1 patients and included (when available) family history, best corrected visual acuity (BCVA), refraction, comprehensive ocular examination, optical coherence tomography (OCT) imaging, visual fields (VF), and full-field electroretinography (ffERG). Results: Out of 228 patients, the majority (197, 86%) were diagnosed with LCA, 18 (7%) with RP, and 13 (5%) with CRD. Age of onset was during early childhood (n = 133, average of 1.7 years). All patients but 6 had moderate hyperopia (n = 59, mean of 4.8D), and average BCVA was 0.06 Snellen (n = 124; only 10 patients had visual acuity [VA] > 0.10 Snellen). On funduscopy, narrowing of blood vessels was noted early in life. Most patients had mild bone spicule-like pigmentation starting in the midperiphery and later encroaching upon the posterior pole. OCT showed thinning of the outer nuclear layer (ONL), while cystoid changes and edema were relatively rare. VF were usually very constricted from early on. ffERG responses were non-detectable in the vast majority of cases. Most of the mutations are predicted to be null (363 alleles), and 93 alleles harbored missense mutations. Missense mutations were identified only in two regions: the RPGR-interacting domain and the C2 domains. Biallelic null mutations are mostly associated with a severe form of the disease, whereas biallelic missense mutations usually cause a milder disease (mostly CRD). Conclusion: Our results indicate that RPGRIP1 biallelic mutations usually cause severe retinal degeneration at an early age with a cone–rod pattern. However, most of the patients exhibit preservation of some (usually low) BCVA for a long period and can potentially benefit from gene therapy. Missense changes appear only in the conserved domains and are associated with a milder phenotype.
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Affiliation(s)
- Avigail Beryozkin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hamzah Aweidah
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Myriam Berman
- Ophthalmology, Clinical Department, Faculty of Medicine, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Oscar Iguzquiza
- Neurology, Clinical Department, Faculty of Medicine, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Muhammad Imran Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Radgonde Amer
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Samer Khateb
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamar Ben-Yosef
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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10
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Biswas P, Villanueva AL, Soto-Hermida A, Duncan JL, Matsui H, Borooah S, Kurmanov B, Richard G, Khan SY, Branham K, Huang B, Suk J, Bakall B, Goldberg JL, Gabriel L, Khan NW, Raghavendra PB, Zhou J, Devalaraja S, Huynh A, Alapati A, Zawaydeh Q, Weleber RG, Heckenlively JR, Hejtmancik JF, Riazuddin S, Sieving PA, Riazuddin SA, Frazer KA, Ayyagari R. Deciphering the genetic architecture and ethnographic distribution of IRD in three ethnic populations by whole genome sequence analysis. PLoS Genet 2021; 17:e1009848. [PMID: 34662339 PMCID: PMC8589175 DOI: 10.1371/journal.pgen.1009848] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 11/12/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
Patients with inherited retinal dystrophies (IRDs) were recruited from two understudied populations: Mexico and Pakistan as well as a third well-studied population of European Americans to define the genetic architecture of IRD by performing whole-genome sequencing (WGS). Whole-genome analysis was performed on 409 individuals from 108 unrelated pedigrees with IRDs. All patients underwent an ophthalmic evaluation to establish the retinal phenotype. Although the 108 pedigrees in this study had previously been examined for mutations in known IRD genes using a wide range of methodologies including targeted gene(s) or mutation(s) screening, linkage analysis and exome sequencing, the gene mutations responsible for IRD in these 108 pedigrees were not determined. WGS was performed on these pedigrees using Illumina X10 at a minimum of 30X depth. The sequence reads were mapped against hg19 followed by variant calling using GATK. The genome variants were annotated using SnpEff, PolyPhen2, and CADD score; the structural variants (SVs) were called using GenomeSTRiP and LUMPY. We identified potential causative sequence alterations in 61 pedigrees (57%), including 39 novel and 54 reported variants in IRD genes. For 57 of these pedigrees the observed genotype was consistent with the initial clinical diagnosis, the remaining 4 had the clinical diagnosis reclassified based on our findings. In seven pedigrees (12%) we observed atypical causal variants, i.e. unexpected genotype(s), including 4 pedigrees with causal variants in more than one IRD gene within all affected family members, one pedigree with intrafamilial genetic heterogeneity (different affected family members carrying causal variants in different IRD genes), one pedigree