51
|
Garces F, Jiang K, Molday LL, Stöhr H, Weber BH, Lyons CJ, Maberley D, Molday RS. Correlating the Expression and Functional Activity of ABCA4 Disease Variants With the Phenotype of Patients With Stargardt Disease. Invest Ophthalmol Vis Sci 2019; 59:2305-2315. [PMID: 29847635 PMCID: PMC5937799 DOI: 10.1167/iovs.17-23364] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Purpose Stargardt disease (STGD1), the most common early-onset recessive macular degeneration, is caused by mutations in the gene encoding the ATP-binding cassette transporter ABCA4. Although extensive genetic studies have identified more than 1000 mutations that cause STGD1 and related ABCA4-associated diseases, few studies have investigated the extent to which mutations affect the biochemical properties of ABCA4. The purpose of this study was to correlate the expression and functional activities of missense mutations in ABCA4 identified in a cohort of Canadian patients with their clinical phenotype. Methods Eleven patients from British Columbia were diagnosed with STGD1. The exons and exon-intron boundaries were sequenced to identify potential pathologic mutations in ABCA4. Missense mutations were expressed in HEK293T cells and their level of expression, retinoid substrate binding properties, and ATPase activities were measured and correlated with the phenotype of the STGD1 patients. Results Of the 11 STGD1 patients analyzed, 7 patients had two mutations in ABCA4, 3 patients had one detected mutation, and 1 patient had no mutations in the exons and flanking regions. Included in this cohort of patients was a severely affected 11-year-old child who was homozygous for the novel p.Ala1794Pro mutation. Expression and functional analysis of this variant and other disease-associated variants compared favorably with the phenotypes of this cohort of STGD1 patients. Conclusions Although many factors contribute to the phenotype of STGD1 patients, the expression and residual activity of ABCA4 mutants play a major role in determining the disease severity of STGD1 patients.
Collapse
Affiliation(s)
- Fabian Garces
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kailun Jiang
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Heidi Stöhr
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Bernhard H Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Christopher J Lyons
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Maberley
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
52
|
Bauwens M, Garanto A, Sangermano R, Naessens S, Weisschuh N, De Zaeytijd J, Khan M, Sadler F, Balikova I, Van Cauwenbergh C, Rosseel T, Bauwens J, De Leeneer K, De Jaegere S, Van Laethem T, De Vries M, Carss K, Arno G, Fakin A, Webster AR, de Ravel de l'Argentière TJL, Sznajer Y, Vuylsteke M, Kohl S, Wissinger B, Cherry T, Collin RWJ, Cremers FPM, Leroy BP, De Baere E. ABCA4-associated disease as a model for missing heritability in autosomal recessive disorders: novel noncoding splice, cis-regulatory, structural, and recurrent hypomorphic variants. Genet Med 2019; 21:1761-1771. [PMID: 30670881 PMCID: PMC6752479 DOI: 10.1038/s41436-018-0420-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 12/17/2018] [Indexed: 12/30/2022] Open
Abstract
Purpose ABCA4-associated disease, a recessive retinal dystrophy, is hallmarked by a large proportion of patients with only one pathogenic ABCA4 variant, suggestive for missing heritability. Methods By locus-specific analysis of ABCA4, combined with extensive functional studies, we aimed to unravel the missing alleles in a cohort of 67 patients (p), with one (p = 64) or no (p = 3) identified coding pathogenic variants of ABCA4. Results We identified eight pathogenic (deep-)intronic ABCA4 splice variants, of which five are novel and six structural variants, four of which are novel, including two duplications. Together, these variants account for the missing alleles in 40.3% of patients. Furthermore, two novel variants with a putative cis-regulatory effect were identified. The common hypomorphic variant c.5603A>T p.(Asn1868Ile) was found as a candidate second allele in 43.3% of patients. Overall, we have elucidated the missing heritability in 83.6% of our cohort. In addition, we successfully rescued three deep-intronic variants using antisense oligonucleotide (AON)-mediated treatment in HEK 293-T cells and in patient-derived fibroblast cells. Conclusion Noncoding pathogenic variants, novel structural variants, and a common hypomorphic allele of the ABCA4 gene explain the majority of unsolved cases with ABCA4-associated disease, rendering this retinopathy a model for missing heritability in autosomal recessive disorders.
Collapse
Affiliation(s)
- Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Riccardo Sangermano
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sarah Naessens
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Nicole Weisschuh
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Françoise Sadler
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Irina Balikova
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Caroline Van Cauwenbergh
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Jim Bauwens
- Department of Computer Science, Free University of Brussels, Brussels, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sarah De Jaegere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Thalia Van Laethem
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Meindert De Vries
- Department of Ophthalmology, Hôpital des Enfants Reine Fabiola, Brussels, Belgium
| | - Keren Carss
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, UK.,UK NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, London, UK
| | - Ana Fakin
- UCL Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | | | - Yves Sznajer
- Centre de Génétique Humaine, Cliniques Universitaires St. Luc, Université Catholique de Louvain, Brussels, Belgium
| | | | - Susanne Kohl
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Timothy Cherry
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bart P Leroy
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology and Center for Cellular & Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
| |
Collapse
|
53
|
Jonsson F, Westin IM, Österman L, Sandgren O, Burstedt M, Holmberg M, Golovleva I. ATP-binding cassette subfamily A, member 4 intronic variants c.4773+3A>G and c.5461-10T>C cause Stargardt disease due to defective splicing. Acta Ophthalmol 2018; 96:737-743. [PMID: 29461686 DOI: 10.1111/aos.13676] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/21/2017] [Indexed: 12/13/2022]
Abstract
PURPOSE Inherited retinal dystrophies (IRDs) represent a group of progressive conditions affecting the retina. There is a great genetic heterogeneity causing IRDs, and to date, more than 260 genes are associated with IRDs. Stargardt disease, type 1 (STGD1) or macular degeneration with flecks, STGD1 represents a disease with early onset, central visual impairment, frequent appearance of yellowish flecks and mutations in the ATP-binding cassette subfamily A, member 4 (ABCA4) gene. A large number of intronic sequence variants in ABCA4 have been considered pathogenic although their functional effect was seldom demonstrated. In this study, we aimed to reveal how intronic variants present in patients with Stargardt from the same Swedish family affect splicing. METHODS The splicing of the ABCA4 gene was studied in human embryonic kidney cells, HEK293T, and in human retinal pigment epithelium cells, ARPE-19, using a minigene system containing variants c.4773+3A>G and c.5461-10T>C. RESULTS We showed that both ABCA4 variants, c.4773+3A>G and c.5461-10T>C, cause aberrant splicing of the ABCA4 minigene resulting in exon skipping. We also demonstrated that splicing of ABCA4 has different outcomes depending on transfected cell type. CONCLUSION Two intronic variants c.4773+3A>G and c.5461-10T>C, both predicted to affect splicing, are indeed disease-causing mutations due to skipping of exons 33, 34, 39 and 40 of ABCA4 gene. The experimental proof that ABCA4 mutations in STGD patients affect protein function is crucial for their inclusion to future clinical trials; therefore, functional testing of all ABCA4 intronic variants associated with Stargardt disease by minigene technology is desirable.
Collapse
Affiliation(s)
- Frida Jonsson
- Medical Biosciences/Medical and Clinical Genetics; University of Umeå; Umeå Sweden
| | - Ida Maria Westin
- Medical Biosciences/Medical and Clinical Genetics; University of Umeå; Umeå Sweden
| | - Lennart Österman
- Medical Biosciences/Medical and Clinical Genetics; University of Umeå; Umeå Sweden
| | - Ola Sandgren
- Clinical Sciences/Ophthalmology; University of Umeå; Umeå Sweden
| | - Marie Burstedt
- Clinical Sciences/Ophthalmology; University of Umeå; Umeå Sweden
| | - Monica Holmberg
- Medical Biosciences/Medical and Clinical Genetics; University of Umeå; Umeå Sweden
| | - Irina Golovleva
- Medical Biosciences/Medical and Clinical Genetics; University of Umeå; Umeå Sweden
| |
Collapse
|
54
|
Sheremet NL, Grushke IG, Zhorzholadze NV, Tanas AS, Strelnikov VV. [Inherited retinal diseases in patients with ABCA4 gene mutations]. Vestn Oftalmol 2018; 134:68-73. [PMID: 30166513 DOI: 10.17116/oftalma201813404168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
ABCA4 is one of the main genes which mutations are associated with various inherited retinal diseases (IRD) such as Stargardt disease, cone dystrophy, cone-rod dystrophy, and retinitis pigmentosa. Wide prevalence of IRD, high heterogeneity of ABCA4 gene mutations that lead to impaired function of the protein with varying expressiveness make studying of the clinical and genetic characteristics of retinal diseases relevant for further investigations into pathogenesis, prognosis and outcome of the disease. This article reviews the literature on incidence of IRD caused by mutations in the ABCA4 gene and characteristics of the clinical progression of retinal diseases associated with various types of mutations, and presents analysis of clinical and genetic correlations in terms of the effect the mutation has on the structure or function of the protein.