carrying a dominant causative variant present in pseudo-recessive form due to consanguinity and one pedigree with a de-novo variant in the affected family member. Combined atypical and large structural variants contributed to about 20% of cases. Among the novel mutations, 75% were detected in Mexican and 50% found in European American pedigrees and have not been reported in any other population while only 20% were detected in Pakistani pedigrees and were not previously reported. The remaining novel IRD causative variants were listed in gnomAD but were found to be very rare and population specific. Mutations in known IRD associated genes contributed to pathology in 63% Mexican, 60% Pakistani and 45% European American pedigrees analyzed. Overall, contribution of known IRD gene variants to disease pathology in these three populations was similar to that observed in other populations worldwide. This study revealed a spectrum of mutations contributing to IRD in three populations, identified a large proportion of novel potentially causative variants that are specific to the corresponding population or not reported in gnomAD and shed light on the genetic architecture of IRD in these diverse global populations.
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Affiliation(s)
- Pooja Biswas
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India
| | - Adda L. Villanueva
- Retina and Genomics Institute, Yucatán, México
- Laboratoire de Diagnostic Moleculaire, Hôpital Maisonneuve Rosemont, Montreal, Quebec, Canada
| | - Angel Soto-Hermida
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Jacque L. Duncan
- Ophthalmology, University of California San Francisco, San Francisco, California, United States of America
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Shyamanga Borooah
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Berzhan Kurmanov
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | | | - Shahid Y. Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kari Branham
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - Bonnie Huang
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - John Suk
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Benjamin Bakall
- Ophthalmology, University of Arizona College of Medicine Phoenix, Phoenix, Arizona, United States of America
| | - Jeffrey L. Goldberg
- Byers Eye Institute, Stanford, Palo Alto, California, United States of America
| | - Luis Gabriel
- Genetics and Ophthalmology, Genelabor, Goiânia, Brazil
| | - Naheed W. Khan
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - Pongali B. Raghavendra
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India
- School of Regenerative Medicine, Manipal University, Bengaluru, Karnataka, India
| | - Jason Zhou
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Sindhu Devalaraja
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Andrew Huynh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Akhila Alapati
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Qais Zawaydeh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Richard G. Weleber
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - John R. Heckenlively
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | - Paul A. Sieving
- National Eye Institute, Bethesda, Maryland, United States of America
- Ophthalmology & Vision Science, UC Davis Medical Center, California, United States of America
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kelly A. Frazer
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, Rady Children’s Hospital, Division of Genome Information Sciences, San Diego, California, United States of America
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
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11
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He Y, Xie RG, Lou JW, Li YW, Wang CL, Zhang VW, Li DZ. Exome-based preconception carrier testing for consanguineous couples in China. Prenat Diagn 2021; 41:1425-1429. [PMID: 34486758 DOI: 10.1002/pd.6018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 05/17/2021] [Accepted: 07/03/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE To evaluate the utility of clinical exome sequencing (ES)-based carrier screening in Chinese consanguineous couples. METHODS Consanguineous couples were screened for autosomal recessive (AR) disorders using the clinical ES of 5000 genes associated with human diseases. RESULTS We recruited 14 couples who elected to have sequencing. One couple was related as first cousins and 13 as second cousins. Both partners carrying the same pathogenic variant were detected in four couples. One couple was found in which one partner carried a splice variant, and the other had a missence variant of the same gene. These five couples were identified as being at risk of having a child affected by an AR disorder. CONCLUSION Our study demonstrates that ES-based preconception screening yields a clinical value for Chinese consanguineous couples. It enables to detect at-risk couples for rare AR diseases.
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Affiliation(s)
- Yi He
- Prenatal Diagnosis Unit, Dongguan Women and Children Healthcare Hospital, Dongguan, Guangdong, China
| | - Run-Gui Xie
- Prenatal Diagnosis Unit, Dongguan Women and Children Healthcare Hospital, Dongguan, Guangdong, China
| | - Ji-Wu Lou
- Prenatal Diagnosis Unit, Dongguan Women and Children Healthcare Hospital, Dongguan, Guangdong, China
| | - Yan-Wei Li
- Amcare Genomic Laboratory, Guangzhou, Guangdong, China
| | - Chun-Li Wang
- Amcare Genomic Laboratory, Guangzhou, Guangdong, China
| | | | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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12
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García Bohórquez B, Aller E, Rodríguez Muñoz A, Jaijo T, García García G, Millán JM. Updating the Genetic Landscape of Inherited Retinal Dystrophies. Front Cell Dev Biol 2021; 9:645600. [PMID: 34327195 PMCID: PMC8315279 DOI: 10.3389/fcell.2021.645600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/30/2021] [Indexed: 12/24/2022] Open
Abstract
Inherited retinal dystrophies (IRD) are a group of diseases characterized by the loss or dysfunction of photoreceptors and a high genetic and clinical heterogeneity. Currently, over 270 genes have been associated with IRD which makes genetic diagnosis very difficult. The recent advent of next generation sequencing has greatly facilitated the diagnostic process, enabling to provide the patients with accurate genetic counseling in some cases. We studied 92 patients who were clinically diagnosed with IRD with two different custom panels. In total, we resolved 53 patients (57.6%); in 12 patients (13%), we found only one mutation in a gene with a known autosomal recessive pattern of inheritance; and 27 patients (29.3%) remained unsolved. We identified 120 pathogenic or likely pathogenic variants; 30 of them were novel. Among the cone-rod dystrophy patients, ABCA4 was the most common mutated gene, meanwhile, USH2A was the most prevalent among the retinitis pigmentosa patients. Interestingly, 10 families carried pathogenic variants in more than one IRD gene, and we identified two deep-intronic variants previously described as pathogenic in ABCA4 and CEP290. In conclusion, the IRD study through custom panel sequencing demonstrates its efficacy for genetic diagnosis, as well as the importance of including deep-intronic regions in their design. This genetic diagnosis will allow patients to make accurate reproductive decisions, enroll in gene-based clinical trials, and benefit from future gene-based treatments.
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Affiliation(s)
- Belén García Bohórquez
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
| | - Elena Aller
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
- Unit of Genetics, University Hospital La Fe, Valencia, Spain
| | - Ana Rodríguez Muñoz
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
| | - Teresa Jaijo
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
- Unit of Genetics, University Hospital La Fe, Valencia, Spain
| | - Gema García García
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
| | - José M. Millán
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
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13
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Simna SP, Han Z. Prospects Of Non-Coding Elements In Genomic Dna Based Gene Therapy. Curr Gene Ther 2021; 22:89-103. [PMID: 33874871 DOI: 10.2174/1566523221666210419090357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 11/22/2022]
Abstract
Gene therapy has made significant development since the commencement of the first clinical trials a few decades ago and has remained a dynamic area of research regardless of obstacles such as immune response and insertional mutagenesis. Progression in various technologies like next-generation sequencing (NGS) and nanotechnology has established the importance of non-coding segments of a genome, thereby taking gene therapy to the next level. In this review, we have summarized the importance of non-coding elements, highlighting the advantages of using full-length genomic DNA loci (gDNA) compared to complementary DNA (cDNA) or minigene, currently used in gene therapy. The focus of this review is to provide an overview of the advances and the future of potential use of gDNA loci in gene therapy, expanding the therapeutic repertoire in molecular medicine.