Collapse
Affiliation(s)
- N L Sheremet
- Research Institute of Eye Diseases, 11, A, B, Rossolimo St., Moscow, Russian Federation, 119021
| | - I G Grushke
- Research Institute of Eye Diseases, 11, A, B, Rossolimo St., Moscow, Russian Federation, 119021
| | - N V Zhorzholadze
- Research Institute of Eye Diseases, 11, A, B, Rossolimo St., Moscow, Russian Federation, 119021
| | - A S Tanas
- Medicogenetic Research Center, 1 Moskvorechye St., Moscow, Russian Federation, 115478
| | - V V Strelnikov
- Medicogenetic Research Center, 1 Moskvorechye St., Moscow, Russian Federation, 115478
| |
Collapse
|
55
|
Nassisi M, Mohand-Saïd S, Dhaenens CM, Boyard F, Démontant V, Andrieu C, Antonio A, Condroyer C, Foussard M, Méjécase C, Eandi CM, Sahel JA, Zeitz C, Audo I. Expanding the Mutation Spectrum in ABCA4: Sixty Novel Disease Causing Variants and Their Associated Phenotype in a Large French Stargardt Cohort. Int J Mol Sci 2018; 19:E2196. [PMID: 30060493 PMCID: PMC6121640 DOI: 10.3390/ijms19082196] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/18/2018] [Accepted: 07/22/2018] [Indexed: 12/18/2022] Open
Abstract
Here we report novel mutations in ABCA4 with the underlying phenotype in a large French cohort with autosomal recessive Stargardt disease. The DNA samples of 397 index subjects were analyzed in exons and flanking intronic regions of ABCA4 (NM_000350.2) by microarray analysis and direct Sanger sequencing. At the end of the screening, at least two likely pathogenic mutations were found in 302 patients (76.1%) while 95 remained unsolved: 40 (10.1%) with no variants identified, 52 (13.1%) with one heterozygous mutation, and 3 (0.7%) with at least one variant of uncertain significance (VUS). Sixty-three novel variants were identified in the cohort. Three of them were variants of uncertain significance. The other 60 mutations were classified as likely pathogenic or pathogenic, and were identified in 61 patients (15.4%). The majority of those were missense (55%) followed by frameshift and nonsense (30%), intronic (11.7%) variants, and in-frame deletions (3.3%). Only patients with variants never reported in literature were further analyzed herein. Recruited subjects underwent complete ophthalmic examination including best corrected visual acuity, kinetic and static perimetry, color vision test, full-field and multifocal electroretinography, color fundus photography, short-wavelength and near-infrared fundus autofluorescence imaging, and spectral domain optical coherence tomography. Clinical evaluation of each subject confirms the tendency that truncating mutations lead to a more severe phenotype with electroretinogram (ERG) impairment (p = 0.002) and an earlier age of onset (p = 0.037). Our study further expands the mutation spectrum in the exonic and flanking regions of ABCA4 underlying Stargardt disease.
Collapse
Affiliation(s)
- Marco Nassisi
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
- Department of Surgical Sciences, Eye Clinic, University of Turin, 10126 Turin, Italy.
| | - Saddek Mohand-Saïd
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, F-75012 Paris, France.
| | - Claire-Marie Dhaenens
- Univ. Lille, Inserm UMR-S 1172, CHU Lille, Biochemistry and Molecular Biology Department-UF Génopathies, F-59000 Lille, France.
| | - Fiona Boyard
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - Vanessa Démontant
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - Camille Andrieu
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, F-75012 Paris, France.
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - Christel Condroyer
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - Marine Foussard
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - Cécile Méjécase
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - Chiara Maria Eandi
- Department of Surgical Sciences, Eye Clinic, University of Turin, 10126 Turin, Italy.
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, F-75012 Paris, France.
- Fondation Ophtalmologique Adolphe de Rothschild, F-75019 Paris, France.
- Académie des Sciences-Institut de France, F-75006 Paris, France.
- Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburg, PA 15213, USA.
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, F-75012 Paris, France.
- Institute of Ophthalmology, University College of London, London EC1V 9EL, UK.
| |
Collapse
|
56
|
Sisk RA, Hufnagel RB, Laham A, Wohler ES, Sobreira N, Ahmed ZM. Peripheral Cone Dystrophy: Expanded Clinical Spectrum, Multimodal and Ultrawide-Field Imaging, and Genomic Analysis. J Ophthalmol 2018; 2018:2984934. [PMID: 30116628 PMCID: PMC6079493 DOI: 10.1155/2018/2984934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/19/2018] [Accepted: 05/02/2018] [Indexed: 12/30/2022] Open
Abstract
PURPOSE To present new clinical features, multimodal and ultrawide-field imaging characteristics of peripheral cone dystrophy (PCD), and results of laboratory and genetic investigation to decipher the etiology. METHODS Retrospective observational case-series. RESULTS Three patients with PCD presented with bilateral paracentral scotomas and a mean visual acuity of 20/25. All exhibited confluent macular hyperautofluorescence with a central bull's eye lesion. Spectral-domain optical coherence tomography revealed loss of outer retinal elements, particularly the inner segment ellipsoid band and external limiting membrane, within the area of macular hyperautofluorescence. This area corresponded with a lightened fundus appearance and variable retinal pigment epithelium (RPE) abnormalities. Full field and multifocal electroretinography distinguished PCD from other photoreceptor dystrophies. Ultrawide-field imaging revealed irregular peripheral retinal lesions in a distribution greater nasally than temporally and not contiguous with the macular lesion. Functional and anatomic testing remained stable over a mean follow-up of 3 years. Laboratory investigation for causes of uveitis was negative. Whole exome sequencing identified rare variants in genes associated with macular or cone dystrophy or degeneration. CONCLUSIONS In contrast to the original description, the funduscopic and fluorescein angiographic appearance of PCD is abnormal, although the defects are subtle. Peripheral lesions may be observed in some patients. Bilateral, symmetric, macular hyperautofluorescence associated with outer retinal atrophy that spares the fovea is a characteristic of PCD. Pathogenic variants in the same gene were not shared across the cohort, suggesting genetic heterogeneity. Further evaluation is warranted.
Collapse
Affiliation(s)
- Robert A. Sisk
- Department of Ophthalmology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Cincinnati Eye Institute, Cincinnati, OH, USA
- Division of Pediatric Ophthalmology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Robert B. Hufnagel
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ailee Laham
- Department of Ophthalmology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Elizabeth S. Wohler
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology, School of Medicine, University of Maryland, Baltimore, MD, USA
| |
Collapse
|
57
|
Mutation Spectrum of the ABCA4 Gene in a Greek Cohort with Stargardt Disease: Identification of Novel Mutations and Evidence of Three Prevalent Mutated Alleles. J Ophthalmol 2018; 2018:5706142. [PMID: 29854428 PMCID: PMC5952432 DOI: 10.1155/2018/5706142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/15/2018] [Indexed: 11/18/2022] Open
Abstract
Aim To evaluate the frequency and pattern of disease-associated mutations of ABCA4 gene among Greek patients with presumed Stargardt disease (STGD1). Materials and Methods A total of 59 patients were analyzed for ABCA4 mutations using the ABCR400 microarray and PCR-based sequencing of all coding exons and flanking intronic regions. MLPA analysis as well as sequencing of two regions in introns 30 and 36 reported earlier to harbor deep intronic disease-associated variants was used in 4 selected cases. Results An overall detection rate of at least one mutant allele was achieved in 52 of the 59 patients (88.1%). Direct sequencing improved significantly the complete characterization rate, that is, identification of two mutations compared to the microarray analysis (93.1% versus 50%). In total, 40 distinct potentially disease-causing variants of the ABCA4 gene were detected, including six previously unreported potentially pathogenic variants. Among the disease-causing variants, in this cohort, the most frequent was c.5714+5G>A representing 16.1%, while p.Gly1961Glu and p.Leu541Pro represented 15.2% and 8.5%, respectively. Conclusions By using a combination of methods, we completely molecularly diagnosed 48 of the 59 patients studied. In addition, we identified six previously unreported, potentially pathogenic ABCA4 mutations.
Collapse
|
58
|
Albert S, Garanto A, Sangermano R, Khan M, Bax NM, Hoyng CB, Zernant J, Lee W, Allikmets R, Collin RW, Cremers FP. Identification and Rescue of Splice Defects Caused by Two Neighboring Deep-Intronic ABCA4 Mutations Underlying Stargardt Disease. Am J Hum Genet 2018. [PMID: 29526278 DOI: 10.1016/j.ajhg.2018.02.008] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Sequence analysis of the coding regions and splice site sequences in inherited retinal diseases is not able to uncover ∼40% of the causal variants. Whole-genome sequencing can identify most of the non-coding variants, but their interpretation is still very challenging, in particular when the relevant gene is expressed in a tissue-specific manner. Deep-intronic variants in ABCA4 have been associated with autosomal-recessive Stargardt disease (STGD1), but the exact pathogenic mechanism is unknown. By generating photoreceptor precursor cells (PPCs) from fibroblasts obtained from individuals with STGD1, we demonstrated that two neighboring deep-intronic ABCA4 variants (c.4539+2001G>A and c.4539+2028C>T) result in a retina-specific 345-nt pseudoexon insertion (predicted protein change: p.Arg1514Leufs∗36), likely due to the creation of exonic enhancers. Administration of antisense oligonucleotides (AONs) targeting the 345-nt pseudoexon can significantly rescue the splicing defect observed in PPCs of two individuals with these mutations. Intriguingly, an AON that is complementary to c.4539+2001G>A rescued the splicing defect only in PPCs derived from an individual with STGD1 with this but not the other mutation, demonstrating the high specificity of AONs. In addition, a single AON molecule rescued splicing defects associated with different neighboring mutations, thereby providing new strategies for the treatment of persons with STGD1. As many genes associated with human genetic conditions are expressed in specific tissues and pre-mRNA splicing may also rely on organ-specific factors, our approach to investigate and treat splicing variants using differentiated cells derived from individuals with STGD1 can be applied to any tissue of interest.