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Affiliation(s)
- S P Simna
- Department of Ophthalmology, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599. United States
| | - Zongchao Han
- Department of Ophthalmology, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599. United States
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14
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Zou G, Zhang T, Cheng X, Igelman AD, Wang J, Qian X, Fu S, Wang K, Koenekoop RK, Fishman GA, Yang P, Li Y, Pennesi ME, Chen R. Noncoding mutation in RPGRIP1 contributes to inherited retinal degenerations. Mol Vis 2021; 27:95-106. [PMID: 33907365 PMCID: PMC8056464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/16/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose Despite the extensive use of next-generation sequencing (NGS) technology to identify disease-causing genomic variations, a major gap in our understanding of Mendelian diseases is the unidentified molecular lesion in a significant portion of patients. For inherited retinal degenerations (IRDs), although currently close to 300 disease-associated genes have been identified, the mutations in approximately one-third of patients remain unknown. With mounting evidence that noncoding mutations might contribute significantly to disease burden, we aimed to systematically investigate the contributions of noncoding regions in the genome to IRDs. Methods In this study, we focused on RPGRIP1, which has been linked to various IRD phenotypes, including Leber congenital amaurosis (LCA), retinitis pigmentosa (RP), and macular dystrophy (MD). As several noncoding mutant alleles have been reported in RPGRIP1, and we observed that the mutation carrier frequency of RPGRIP1 is higher in patient cohorts with unsolved IRDs, we hypothesized that mutations in the noncoding regions of RPGRIP1 might be a significant contributor to pathogenicity. To test this hypothesis, we performed whole-genome sequencing (WGS) for 25 patients with unassigned IRD who carry a single mutation in RPGRIP1. Results Three noncoding variants in RPGRIP1, including a 2,890 bp deletion and two deep-intronic variants (c.2710+233G>A and c.1468-263G>C), were identified as putative second hits of RPGRIP1 in three patients with LCA. The mutant alleles were validated with direct sequencing or in vitro assays. Conclusions The results highlight the significance of the contribution of noncoding pathogenic variants to unsolved IRD cases.
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Affiliation(s)
- Gang Zou
- Department of Ophthalmology, Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest University for Nationalities, Ningxia Clinical Research Center on Diseases of Blindness in Eye, Yinchuan, China
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Tao Zhang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Xuesen Cheng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Austin D. Igelman
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon
| | - Jun Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Xinye Qian
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Shangyi Fu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Keqing Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Robert K. Koenekoop
- Department of Paediatric Surgery, Human Genetics and Adult Ophthalmology, MUHC, Montréal, Quebec, Canada
| | - Gerald A. Fishman
- Pangere Center for Inherited Retinal Diseases, The Chicago Lighthouse, Chicago, IL
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Mark E. Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
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15
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Qian X, Wang J, Wang M, Igelman AD, Jones KD, Li Y, Wang K, Goetz KE, Birch DG, Yang P, Pennesi ME, Chen R. Identification of Deep-Intronic Splice Mutations in a Large Cohort of Patients With Inherited Retinal Diseases. Front Genet 2021; 12:647400. [PMID: 33737949 PMCID: PMC7960924 DOI: 10.3389/fgene.2021.647400] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
High throughput sequencing technologies have revolutionized the identification of mutations responsible for a diverse set of Mendelian disorders, including inherited retinal disorders (IRDs). However, the causal mutations remain elusive for a significant proportion of patients. This may be partially due to pathogenic mutations located in non-coding regions, which are largely missed by capture sequencing targeting the coding regions. The advent of whole-genome sequencing (WGS) allows us to systematically detect non-coding variations. However, the interpretation of these variations remains a significant bottleneck. In this study, we investigated the contribution of deep-intronic splice variants to IRDs. WGS was performed for a cohort of 571 IRD patients who lack a confident molecular diagnosis, and potential deep intronic variants that affect proper splicing were identified using SpliceAI. A total of six deleterious deep intronic variants were identified in eight patients. An in vitro minigene system was applied to further validate the effect of these variants on the splicing pattern of the associated genes. The prediction scores assigned to splice-site disruption positively correlated with the impact of mutations on splicing, as those with lower prediction scores demonstrated partial splicing. Through this study, we estimated the contribution of deep-intronic splice mutations to unassigned IRD patients and leveraged in silico and in vitro methods to establish a framework for prioritizing deep intronic variant candidates for mechanistic and functional analyses.