Collapse
|
59
|
Phenotypic Progression of Stargardt Disease in a Large Consanguineous Tunisian Family Harboring New ABCA4 Mutations. J Ophthalmol 2018; 2018:1030184. [PMID: 29736279 PMCID: PMC5875050 DOI: 10.1155/2018/1030184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 12/29/2017] [Accepted: 02/01/2018] [Indexed: 12/01/2022] Open
Abstract
To assess the progression of Stargardt (STGD) disease over nine years in two branches of a large consanguineous Tunisian family. Initially, different phenotypes were observed with clinical intra- and interfamilial variations. At presentation, four different retinal phenotypes were observed. In phenotype 1, bull's eye maculopathy and slight alteration of photopic responses in full-field electroretinography were observed in the youngest child. In phenotype 2, macular atrophy and yellow white were observed in two brothers. In phenotype 3, diffuse macular, peripapillary, and peripheral RPE atrophy and hyperfluorescent dots were observed in two sisters. In phenotype 4, Stargardt disease-fundus flavimaculatus phenotype was observed in two cousins with later age of onset. After a progression of 9 years, all seven patients displayed the same phenotype 3 with advanced stage STGD and diffuse atrophy. WES and MLPA identified two ABCA4 mutations M1: c.[(?_4635)_(5714+?)dup; (?_6148)_(6479_+?) del] and M2: c.[2041C>T], p.[R681∗]. In one branch, the three affected patients had M1/M1 causal mutations and in the other branch the two affected patients had M1/M2 causal mutations. After 9-year follow-up, all patients showed the same phenotypic evolution, confirming the progressive nature of the disease. Genetic variations in the two branches made no difference to similar end-stage disease.
Collapse
|
60
|
Stenirri S, Battistella S, Soriani N, Bernal S, Baiget M, Ferrari M, Cremonesi L. Molecular Scanning of the ABCA4 Gene in Spanish Patients with Retinitis Pigmentosa and Stargardt Disease: Identification of Novel Mutations. Eur J Ophthalmol 2018; 17:749-54. [DOI: 10.1177/112067210701700510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- S. Stenirri
- Genomic Unit for Diagnosis of Human Pathologies, San Raffaele Scientific Institute, Milano - Italy
| | - S. Battistella
- Genomic Unit for Diagnosis of Human Pathologies, San Raffaele Scientific Institute, Milano - Italy
| | - N. Soriani
- Genomic Unit for Diagnosis of Human Pathologies, San Raffaele Scientific Institute, Milano - Italy
| | - S. Bernal
- Servei de Genètica, Hospital Sant Pau, Barcelona - Spain
| | - M. Baiget
- Servei de Genètica, Hospital Sant Pau, Barcelona - Spain
| | - M. Ferrari
- Genomic Unit for Diagnosis of Human Pathologies, San Raffaele Scientific Institute, Milano - Italy
- Diagnostica e Ricerca San Raffaele SpA, Milano
- Università Vita-Salute San Raffaele, Milano - Italy
| | - L. Cremonesi
- Genomic Unit for Diagnosis of Human Pathologies, San Raffaele Scientific Institute, Milano - Italy
| |
Collapse
|
61
|
Schroeder M, Kjellström U. Full-field ERG as a predictor of the natural course of ABCA4-associated retinal degenerations. Mol Vis 2018; 24:1-16. [PMID: 29386879 PMCID: PMC5757858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 01/02/2018] [Indexed: 12/03/2022] Open
Abstract
PURPOSE To assess retinal function in combination with the retinal structure in ABCA4-associated retinal degenerations. Moreover, to evaluate the possibility of predicting the natural course of these disorders. METHODS 34 patients with Stargardt disease or cone rod dystrophy carrying confirmed mutations in ABCA4 were selected from our retinitis pigmentosa (RP) register. Sequence analysis of the entire coding region of the ABCA4 gene was performed. The patients were subdivided into three groups based on their most recent visual fields. Group 1 included ten patients with central scotomas within 10°, group 2 included 19 patients with larger central scotomas of 10-35°, and group 3 included five patients with mere temporal residues. The patients underwent slit-lamp and fundus examinations, visual acuity testing, optical coherence tomography (OCT), fundus photography (color, red-free, and autofluorescence (AF) images), full-field electroretinography (ffERG), and multifocal electroretinography (mERG). FfERG and mERG results were analyzed statistically. Total rod and cone function, as well as macular function, was compared between the three groups and of each group to a normal material. In 23 patients who had undergone ffERG on a previous occasion, the 30 Hz flicker implicit time (IT) from the first visit was also analyzed. RESULTS The ffERG statistics revealed significant differences between the groups regarding cone and rod function with group 1 showing the highest amplitudes and the shortest ITs while group 3 demonstrated the lowest amplitudes and the most delayed ITs. When compared to controls, group 1 did not show any significant changes while groups 2 and 3 demonstrated reduced amplitudes and delayed 30 Hz ITs. Regarding estimation of the natural course, identical results of the 30 Hz IT were encountered for the groups also at the first visit early in the course of disease. Comparison of the mERGs showed significant differences with group 1 demonstrating the highest amplitudes and group 3 the lowest for all rings but rings 2 and 3 in the right eye for which the amplitudes were the second highest. The mERGs for each group were also compared to controls showing reduced mERG amplitudes for all rings in all groups, except group 1, left eye. OCT showed macular attenuation in all patients. Evaluation of the inner and outer photoreceptor junction (IS/OS) morphology revealed alterations related to macular function measured with mERG in all eyes. Eight patients in group 1 showed foveal IS/OS junction loss, one had foveal IS/OS junction disorganization, and one had IS/OS loss also beyond the fovea. In group 2, one patient had IS/OS junction loss confined to the fovea, and the rest showed total loss of IS/OS junctions. Group 3 was devoid of IS/OS junctions. Concerning the AF images, group 1 showed small areas of absent AF in the macula, peripapillary sparing, and flecks of increased and reduced AF in the posterior pole. In group 2, the central areas of absent AF were larger. Flecks of reduced AF were the most dominant and reached beyond the posterior pole. Seven of 19 patients had peripapillary sparing. In group 3, large confluent areas of reduced AF were found in the posterior pole and beyond with small areas of increased AF in the far periphery. No peripapillary sparing was seen. CONCLUSIONS The current study demonstrates a significant difference in total retinal function, as well as macular function, between patients with ABCA4-associated retinal degeneration and a different degree of visual field defects with gradual deterioration of function along with increased visual field constriction. Likewise, the morphological changes, including the deviant AF pattern and loss of IS/OS junctions, that were related to macular function measured with mERG worsened with the degree of visual field defects. Moreover, in these groups of patients with ABCA4-associated retinal degenerations, full-field cone 30 Hz flicker IT seems to be a predictor of the natural course of the disease also on long-term follow-up.
Collapse
|
62
|
Sangermano R, Khan M, Cornelis SS, Richelle V, Albert S, Garanto A, Elmelik D, Qamar R, Lugtenberg D, van den Born LI, Collin RWJ, Cremers FPM. ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease. Genome Res 2018. [PMID: 29162642 DOI: 10.1101/gr.226621.117/-/dc1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Stargardt disease is caused by variants in the ABCA4 gene, a significant part of which are noncanonical splice site (NCSS) variants. In case a gene of interest is not expressed in available somatic cells, small genomic fragments carrying potential disease-associated variants are tested for splice abnormalities using in vitro splice assays. We recently discovered that when using small minigenes lacking the proper genomic context, in vitro results do not correlate with splice defects observed in patient cells. We therefore devised a novel strategy in which a bacterial artificial chromosome was employed to generate midigenes, splice vectors of varying lengths (up to 11.7 kb) covering almost the entire ABCA4 gene. These midigenes were used to analyze the effect of all 44 reported and three novel NCSS variants on ABCA4 pre-mRNA splicing. Intriguingly, multi-exon skipping events were observed, as well as exon elongation and intron retention. The analysis of all reported NCSS variants in ABCA4 allowed us to reveal the nature of aberrant splicing events and to classify the severity of these mutations based on the residual fraction of wild-type mRNA. Our strategy to generate large overlapping splice vectors carrying multiple exons, creating a toolbox for robust and high-throughput analysis of splice variants, can be applied to all human genes.
Collapse
Affiliation(s)
- Riccardo Sangermano
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Mubeen Khan
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.,Department of Biosciences, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan
| | - Stéphanie S Cornelis
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Valerie Richelle
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Silvia Albert
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Duaa Elmelik
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Raheel Qamar
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan
| | - Dorien Lugtenberg
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - L Ingeborgh van den Born
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands.,The Rotterdam Ophthalmic Institute, 3011 BH Rotterdam, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| |
Collapse
|
63
|
ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease. Genome Res 2017; 28:100-110. [PMID: 29162642 PMCID: PMC5749174 DOI: 10.1101/gr.226621.117] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/17/2017] [Indexed: 12/13/2022]
Abstract
Stargardt disease is caused by variants in the ABCA4 gene, a significant part of which are noncanonical splice site (NCSS) variants. In case a gene of interest is not expressed in available somatic cells, small genomic fragments carrying potential disease-associated variants are tested for splice abnormalities using in vitro splice assays. We recently discovered that when using small minigenes lacking the proper genomic context, in vitro results do not correlate with splice defects observed in patient cells. We therefore devised a novel strategy in which a bacterial artificial chromosome was employed to generate midigenes, splice vectors of varying lengths (up to 11.7 kb) covering almost the entire ABCA4 gene. These midigenes were used to analyze the effect of all 44 reported and three novel NCSS variants on ABCA4 pre-mRNA splicing. Intriguingly, multi-exon skipping events were observed, as well as exon elongation and intron retention. The analysis of all reported NCSS variants in ABCA4 allowed us to reveal the nature of aberrant splicing events and to classify the severity of these mutations based on the residual fraction of wild-type mRNA. Our strategy to generate large overlapping splice vectors carrying multiple exons, creating a toolbox for robust and high-throughput analysis of splice variants, can be applied to all human genes.