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Affiliation(s)
- Xinye Qian
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Jun Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Meng Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Austin D Igelman
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR, United States
| | - Kaylie D Jones
- Retina Foundation of the Southwest and Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Keqing Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Kerry E Goetz
- Office of the Director, National Eye Institute/National Institutes of Health, Bethesda, MD, United States
| | - David G Birch
- Retina Foundation of the Southwest and Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR, United States
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR, United States
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
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16
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Perrault I, Hanein S, Gérard X, Mounguengue N, Bouyakoub R, Zarhrate M, Fourrage C, Jabot-Hanin F, Bocquet B, Meunier I, Zanlonghi X, Kaplan J, Rozet JM. Whole Locus Sequencing Identifies a Prevalent Founder Deep Intronic RPGRIP1 Pathologic Variant in the French Leber Congenital Amaurosis Cohort. Genes (Basel) 2021; 12:genes12020287. [PMID: 33670832 PMCID: PMC7922592 DOI: 10.3390/genes12020287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/10/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023] Open
Abstract
Leber congenital amaurosis (LCA) encompasses the earliest and most severe retinal dystrophies and can occur as a non-syndromic or a syndromic disease. Molecular diagnosis in LCA is of particular importance in clinical decision-making and patient care since it can provide ocular and extraocular prognostics and identify patients eligible to develop gene-specific therapies. Routine high-throughput molecular testing in LCA yields 70%–80% of genetic diagnosis. In this study, we aimed to investigate the non-coding regions of one non-syndromic LCA gene, RPGRIP1, in a series of six families displaying one single disease allele after a gene-panel screening of 722 LCA families which identified 26 biallelic RPGRIP1 families. Using trio-based high-throughput whole locus sequencing (WLS) for second disease alleles, we identified a founder deep intronic mutation (NM_020366.3:c.1468-128T>G) in 3/6 families. We employed Sanger sequencing to search for the pathologic variant in unresolved LCA cases (106/722) and identified three additional families (two homozygous and one compound heterozygous with the NM_020366.3:c.930+77A>G deep intronic change). This makes the c.1468-128T>G the most frequent RPGRIP1 disease allele (8/60, 13%) in our cohort. Studying patient lymphoblasts, we show that the pathologic variant creates a donor splice-site and leads to the insertion of the pseudo-exon in the mRNA, which we were able to hamper using splice-switching antisense oligonucleotides (AONs), paving the way to therapies.
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Affiliation(s)
- Isabelle Perrault
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
- Correspondence:
| | - Sylvain Hanein
- Translational Genetics, Institute of Genetic Diseases, INSERM UMR1163, Imagine and Paris Descartes University, 75015 Paris, France;
| | - Xavier Gérard
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
| | - Nelson Mounguengue
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
| | - Ryme Bouyakoub
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
| | - Mohammed Zarhrate
- Genomics Platform, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France;
| | - Cécile Fourrage
- Bioinformatic Platform, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (C.F.); (F.J.-H.)
| | - Fabienne Jabot-Hanin
- Bioinformatic Platform, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (C.F.); (F.J.-H.)