Collapse
|
64
|
Abeshi A, Zulian A, Beccari T, Dundar M, Ziccardi L, Bertelli M. Genetic testing for cone rod dystrophies. EUROBIOTECH JOURNAL 2017. [DOI: 10.24190/issn2564-615x/2017/s1.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Abstract
We studied the scientific literature and disease guidelines in order to summarize the clinical utility of the genetic test for cone rod dystrophies (CORDs). CORDs are caused by variations in the ABCA4, ADAM9, AIPL1, C8orf37, CACNA1F, CACNA2D4, CDHR1, CNGA3, CRX, DRAM2, GUCA1A, GUCY2D, HRG4, KCNV2, PDE6C, PITPNM3, POC1B, PROM1, PRPH2, RAB28, RAX2, RIMS1, RPGRIP1, RPGR SEMA4A, TTLL5 genes, with an overall prevalence of 1 per 40 000. Most genes have autosomal recessive inheritance; the others have autosomal dominant or X-linked recessive transmission. Clinical diagnosis is based on clinical findings, color vision testing, ophthalmological examination and electroretinography. The genetic test is useful for confirming diagnosis, and for differential diagnosis, couple risk assessment and access to clinical trials.
Collapse
Affiliation(s)
- Andi Abeshi
- MAGI Balkans, Tirana , Albania
- MAGI’S Lab, Rovereto , Italy
| | | | - Tommaso Beccari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia , Italy
| | - Munis Dundar
- Department of Medical Genetics, Erciyes University Medical School, Kayseri , Turkey
| | - Lucia Ziccardi
- Neurophthalmology Unit, “G.B. Bietti” Foundation IRCCS, Rome , Italy
| | | |
Collapse
|
65
|
Schulz HL, Grassmann F, Kellner U, Spital G, Rüther K, Jägle H, Hufendiek K, Rating P, Huchzermeyer C, Baier MJ, Weber BHF, Stöhr H. Mutation Spectrum of the ABCA4 Gene in 335 Stargardt Disease Patients From a Multicenter German Cohort-Impact of Selected Deep Intronic Variants and Common SNPs. Invest Ophthalmol Vis Sci 2017; 58:394-403. [PMID: 28118664 PMCID: PMC5270621 DOI: 10.1167/iovs.16-19936] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Purpose Stargardt disease (STGD1) is an autosomal recessive retinopathy, caused by mutations in the retina-specific ATP-binding cassette transporter (ABCA4) gene. To establish the mutational spectrum and to assess effects of selected deep intronic and common genetic variants on disease, we performed a comprehensive sequence analysis in a large cohort of German STGD1 patients. Methods DNA samples of 335 STGD1 patients were analyzed for ABCA4 mutations in its 50 coding exons and adjacent intronic sequences by resequencing array technology or next generation sequencing (NGS). Parts of intron 30 and 36 were screened by Sanger chain-terminating dideoxynucleotide sequencing. An in vitro splicing assay was used to test selected variants for their splicing behavior. By logistic regression analysis we assessed the association of common ABCA4 alleles while a multivariate logistic regression model calculated a genetic risk score (GRS). Results Our analysis identified 148 pathogenic or likely pathogenic mutations, of which 48 constitute so far unpublished ABCA4-associated disease alleles. Four rare deep intronic variants were found once in 472 alleles analyzed. In addition, we identified six risk-modulating common variants. Genetic risk score estimates suggest that defined common ABCA4 variants influence disease risk in carriers of a single pathogenic ABCA4 allele. Conclusions Our study adds to the mutational spectrum of the ABCA4 gene. Moreover, in our cohort, deep intronic variants in intron 30 and 36 likely play no or only a minor role in disease pathology. Of note, our findings demonstrate a possible modifying effect of common sequence variants on ABCA4-associated disease.
Collapse
Affiliation(s)
- Heidi L Schulz
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Felix Grassmann
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Ulrich Kellner
- Rare Retinal Disease Center, AugenZentrum Siegburg, MVZ ADTC Siegburg GmbH, Siegburg, Germany 3RetinaScience, Bonn, Germany
| | - Georg Spital
- Department of Ophthalmology, St. Franziskus-Hospital, Münster, Germany
| | | | - Herbert Jägle
- Department of Ophthalmology, University Hospital Regensburg, Regensburg, Germany
| | | | - Philipp Rating
- Department of Ophthalmology, University Hospital Essen, Essen, Germany
| | - Cord Huchzermeyer
- Department of Ophthalmology, University Hospital Erlangen, Erlangen, Germany
| | - Maria J Baier
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Heidi Stöhr
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| |
Collapse
|
66
|
Lee W, Schuerch K, Xie Y, Zernant J, Tsang SH, Sparrow JR, Allikmets R. Simultaneous Expression of ABCA4 and GPR143 Mutations: A Complex Phenotypic Manifestation. Invest Ophthalmol Vis Sci 2017; 57:3409-15. [PMID: 27367509 PMCID: PMC4961055 DOI: 10.1167/iovs.16-19621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Purpose To describe the complex, overlapping phenotype expressed in a two generation family harboring pathogenic mutations in the ABCA4 and GPR143 genes. Methods Clinical evaluation of a two generation family included quantitative autofluorescence imaging (qAF, 488-nm excitation) using a modified confocal scanning laser ophthalmoscope equipped with an internal fluorescent reference to account for varying laser power detector sensitivity, spectral-domain optical coherence tomography, and full-field ERG testing. Complete sequencing of the ABCA4 and GPR143 genes was carried out in each individual. Results Affected individuals presented with bull's eye lesions and qAF levels above the 95% confidence interval for healthy eyes; full-field ERG revealed no generalized rod dysfunction but mild implicit time delays in cone responses. Complete sequencing of the ABCA4 gene revealed two disease-causing mutations, p.L541P and p.G1961E; and mutational phase was confirmed in each unaffected parent. Further examination in the affected patients revealed a peripheral “mud-splattered” pattern of hypopigmented RPE after which sequencing of GPR143 revealed a novel missense variant, p.Y157C. The GPR143 variant segregated from the father who did not exhibit any indications of retinal disease with the exception of an abnormal near-infrared autofluorescence (NIR-AF) signal distribution in the macula. Conclusions An individual carrying both ABCA4 and GPR143 disease-causing mutations can express a complex, overlapping phenotype associated with both Stargardt disease and X-linked ocular albinism (OA1). The absence of OA1-related disease changes (with the exception of NIR-AF changes associated with melanin distribution) in the father may be indicative of mild expressivity or variable gene penetrance.
Collapse
Affiliation(s)
- Winston Lee
- Department of Ophthalmology, Columbia University, New York, New York, United States
| | - Kaspar Schuerch
- Department of Ophthalmology, Columbia University, New York, New York, United States
| | - Yajing Xie
- Department of Ophthalmology, Columbia University, New York, New York, United States
| | - Jana Zernant
- Department of Ophthalmology, Columbia University, New York, New York, United States
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University, New York, New York, United States 2Department of Pathology & Cell Biology, Columbia University, New York, New York, United States
| | - Janet R Sparrow
- Department of Ophthalmology, Columbia University, New York, New York, United States 2Department of Pathology & Cell Biology, Columbia University, New York, New York, United States
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, New York, United States 2Department of Pathology & Cell Biology, Columbia University, New York, New York, United States
| |
Collapse
|
67
|
Aukrust I, Jansson RW, Bredrup C, Rusaas HE, Berland S, Jørgensen A, Haug MG, Rødahl E, Houge G, Knappskog PM. The intronic ABCA4 c.5461-10T>C variant, frequently seen in patients with Stargardt disease, causes splice defects and reduced ABCA4 protein level. Acta Ophthalmol 2017; 95:240-246. [PMID: 27775217 DOI: 10.1111/aos.13273] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/27/2016] [Indexed: 12/23/2022]
Abstract
PURPOSE Despite being the third most common ABCA4 variant observed in patients with Stargardt disease, the functional effect of the intronic ABCA4 variant c.5461-10T>C is unknown. The purpose of this study was to investigate the molecular effect of this variant. METHODS Fibroblast samples from patients carrying the ABCA4 variant c.5461-10T>C were analysed by isolating total RNA, followed by real-time polymerase chain reaction (RT-PCR) using specific primers spanning the variant. For detection of ABCA4 protein, fibroblast samples were lysed and analysed by SDS-PAGE followed by immunoblotting using a monoclonal ABCA4 antibody. RESULTS The ABCA4 variant c.5461-10T>C causes a splicing defect resulting in the reduction of full-length mRNA in fibroblasts from patients and the presence of alternatively spliced mRNAs where exon 39-40 is skipped. A reduced level of full-length ABCA4 protein is observed compared to controls not carrying the variant. CONCLUSIONS This study describes the functional effect and the molecular mechanism of the pathogenic ABCA4 variant c.5461-10T>C. The variant is functionally important as it leads to splicing defects and a reduced level of ABCA4 protein.
Collapse
Affiliation(s)
- Ingvild Aukrust
- Center for Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen Norway
| | - Ragnhild W. Jansson
- Department of Ophthalmology; Haukeland University Hospital; Bergen Norway
- Department of Clinical Medicine; University of Bergen; Bergen Norway
| | - Cecilie Bredrup
- Department of Ophthalmology; Haukeland University Hospital; Bergen Norway
| | - Hilde E. Rusaas
- Center for Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen Norway
| | - Siren Berland
- Center for Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen Norway
| | - Agnete Jørgensen
- Division of Child and Adolescent Health; Medical Genetics Department; University Hospital of North Norway; Tromsø Norway
| | - Marte G. Haug
- Department of Pathology and Medical Genetics; St. Olav's University Hospital; Trondheim Norway
| | - Eyvind Rødahl
- Department of Ophthalmology; Haukeland University Hospital; Bergen Norway
- Department of Clinical Medicine; University of Bergen; Bergen Norway
| | - Gunnar Houge
- Center for Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen Norway
| | - Per M. Knappskog
- Center for Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen Norway
- Department of Clinical Science; University of Bergen; Bergen Norway
| |
Collapse
|
68
|
Zernant J, Lee W, Collison FT, Fishman GA, Sergeev YV, Schuerch K, Sparrow JR, Tsang SH, Allikmets R. Frequent hypomorphic alleles account for a significant fraction of ABCA4 disease and distinguish it from age-related macular degeneration. J Med Genet 2017; 54:404-412. [PMID: 28446513 DOI: 10.1136/jmedgenet-2017-104540] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/28/2017] [Accepted: 03/07/2017] [Indexed: 12/24/2022]
Abstract
BACKGROUND Variation in the ABCA4 gene is causal for, or associated with, a wide range of phenotypes from early onset Mendelian retinal dystrophies to late-onset complex disorders such as age-related macular degeneration (AMD). Despite substantial progress in determining the causal genetic variation, even complete sequencing of the entire open reading frame and splice sites of ABCA4 identifies biallelic mutations in only 60%-70% of cases; 20%-25% remain with one mutation and no mutations are found in 10%-15% of cases with clinically confirmed ABCA4 disease. This study was designed to identify missing causal variants specifically in monoallelic cases of ABCA4 disease. METHODS Direct sequencing and analysis were performed in a large familial ABCA4 disease cohort of predominately European descent (n=643). Patient phenotypes were assessed from clinical and retinal imaging data. RESULTS We determined that a hypomorphic ABCA4 variant c.5603A>T (p.Asn1868Ile), previously considered benign due to high minor allele frequency (MAF) (~7%) in the general population, accounts for 10% of the disease, >50% of the missing causal alleles in monoallelic cases, ~80% of late-onset cases and distinguishes ABCA4 disease from AMD. It results in a distinct clinical phenotype characterised by late-onset of symptoms (4th decade) and foveal sparing (85%). Intragenic modifying effects involving this variant and another, c.2588G>C (p.Gly863Ala) allele, were also identified. CONCLUSIONS These findings substantiate the causality of frequent missense variants and their phenotypic outcomes as a significant contribution to ABCA4 disease, particularly the late-onset phenotype, and its clinical variation. They also suggest a significant revision of diagnostic screening and assessment of ABCA4 variation in aetiology of retinal diseases.
Collapse
Affiliation(s)
- Jana Zernant
- Department of Ophthalmology, Columbia University, New York, New York, USA
| | - Winston Lee
- Department of Ophthalmology, Columbia University, New York, New York, USA
| | - Frederick T Collison
- The Pangere Center for Hereditary Retinal Diseases, The Chicago Lighthouse, Chicago, Illinois, USA
| | - Gerald A Fishman
- The Pangere Center for Hereditary Retinal Diseases, The Chicago Lighthouse, Chicago, Illinois, USA
| | - Yuri V Sergeev
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kaspar Schuerch
- Department of Ophthalmology, Columbia University, New York, New York, USA
| | - Janet R Sparrow
- Department of Ophthalmology, Columbia University, New York, New York, USA.,Department of Pathology & Cell Biology, Columbia University, New York, New York, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University, New York, New York, USA.,Department of Pathology & Cell Biology, Columbia University, New York, New York, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, New York, USA.,Department of Pathology & Cell Biology, Columbia University, New York, New York, USA
| |
Collapse
|
69
|
Lee W, Schuerch K, Zernant J, Collison FT, Bearelly S, Fishman GA, Tsang SH, Sparrow JR, Allikmets R. Genotypic spectrum and phenotype correlations of ABCA4-associated disease in patients of south Asian descent. Eur J Hum Genet 2017; 25:735-743. [PMID: 28327576 DOI: 10.1038/ejhg.2017.13] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/12/2016] [Accepted: 01/11/2017] [Indexed: 11/09/2022] Open
Abstract
Variants in the ABCA4 gene are the most common cause of juvenile-onset blindness affecting close to 1 in 10 000 people worldwide. Disease severity varies largely according to genotype, which can be specific to ethnic and racial groups. Here we investigate the spectrum of ABCA4 variation and its phenotypic expression in 38 patients of South Asian descent, notably from India, Pakistan, Bangladesh and Sri Lanka. Sequencing of all exons and flanking intronic sequences of ABCA4 revealed disease-causing variants in all patients: 3 in 2.6%, 2 in 81.6% and 1 in 15.8%. Altogether, 36 distinct variants were identified, including 9 previously not described. The most frequent variant c.5882G>A, p.(G1961E) was found in half the patients, the highest ever reported in a single study cohort. The South Asian founder variant c.859-9T>C was identified along with other founder variants ascribed to Danish, Chinese, Mexican and African patients. Patients carrying c.5882G>A, p.(G1961E) exhibited a consistently confined disease phenotype, normal quantitative autofluorescence (qAF) levels and preserved full-field ERG (ffERG) while c.859-9T>C resulted in widespread disease, significantly elevated qAF and reduced to non-detectable ffERG. South Asian patients present with a relatively unique ABCA4 profile comprised of various ethnic founder variants resulting in two or three major retinal phenotypes.
Collapse
Affiliation(s)
- Winston Lee
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Kaspar Schuerch
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Jana Zernant
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Frederick T Collison
- The Pangere Center for Inherited Retinal Diseases, The Chicago Lighthouse, Chicago, IL, USA
| | | | - Gerald A Fishman
- The Pangere Center for Inherited Retinal Diseases, The Chicago Lighthouse, Chicago, IL, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Janet R Sparrow
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| |
Collapse
|
70
|
Whole exome sequencing using Ion Proton system enables reliable genetic diagnosis of inherited retinal dystrophies. Sci Rep 2017; 7:42078. [PMID: 28181551 PMCID: PMC5299602 DOI: 10.1038/srep42078] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/05/2017] [Indexed: 01/17/2023] Open
Abstract
Inherited retinal dystrophies (IRD) comprise a wide group of clinically and genetically complex diseases that progressively affect the retina. Over recent years, the development of next-generation sequencing (NGS) methods has transformed our ability to diagnose heterogeneous diseases. In this work, we have evaluated the implementation of whole exome sequencing (WES) for the molecular diagnosis of IRD. Using Ion ProtonTM system, we simultaneously analyzed 212 genes that are responsible for more than 25 syndromic and non-syndromic IRD. This approach was used to evaluate 59 unrelated families, with the pathogenic variant(s) successfully identified in 71.18% of cases. Interestingly, the mutation detection rate varied substantially depending on the IRD subtype. Overall, we found 63 different mutations (21 novel) in 29 distinct genes, and performed in vivo functional studies to determine the deleterious impact of variants identified in MERTK, CDH23, and RPGRIP1. In addition, we provide evidences that support CDHR1 as a gene responsible for autosomal recessive retinitis pigmentosa with early macular affectation, and present data regarding the disease mechanism of this gene. Altogether, these results demonstrate that targeted WES of all IRD genes is a reliable, hypothesis-free approach, and a cost- and time-effective strategy for the routine genetic diagnosis of retinal dystrophies.
Collapse
|
71
|
Cornelis SS, Bax NM, Zernant J, Allikmets R, Fritsche LG, den Dunnen JT, Ajmal M, Hoyng CB, Cremers FPM. In Silico Functional Meta-Analysis of 5,962 ABCA4 Variants in 3,928 Retinal Dystrophy Cases. Hum Mutat 2017; 38:400-408. [PMID: 28044389 DOI: 10.1002/humu.23165] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 12/20/2016] [Accepted: 12/27/2016] [Indexed: 12/26/2022]
Abstract
Variants in the ABCA4 gene are associated with a spectrum of inherited retinal diseases (IRDs), most prominently with autosomal recessive (ar) Stargardt disease (STGD1) and ar cone-rod dystrophy. The clinical outcome to a large degree depends on the severity of the variants. To provide an accurate prognosis and to select patients for novel treatments, functional significance assessment of nontruncating ABCA4 variants is important. We collected all published ABCA4 variants from 3,928 retinal dystrophy cases in a Leiden Open Variation Database, and compared their frequency in 3,270 Caucasian IRD cases with 33,370 non-Finnish European control individuals. Next to the presence of 270 protein-truncating variants, 191 nontruncating variants were significantly enriched in the patient cohort. Furthermore, 30 variants were deemed benign. Assessing the homozygous occurrence of frequent variants in IRD cases based on the allele frequencies in control individuals confirmed the mild nature of the p.[Gly863Ala, Gly863del] variant and identified three additional mild variants (p.(Ala1038Val), c.5714+5G>A, and p.(Arg2030Gln)). The p.(Gly1961Glu) variant was predicted to act as a mild variant in most cases. Based on these data, in silico analyses, and American College of Medical Genetics and Genomics guidelines, we provide pathogenicity classifications on a five-tier scale from benign to pathogenic for all variants in the ABCA4-LOVD database.