- Bioinformatics Core Facility, Université Paris Descartes-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, 75015 Paris, France
| | - Béatrice Bocquet
- Centre de Référence des Affections Sensorielles Génétiques, Institut des Neurosciences de Montpellier, CHU-Saint Eloi Montpellier, 34091 Montpellier, France; (B.B.); (I.M.)
| | - Isabelle Meunier
- Centre de Référence des Affections Sensorielles Génétiques, Institut des Neurosciences de Montpellier, CHU-Saint Eloi Montpellier, 34091 Montpellier, France; (B.B.); (I.M.)
- National Reference Centre for Inherited Sensory Diseases, Univ Montpellier, CHU, 34091 Montpellier, France
| | - Xavier Zanlonghi
- Eye Clinic Jules Verne, 44300 Nantes, France;
- CHU, 35000 Rennes, France
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
- Ophthalmology Department, University Hospital Henri Mondor, APHP, 94000 Créteil, France
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
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17
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Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2021. [DOI: 10.1016/j.preteyeres.2020.100874
expr 921883647 + 833887994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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18
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The Role of Noncoding Variants in Heritable Disease. Trends Genet 2020; 36:880-891. [PMID: 32741549 DOI: 10.1016/j.tig.2020.07.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/26/2022]
Abstract
The genetic basis of disease has largely focused on coding regions. However, it has become clear that a large proportion of the noncoding genome is functional and harbors genetic variants that contribute to disease etiology. Here, we review recent examples of inherited noncoding alterations that are responsible for Mendelian disorders or act to influence complex traits. We explore both rare and common genetic variants and discuss the wide range of mechanisms by which they affect gene regulation to promote disease. We also debate the challenges and progress associated with identifying and interpreting the functional and clinical significance of genetic variation in the context of the noncoding regulatory landscape.
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19
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Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2020; 80:100874. [PMID: 32553897 DOI: 10.1016/j.preteyeres.2020.100874] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/15/2022]
Abstract
Mutations which induce aberrant transcript splicing represent a distinct class of disease-causing genetic variants in retinal disease genes. Such mutations may either weaken or erase regular splice sites or create novel splice sites which alter exon recognition. While mutations affecting the canonical GU-AG dinucleotides at the splice donor and splice acceptor site are highly predictive to cause a splicing defect, other variants in the vicinity of the canonical splice sites or those affecting additional cis-acting regulatory sequences within exons or introns are much more difficult to assess or even to recognize and require additional experimental validation. Splicing mutations are unique in that the actual outcome for the transcript (e.g. exon skipping, pseudoexon inclusion, intron retention) and the encoded protein can be quite different depending on the individual mutation. In this article, we present an overview on the current knowledge about and impact of splicing mutations in inherited retinal diseases. We introduce the most common sub-classes of splicing mutations including examples from our own work and others and discuss current strategies for the identification and validation of splicing mutations, as well as therapeutic approaches, open questions, and future perspectives in this field of research.
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20
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Copy-number variation contributes 9% of pathogenicity in the inherited retinal degenerations. Genet Med 2020; 22:1079-1087. [PMID: 32037395 PMCID: PMC7272325 DOI: 10.1038/s41436-020-0759-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/27/2020] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Current sequencing strategies can genetically solve 55-60% of inherited retinal degeneration (IRD) cases, despite recent progress in sequencing. This can partially be attributed to elusive pathogenic variants (PVs) in known IRD genes, including copy-number variations (CNVs), which have been shown as major contributors to unsolved IRD cases. METHODS Five hundred IRD patients were analyzed with targeted next-generation sequencing (NGS). The NGS data were used to detect CNVs with ExomeDepth and gCNV and the results were compared with CNV detection with a single-nucleotide polymorphism (SNP) array. Likely causal CNV predictions were validated by quantitative polymerase chain reaction (qPCR). RESULTS Likely disease-causing single-nucleotide variants (SNVs) and small indels were found in 55.6% of subjects. PVs in USH2A (11.6%), RPGR (4%), and EYS (4%) were the most common. Likely causal CNVs were found in an additional 8.8% of patients. Of the three CNV detection methods, gCNV showed the highest accuracy. Approximately 30% of unsolved subjects had a single likely PV in a recessive IRD gene. CONCLUSION CNV detection using NGS-based algorithms is a reliable method that greatly increases the genetic diagnostic rate of IRDs. Experimentally validating CNVs helps estimate the rate at which IRDs might be solved by a CNV plus a more elusive variant.