Collapse
Affiliation(s)
- Stéphanie S Cornelis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nathalie M Bax
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Jana Zernant
- Department of Ophthalmology, Columbia University, New York, New York
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, New York.,Department of Pathology & Cell Biology, Columbia University, New York, New York
| | - Lars G Fritsche
- Department of Public Health, K.G. Jebsen Center for Genetic Epidemiology, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Johan T den Dunnen
- Departments of Clinical Genetics and Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Muhammad Ajmal
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| |
Collapse
|
72
|
Zolnikova IV, Strelnikov VV, Skvortsova NA, Tanas AS, Barh D, Rogatina EV, Egorova IV, Levina DV, Demenkova ON, Prikaziuk EG, Ivanova ME. Stargardt disease-associated mutation spectrum of a Russian Federation cohort. Eur J Med Genet 2016; 60:140-147. [PMID: 27939946 DOI: 10.1016/j.ejmg.2016.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/26/2016] [Accepted: 12/01/2016] [Indexed: 12/24/2022]
Abstract
ABCA4-associated mutation screening is extensively performed in European, African, American and several other populations for various retinopathies. However, it has not been well studied in a Russian cohort. Using next-generation (325 genes inherited disease panel) and Sanger sequencing technologies for the first time we documented the spectrum of genetic variations in a Russian retinopathy cohort of 51 patients from 10 ethnic groups. We found ABCA4 variations in 70.5% cases and one case with BEST1 variation. Multiple ABCA4 variations, ABCA4 + RDH12, and ABCA4 + BEST1 variations are also observed and the disease severity is found proportionate to the variation burden. Ten novel ABCA4 variations are detected of which 8 belongs to non-Slavonian population. Most of the detected known variations are found in European and American Stargardt disease populations. No retinopathy causing variation is detected in 14 (27%) cases suggesting that in this Russian retinopathies cohort the causal variants could be in genes that are not covered by our 325 gene panel. Therefore, whole genome/exome analysis is required to identify novel retinopathy associated genes and provide better disease management for this heterogeneous cohort.
Collapse
Affiliation(s)
- Inna V Zolnikova
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | | | - Natalia A Skvortsova
- Posterior Eye Segment Diagnostics and Surgery Centre, 2nd Vladimirskaya Str. b.2, 4th Floor, Moscow 111123, Russia
| | - Alexander S Tanas
- Research Centre for Medical Genetics, Moskvorechie Str. 1, Moscow 15478, Russia
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB 721172, India; Xcode Life Sciences, 3D Eldorado, 112 Nungambakkam High Road, Nungambakkam, Chennai, Tamil Nadu 600034, India.
| | - Elena V Rogatina
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Irina V Egorova
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Darja V Levina
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Olga N Demenkova
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Egor G Prikaziuk
- Bioinformatics Institute, Kantemirovskaya Str. b.2a, Saint Petersburg 197342, Russia
| | | |
Collapse
|
73
|
Wang X, Feng Y, Li J, Zhang W, Wang J, Lewis RA, Wong LJ. Retinal Diseases Caused by Mutations in Genes Not Specifically Associated with the Clinical Diagnosis. PLoS One 2016; 11:e0165405. [PMID: 27788217 PMCID: PMC5082937 DOI: 10.1371/journal.pone.0165405] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 10/11/2016] [Indexed: 12/15/2022] Open
Abstract
Purpose When seeking a confirmed molecular diagnosis in the research setting, patients with one descriptive diagnosis of retinal disease could carry pathogenic variants in genes not specifically associated with that description. However, this event has not been evaluated systematically in clinical diagnostic laboratories that validate fully all target genes to minimize false negatives/positives. Methods We performed targeted next-generation sequencing analysis on 207 ocular disease-related genes for 42 patients whose DNA had been tested negative for disease-specific panels of genes known to be associated with retinitis pigmentosa, Leber congenital amaurosis, or exudative vitreoretinopathy. Results Pathogenic variants, including single nucleotide variations and copy number variations, were identified in 9 patients, including 6 with variants in syndromic retinal disease genes and 3 whose molecular diagnosis could not be distinguished easily from their submitted clinical diagnosis, accounting for 21% (9/42) of the unsolved cases. Conclusion Our study underscores the clinical and genetic heterogeneity of retinal disorders and provides valuable reference to estimate the fraction of clinical samples whose retinal disorders could be explained by genes not specifically associated with the corresponding clinical diagnosis. Our data suggest that sequencing a larger set of retinal disorder related genes can increase the molecular diagnostic yield, especially for clinically hard-to-distinguish cases.
Collapse
Affiliation(s)
- Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Yanming Feng
- Baylor Genetics, Houston, Texas, United States of America
| | - Jianli Li
- Baylor Genetics, Houston, Texas, United States of America
| | - Wei Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jing Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Baylor Genetics, Houston, Texas, United States of America
- * E-mail:
| |
Collapse
|
74
|
Sangermano R, Bax NM, Bauwens M, van den Born LI, De Baere E, Garanto A, Collin RWJ, Goercharn-Ramlal ASA, den Engelsman-van Dijk AHA, Rohrschneider K, Hoyng CB, Cremers FPM, Albert S. Photoreceptor Progenitor mRNA Analysis Reveals Exon Skipping Resulting from the ABCA4 c.5461-10T→C Mutation in Stargardt Disease. Ophthalmology 2016; 123:1375-85. [PMID: 26976702 DOI: 10.1016/j.ophtha.2016.01.053] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/29/2016] [Accepted: 01/29/2016] [Indexed: 02/06/2023] Open
Abstract
PURPOSE To elucidate the functional effect of the ABCA4 variant c.5461-10T→C, one of the most frequent variants associated with Stargardt disease (STGD1). DESIGN Case series. PARTICIPANTS Seventeen persons with STGD1 carrying ABCA4 variants and 1 control participant. METHODS Haplotype analysis of 4 homozygotes and 11 heterozygotes for c.5461-10T→C and sequence analysis of the ABCA4 gene for a homozygous proband. Fibroblasts were reprogrammed from 3 persons with STGD1 into induced pluripotent stem cells, which were differentiated into photoreceptor progenitor cells (PPCs). The effect of the c.5461-10T→C variant on RNA splicing by reverse-transcription polymerase chain reaction was analyzed using PPC mRNA. In vitro assays were performed with minigene constructs containing ABCA4 exon 39. We analyzed the natural history and ophthalmologic characteristics of 4 persons homozygous for c.5461-10T→C. MAIN OUTCOME MEASURES Haplotype and rare variant data for ABCA4, RNA splice defects, age at diagnosis, visual acuity, fundus appearance, visual field, electroretinography (ERG) results, fluorescein angiography results, and fundus autofluorescence findings. RESULTS The frequent ABCA4 variant c.5461-10T→C has a subtle effect on splicing based on prediction programs. A founder haplotype containing c.5461-10T→C was found to span approximately 96 kb of ABCA4 and did not contain other rare sequence variants. Patient-derived PPCs showed skipping of exon 39 or exons 39 and 40 in the mRNA. HEK293T cell transduction with minigenes carrying exon 39 showed that the splice defects were the result of the c.5461-10T→C variant. All 4 subjects carrying the c.5461-10T→C variant in a homozygous state showed a young age of STGD1 onset, with low visual acuity at presentation and abnormal cone ERG results. All 4 demonstrated severe cone-rod dystrophy before 20 years of age and were legally blind by 25 years of age. CONCLUSIONS The ABCA4 variant c.5461-10T→C is located on a founder haplotype lacking other disease-causing rare sequence variants. In vitro studies revealed that it leads to mRNA exon skipping and ABCA4 protein truncation. Given the severe phenotype in persons homozygous for this variant, we conclude that this variant results in the absence of ABCA4 activity.
Collapse
Affiliation(s)
- Riccardo Sangermano
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Nathalie M Bax
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Miriam Bauwens
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | | | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | | | | | - Klaus Rohrschneider
- Universitätsaugenklinik, Ruprecht-Karls-Universität, Heidelberg, Heidelberg, Germany
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands.
| | - Silvia Albert
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands.
| |
Collapse
|
75
|
Abstract
PURPOSE OF REVIEW We are witnessing lightning-fast advances in the molecular diagnosis of inherited retinal dystrophies, mainly due to the widespread use of next-generation sequencing technologies. The purpose of this review is to highlight the breadth of findings from this in-depth testing approach, and to propose changes to our traditional testing and diagnostic paradigms. Lessons learned from modern molecular testing suggest that the previous concept of inherited retinal dystrophies as a group of 'single gene diseases' may require a significant update. RECENT FINDINGS All of the known retinal dystrophies genes can now be sequenced. In many cases, this nonhypothesis driven testing strategy is uncovering mutations in unsuspected genes, generating data that challenges established concepts of genetic mechanisms and provides insights regarding genes previously thought to be exclusively related to syndromic disease. Recent advances in testing have improved not only the breadth, but also the depth of genetic data. For example, deep intronic sequencing has uncovered many novel intronic mutations/variations in the ABCA4 gene. SUMMARY Currently, in approximately 50-60% of patients with nonsyndromic retinal dystrophy, the disease mechanism can be identified. The presence of pathogenic alleles in more than one gene is not uncommon. Retinal dystrophy, with relatively defined clinical presentations and a large but limited number of genes involved, is becoming a model for the next-generation study of molecular disease mechanisms.