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21
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Gonzàlez-Duarte R, de Castro-Miró M, Tuson M, Ramírez-Castañeda V, Gils RV, Marfany G. Scaling New Heights in the Genetic Diagnosis of Inherited Retinal Dystrophies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1185:215-219. [PMID: 31884614 DOI: 10.1007/978-3-030-27378-1_35] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
During the last 20 years, our group has focused on identifying the genes and mutations causative of inherited retinal dystrophies (IRDs). By applying massive sequencing approaches (NGS) in more than 500 familial and sporadic cases, we attained high diagnostic efficiency (85%) with a custom target gene panel and over 75% using whole exome sequencing (WES). Close to 40% of pathogenic alleles are novel mutations, which demand specific in silico tests and in vitro assays. Notably, missense variants are by far the most common type of mutation identified (around 40%), with small in-frame indels being less frequent (2%). To fill the gap of unsolved cases, when no candidate gene or only a single pathogenic allele has been identified, additional scientific and technical issues remain to be addressed. Reliable detection of genomic rearrangements and copy number variants (partial or complete), deep intronic mutations, variants that cause aberrant splicing events in retina-specific transcripts, functional assessment of hypomorphic missense alleles, mutations in regulatory sequences, the contribution of modifier genes to the IRD phenotype, and detection of low heteroplasmy mtDNA mutations are among the new challenges to be met.
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Affiliation(s)
- Roser Gonzàlez-Duarte
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.
| | | | | | | | | | - Gemma Marfany
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.,DBGen Ocular Genomics SL, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain.,Institut de Biomedicina (IBUB-IRSJD), Universitat de Barcelona, Barcelona, Spain
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22
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Zeitz C, Michiels C, Neuillé M, Friedburg C, Condroyer C, Boyard F, Antonio A, Bouzidi N, Milicevic D, Veaux R, Tourville A, Zoumba A, Seneina I, Foussard M, Andrieu C, N Preising M, Blanchard S, Saraiva JP, Mesrob L, Le Floch E, Jubin C, Meyer V, Blanché H, Boland A, Deleuze JF, Sharon D, Drumare I, Defoort-Dhellemmes S, De Baere E, Leroy BP, Zanlonghi X, Casteels I, de Ravel TJ, Balikova I, Koenekoop RK, Laffargue F, McLean R, Gottlob I, Bonneau D, Schorderet DF, L Munier F, McKibbin M, Prescott K, Pelletier V, Dollfus H, Perdomo-Trujillo Y, Faure C, Reiff C, Wissinger B, Meunier I, Kohl S, Banin E, Zrenner E, Jurklies B, Lorenz B, Sahel JA, Audo I. Where are the missing gene defects in inherited retinal disorders? Intronic and synonymous variants contribute at least to 4% of CACNA1F-mediated inherited retinal disorders. Hum Mutat 2019; 40:765-787. [PMID: 30825406 DOI: 10.1002/humu.23735] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/15/2019] [Accepted: 02/26/2019] [Indexed: 12/27/2022]
Abstract
Inherited retinal disorders (IRD) represent clinically and genetically heterogeneous diseases. To date, pathogenic variants have been identified in ~260 genes. Albeit that many genes are implicated in IRD, for 30-50% of the cases, the gene defect is unknown. These cases may be explained by novel gene defects, by overlooked structural variants, by variants in intronic, promoter or more distant regulatory regions, and represent synonymous variants of known genes contributing to the dysfunction of the respective proteins. Patients with one subgroup of IRD, namely incomplete congenital stationary night blindness (icCSNB), show a very specific phenotype. The major cause of this condition is the presence of a hemizygous pathogenic variant in CACNA1F. A comprehensive study applying direct Sanger sequencing of the gene-coding regions, exome and genome sequencing applied to a large cohort of patients with a clinical diagnosis of icCSNB revealed indeed that seven of the 189 CACNA1F-related cases have intronic and synonymous disease-causing variants leading to missplicing as validated by minigene approaches. These findings highlight that gene-locus sequencing may be a very efficient method in detecting disease-causing variants in clinically well-characterized patients with a diagnosis of IRD, like icCSNB.