Collapse
|
76
|
Ścieżyńska A, Oziębło D, Ambroziak AM, Korwin M, Szulborski K, Krawczyński M, Stawiński P, Szaflik J, Szaflik JP, Płoski R, Ołdak M. Next-generation sequencing of ABCA4: High frequency of complex alleles and novel mutations in patients with retinal dystrophies from Central Europe. Exp Eye Res 2015; 145:93-99. [PMID: 26593885 DOI: 10.1016/j.exer.2015.11.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 09/04/2015] [Accepted: 11/11/2015] [Indexed: 10/22/2022]
Abstract
Variation in the ABCA4 locus has emerged as the most prevalent cause of monogenic retinal diseases. The study aimed to discover causative ABCA4 mutations in a large but not previously investigated cohort with ABCA4-related diseases originating from Central Europe and to refine the genetic relevance of all identified variants based on population evidence. Comprehensive clinical studies were performed to identify patients with Stargardt disease (STGD, n = 76) and cone-rod dystrophy (CRD, n = 16). Next-generation sequencing targeting ABCA4 was applied for a widespread screening of the gene. The results were analyzed in the context of exome data from a corresponding population (n = 594) and other large genomic databases. Our data disprove the pathogenic status of p.V552I and provide more evidence against a causal role of four further ABCA4 variants as drivers of the phenotype under a recessive paradigm. The study identifies 12 novel potentially pathogenic mutations (four of them recurrent) and a novel complex allele p.[(R152*; V2050L)]. In one third (31/92) of our cohort we detected the p.[(L541P; A1038V)] complex allele, which represents an unusually high level of genetic homogeneity for ABCA4-related diseases. Causative ABCA4 mutations account for 79% of STGD and 31% of CRD cases. A combination of p.[(L541P; A1038V)] and/or a truncating ABCA4 mutation always resulted in an early disease onset. Identification of ABCA4 retinopathies provides a specific molecular diagnosis and justifies a prompt introduction of simple precautions that may slow disease progression. The comprehensive, population-specific study expands our knowledge on the genetic landscape of retinal diseases.
Collapse
Affiliation(s)
- Aneta Ścieżyńska
- Department of Histology and Embryology, Medical University of Warsaw, Warsaw, Poland
| | - Dominika Oziębło
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw/Kajetany, Poland
| | - Anna M Ambroziak
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland; Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Magdalena Korwin
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Kamil Szulborski
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Maciej Krawczyński
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland; Center for Medical Genetics GENESIS, Poznan, Poland
| | - Piotr Stawiński
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw/Kajetany, Poland
| | - Jerzy Szaflik
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Jacek P Szaflik
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.
| | - Monika Ołdak
- Department of Histology and Embryology, Medical University of Warsaw, Warsaw, Poland; Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw/Kajetany, Poland.
| |
Collapse
|
77
|
Complex inheritance of ABCA4 disease: four mutations in a family with multiple macular phenotypes. Hum Genet 2015; 135:9-19. [PMID: 26527198 DOI: 10.1007/s00439-015-1605-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/01/2015] [Indexed: 01/12/2023]
Abstract
Over 800 mutations in the ABCA4 gene cause autosomal recessive Stargardt disease. Due to extensive genetic heterogeneity, observed variant-associated phenotypes can manifest tremendous variability of expression. Furthermore, the high carrier frequency of pathogenic ABCA4 alleles in the general population (~1:20) often results in pseudo-dominant inheritance patterns further complicating the diagnosis and characterization of affected individuals. This study describes a genotype/phenotype analysis of an unusual family with multiple macular disease phenotypes spanning across two generations and segregating four distinct ABCA4 mutant alleles. Complete sequencing of ABCA4 discovered two known missense mutations, p.C54Y and p.G1961E. Array comparative genomic hybridization revealed a large novel deletion combined with a small insertion, c.6148-698_c.6670del/insTGTGCACCTCCCTAG, and complete sequencing of the entire ABCA4 genomic locus uncovered a new deep intronic variant, c.302+68C>T. Patients with the p.G1961E mutation had the mildest, confined maculopathy phenotype with peripheral flecks while those with all other mutant allele combinations exhibited a more advanced stage of generalized retinal and choriocapillaris atrophy. This family epitomizes the clinical and genetic complexity of ABCA4-associated diseases. It contained variants from all classes of mutations, in the coding region, deep intronic, both single nucleotide variants and copy number variants that accounted for varying phenotypes segregating in an apparent dominant fashion. Unequivocally defining disease-associated alleles in the ABCA4 locus requires a multifaceted approach that includes advanced mutation detection methods and a thorough analysis of clinical phenotypes.
Collapse
|
78
|
Bax NM, Sangermano R, Roosing S, Thiadens AAHJ, Hoefsloot LH, van den Born LI, Phan M, Klevering BJ, Westeneng-van Haaften C, Braun TA, Zonneveld-Vrieling MN, de Wijs I, Mutlu M, Stone EM, den Hollander AI, Klaver CCW, Hoyng CB, Cremers FPM. Heterozygous deep-intronic variants and deletions in ABCA4 in persons with retinal dystrophies and one exonic ABCA4 variant. Hum Mutat 2015; 36:43-7. [PMID: 25363634 DOI: 10.1002/humu.22717] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/18/2014] [Indexed: 11/05/2022]
Abstract
Variants in ABCA4 are responsible for autosomal-recessive Stargardt disease and cone-rod dystrophy. Sequence analysis of ABCA4 exons previously revealed one causative variant in each of 45 probands. To identify the "missing" variants in these cases, we performed multiplex ligation-dependent probe amplification-based deletion scanning of ABCA4. In addition, we sequenced the promoter region, fragments containing five deep-intronic splice variants, and 15 deep-intronic regions containing weak splice sites. Heterozygous deletions spanning ABCA4 exon 5 or exons 20-22 were found in two probands, heterozygous deep-intronic variants were identified in six probands, and a deep-intronic variant was found together with an exon 20-22 deletion in one proband. Based on ophthalmologic findings and characteristics of the identified exonic variants present in trans, the deep-intronic variants V1 and V4 were predicted to be relatively mild and severe, respectively. These findings are important for proper genetic counseling and for the development of variant-specific therapies.
Collapse
Affiliation(s)
- Nathalie M Bax
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
79
|
Kjellström U. Reduced macular function in ABCA4 carriers. Mol Vis 2015; 21:767-82. [PMID: 26261413 PMCID: PMC4506055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 07/15/2015] [Indexed: 11/30/2022] Open
Abstract
PURPOSE To study retinal function and morphology in ABCA4 carriers to investigate if ABCA4 carriership is associated with any functional or morphological changes and, if so, to explore whether certain mutations may be associated with particularly severe alterations. METHODS Eighteen subjects were recruited by means of being the parents of 10 teenagers/young adults with genetically confirmed ABCA4-associated retinal degenerations. The teenagers/young adults are well-known patients and have been followed in our clinic for many years. The eighteen subjects underwent careful ophthalmological examinations, including fundus photography and autofluorescence imaging, Goldmann perimetry, optical coherence tomography (OCT), full-field electroretinography (ffERG), multifocal electroretinography (mERG), and ABCA4 gene sequencing. The ffERG and mERG results were compared with those of healthy controls. RESULTS All subjects carried at least one ABCA4 mutation. Two subjects were compound heterozygous and therefore were excluded from the group-wise statistical analysis. Thirteen different ABCA4 mutations were found. C.2894 A>G (5/18) and c.768 G>T (4/18) were most common. Fourteen of 16 ABCA4 carriers demonstrated significantly altered mERG parameters (reduced amplitudes and/or delayed implicit times (ITs)) compared to normal values. In addition, the two subjects with compound heterozygous ABCA4 mutations had altered mERG parameters. A statistical comparison to the control group showed significantly reduced amplitudes and delayed ITs; p≤0.003 for all mERG parameters. FfERG parameters were altered in two ABCA4 carriers and one of the subjects with compound heterozygous ABCA4 mutations (reduced amplitude and delayed IT for the 30 Hz flicker ERG). No significant alterations were found for the whole group of ABCA4 carriers compared to the ffERG control group. Fundus photographs showed subtle to extensive pigmentary changes in several ABCA4 carriers. CONCLUSIONS In this study, ABCA4 carriers demonstrated reduced macular function measured by mERG along with none to subtle and even extensive morphological retinal changes. The c.768 G>T, c.5461-10T>C, and c.319 C>T mutations were associated with the most deviant ERGs, including both significant reduction of mERG amplitudes and prolongation of mERG ITs, as well as with reduced amplitude or delayed IT for the 30 Hz flicker ffERG in a few cases. They may therefore be considered serious mutations. The c.5917delG and c.4469 G>A mutations were associated with milder or no macular alteration. Long-term follow-up of these and other ABCA4 carriers may be of importance to elucidate the role of ABCA4 mutations in age-related macular degeneration. Moreover, improved knowledge of separate ABCA4 mutations may help us to better understand their role in ABCA4-associated retinal degenerations.
Collapse
|
80
|
Zernant J, Collison FT, Lee W, Fishman GA, Noupuu K, Yuan B, Cai C, Lupski JR, Yannuzzi LA, Tsang SH, Allikmets R. Genetic and clinical analysis of ABCA4-associated disease in African American patients. Hum Mutat 2015; 35:1187-94. [PMID: 25066811 PMCID: PMC4283973 DOI: 10.1002/humu.22626] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/25/2014] [Indexed: 12/30/2022]
Abstract
Autosomal recessive Stargardt disease (STGD1) is caused by hundreds of mutations in the ABCA4 gene, which are often specific to racial and ethnic groups. Here, we investigated the ABCA4 variation and their phenotypic expression in a cohort of 44 patients of African American descent, a previously under-characterized racial group. Patients were screened for mutations in ABCA4 by next-generation sequencing and array-comparative genomic hybridization (aCGH), followed by analyses for pathogenicity by in silico programs. Thorough ophthalmic examination was performed on all patients. At least two (expected) disease-causing alleles in the ABCA4 gene were identified in 27 (61.4%) patients, one allele in 11 (25%) patients, and no ABCA4 mutations were found in six (13.6%) patients. Altogether, 39 different disease-causing ABCA4 variants, including seven new, were identified on 65 (74%) chromosomes, most of which were unique for this racial group. The most frequent ABCA4 mutation in this cohort was c.6320G>A (p.(R2107H)), representing 19.3% of all disease-associated alleles. No large copy number variants were identified in any patient. Most patients reported later onset of symptoms. In summary, the ABCA4 mutation spectrum in patients of West African descent differs significantly from that in patients of European descent, resulting in a later onset and "milder" disease.