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Affiliation(s)
- Christina Zeitz
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | | | - Marion Neuillé
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | | | | | - Fiona Boyard
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Aline Antonio
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France
| | - Nassima Bouzidi
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Diana Milicevic
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Robin Veaux
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Aurore Tourville
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Axelle Zoumba
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Imene Seneina
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Marine Foussard
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Camille Andrieu
- CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France
| | - Markus N Preising
- Department of Ophthalmology, Justus-Liebig-University Giessen, Germany
| | | | | | - Lilia Mesrob
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France.,INSERM, Sorbonne Université, Paris, France
| | - Edith Le Floch
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Claire Jubin
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Hélène Blanché
- Fondation Jean Dausset-CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France.,Fondation Jean Dausset-CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Isabelle Drumare
- Service d'Exploration de la Vision et Neuro-ophtalmologie, CHRU de Lille, Lille, France
| | | | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Xavier Zanlonghi
- Clinique Jules Verne, Centre de Compétence Maladies Rares, Nantes, France
| | - Ingele Casteels
- Department of Ophthalmology, University Hospitals Leuven, Leuven, Belgium
| | | | - Irina Balikova
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Queen Fabiola Children's University Hospital, Brussels, Belgium
| | - Rob K Koenekoop
- Departments of Ophthalmology, Human Genetics, and Pediatric Surgery, Montreal Children's Hospital, McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | | | - Rebecca McLean
- Department of Neuroscience, Psychology and Behaviour, Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - Irene Gottlob
- Department of Neuroscience, Psychology and Behaviour, Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - Dominique Bonneau
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, Angers, France.,Mitovasc, UMR CNRS 6015-INSERM 1083, Université d'Angers, France
| | - Daniel F Schorderet
- Department of Ophthalmology, Jules-Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland.,IRO-Institute for Research in Ophthalmology, Sion, Switzerland.,Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Francis L Munier
- Department of Ophthalmology, Jules-Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland
| | - Martin McKibbin
- Department of Ophthalmology, St. James's University Hospital, Leeds, United Kingdom
| | | | - Valerie Pelletier
- Centre de référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Civil, Strasbourg, France.,Service de Génétique Médicale, Hôpital de Hautepierre, Strasbourg, France
| | - Hélène Dollfus
- Centre de référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Civil, Strasbourg, France.,Service de Génétique Médicale, Hôpital de Hautepierre, Strasbourg, France.,Laboratoire de Génétique Médicale, INSERM U1112, Strasbourg, France
| | - Yaumara Perdomo-Trujillo
- Centre de référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Civil, Strasbourg, France
| | - Céline Faure
- CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France.,Hôpital Privé Saint Martin, Ramsay Générale de Santé, Caen, France
| | | | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Isabelle Meunier
- Centre de Référence Maladies Sensorielles Génétiques, Hôpital Gui de Chauliac, Montpellier, France.,Institute for Neurosciences of Montpellier, Montpellier University and INSERM U1051, Montpellier, France
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eberhart Zrenner
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany.,Werner Reichardt Center for Integrative Neuroscience, University of Tübingen, Tübingen, Germany
| | | | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig-University Giessen, Germany
| | - José-Alain Sahel
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Academie des Sciences, Institut de France, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Isabelle Audo
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France.,Institute of Ophthalmology, University College of London, London, United Kingdom
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