Collapse
Affiliation(s)
- Jana Zernant
- Department of Ophthalmology, Columbia University, New York, New York
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
81
|
Clinical Utility Gene Card for: autosomal recessive cone-rod dystrophy. Eur J Hum Genet 2015; 23:ejhg201567. [PMID: 25873014 DOI: 10.1038/ejhg.2015.67] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 03/05/2015] [Accepted: 03/20/2015] [Indexed: 11/08/2022] Open
|
82
|
Bauwens M, De Zaeytijd J, Weisschuh N, Kohl S, Meire F, Dahan K, Depasse F, De Jaegere S, De Ravel T, De Rademaeker M, Loeys B, Coppieters F, Leroy BP, De Baere E. An AugmentedABCA4Screen Targeting Noncoding Regions Reveals a Deep Intronic Founder Variant in Belgian Stargardt Patients. Hum Mutat 2014; 36:39-42. [DOI: 10.1002/humu.22716] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/18/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Miriam Bauwens
- Center for Medical Genetics; Ghent University and Ghent University Hospital; Ghent Belgium
| | - Julie De Zaeytijd
- Department of Ophthalmology; Ghent University Hospital; Ghent Belgium
| | - Nicole Weisschuh
- Molecular Genetics Laboratory; Institute for Ophthalmic Research; Centre for Ophthalmology; University of Tuebingen; Tuebingen Germany
| | - Susanne Kohl
- Molecular Genetics Laboratory; Institute for Ophthalmic Research; Centre for Ophthalmology; University of Tuebingen; Tuebingen Germany
| | - Françoise Meire
- Department of Ophthalmology; Queen Fabiola Children's University Hospital; Brussels Belgium
| | - Karin Dahan
- Centre de génétique humaine; Institut de Pathologie et de Génétique; Gosselies Belgium
| | - Fanny Depasse
- Department of Ophthalmology; Queen Fabiola Children's University Hospital; Brussels Belgium
| | - Sarah De Jaegere
- Center for Medical Genetics; Ghent University and Ghent University Hospital; Ghent Belgium
| | - Thomy De Ravel
- Center for Human Genetics; Leuven University Hospitals; Leuven Belgium
| | | | - Bart Loeys
- Center for Medical Genetics; University of Antwerp and Antwerp University Hospital; Antwerp Belgium
| | - Frauke Coppieters
- 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 Hospital; Ghent Belgium
- Division of Ophthalmology; The Children's Hospital of Philadelphia; Philadelphia Pennsylvania
| | - Elfride De Baere
- Center for Medical Genetics; Ghent University and Ghent University Hospital; Ghent Belgium
| |
Collapse
|
83
|
Pozo MGD, Méndez-Vidal C, Bravo-Gil N, Vela-Boza A, Dopazo J, Borrego S, Antiñolo G. Exome sequencing reveals novel and recurrent mutations with clinical significance in inherited retinal dystrophies. PLoS One 2014; 9:e116176. [PMID: 25544989 PMCID: PMC4278866 DOI: 10.1371/journal.pone.0116176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 12/02/2014] [Indexed: 12/02/2022] Open
Abstract
This study aimed to identify the underlying molecular genetic cause in four Spanish families clinically diagnosed of Retinitis Pigmentosa (RP), comprising one autosomal dominant RP (adRP), two autosomal recessive RP (arRP) and one with two possible modes of inheritance: arRP or X-Linked RP (XLRP). We performed whole exome sequencing (WES) using NimbleGen SeqCap EZ Exome V3 sample preparation kit and SOLID 5500xl platform. All variants passing filter criteria were validated by Sanger sequencing to confirm familial segregation and the absence in local control population. This strategy allowed the detection of: (i) one novel heterozygous splice-site deletion in RHO, c.937-2_944del, (ii) one rare homozygous mutation in C2orf71, c.1795T>C; p.Cys599Arg, not previously associated with the disease, (iii) two heterozygous null mutations in ABCA4, c.2041C>T; p.R681* and c.6088C>T; p.R2030*, and (iv) one mutation, c.2405-2406delAG; p.Glu802Glyfs*31 in the ORF15 of RPGR. The molecular findings for RHO and C2orf71 confirmed the initial diagnosis of adRP and arRP, respectively, while patients with the two ABCA4 mutations, both previously associated with Stargardt disease, presented symptoms of RP with early macular involvement. Finally, the X-Linked inheritance was confirmed for the family with the RPGR mutation. This latter finding allowed the inclusion of carrier sisters in our preimplantational genetic diagnosis program.
Collapse
Affiliation(s)
- María González-del Pozo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Cristina Méndez-Vidal
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Nereida Bravo-Gil
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Alicia Vela-Boza
- Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spain
| | - Joaquin Dopazo
- Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spain
- Department of Bioinformatics, Prince Felipe Research Centre (CIPF), Valencia, Spain
- Functional Genomics Node (INB), Prince Felipe Research Centre (CIPF), Valencia, Spain
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Guillermo Antiñolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
- Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spain
- * E-mail:
| |
Collapse
|
84
|
Sisk RA, Leng T. Multimodal imaging and multifocal electroretinography demonstrate autosomal recessive Stargardt disease may present like occult macular dystrophy. Retina 2014; 34:1567-75. [PMID: 24743636 DOI: 10.1097/iae.0000000000000136] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE To describe multimodal imaging and electrophysiologic characteristics of an unusual subset of patients with genetically confirmed autosomal recessive Stargardt disease (STGD1) who exhibited a central form of cone dysfunction resembling occult macular dystrophy that preceded the development of lipofuscin flecks, atrophy of retinal pigment epithelium (RPE), or full-field electroretinography abnormalities. METHODS Retrospective, observational descriptive case series. RESULTS Five patients with compound heterozygous ABCA4 mutations presented with bilateral visual acuity reduction, normal-appearing fundi, and blocked choroidal fluorescence on fluorescein angiography. One sibling each of two probands with identical genotypes was also included for analysis. Full-field electroretinography testing was normal in all patients, but multifocal electroretinography demonstrated centripetally depressed amplitudes exceeding areas of fundus autofluorescence, infrared imaging, and spectral domain optical coherence tomography abnormalities. Spectral domain optical coherence tomography initially revealed disruption of the inner segment ellipsoid band accompanying an ovoid hypofluorescent foveolar lesion. Progression to later stages was accompanied by the loss of the foveal photoreceptor outer segments, creating foveal cavitation with preservation of the RPE. Fundus autofluorescence and infrared imaging demonstrated corresponding bull's eye lesions. Over time, the foveal potential space on spectral domain optical coherence tomography collapsed, and three patients developed RPE atrophy and visible lipofuscin flecks. The flecks were detectable by fundus autofluorescence and infrared imaging earlier than by biomicroscopy. From these findings, a staging system for this subset of Stargardt disease presenting with central cone dysfunction was developed and presented herein. CONCLUSION Autosomal recessive Stargardt disease may present as a central cone dysfunction syndrome before the development of lipofuscin flecks, atrophy of RPE, or full-field electroretinography abnormalities. If emerging therapies for Stargardt disease succeed, early recognition and treatment of patients with preserved foveal photoreceptor and RPE cell bodies may yield a more favorable visual prognosis.
Collapse
Affiliation(s)
- Robert A Sisk
- *Cincinnati Eye Institute, Cincinnati, Ohio; †Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; ‡Department of Ophthalmology, University of Cincinnati, Cincinnati, Ohio; and §Byers Eye Institute, Stanford University School of Medicine, Palo Alto, California
| | | |
Collapse
|
85
|
Zhao L, Wang F, Wang H, Li Y, Alexander S, Wang K, Willoughby CE, Zaneveld JE, Jiang L, Soens ZT, Earle P, Simpson D, Silvestri G, Chen R. Next-generation sequencing-based molecular diagnosis of 82 retinitis pigmentosa probands from Northern Ireland. Hum Genet 2014; 134:217-30. [PMID: 25472526 DOI: 10.1007/s00439-014-1512-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/20/2014] [Indexed: 11/24/2022]
Abstract
Retinitis pigmentosa (RP) is a group of inherited retinal disorders characterized by progressive photoreceptor degeneration. An accurate molecular diagnosis is essential for disease characterization and clinical prognoses. A retinal capture panel that enriches 186 known retinal disease genes, including 55 known RP genes, was developed. Targeted next-generation sequencing was performed for a cohort of 82 unrelated RP cases from Northern Ireland, including 46 simplex cases and 36 familial cases. Disease-causing mutations were identified in 49 probands, including 28 simplex cases and 21 familial cases, achieving a solving rate of 60 %. In total, 65 pathogenic mutations were found, and 29 of these were novel. Interestingly, the molecular information of 12 probands was neither consistent with their initial inheritance pattern nor clinical diagnosis. Further clinical reassessment resulted in a refinement of the clinical diagnosis in 11 patients. This is the first study to apply next-generation sequencing-based, comprehensive molecular diagnoses to a large number of RP probands from Northern Ireland. Our study shows that molecular information can aid clinical diagnosis, potentially changing treatment options, current family counseling and management.
Collapse
Affiliation(s)
- Li Zhao
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
86
|
Lambertus S, van Huet RAC, Bax NM, Hoefsloot LH, Cremers FPM, Boon CJF, Klevering BJ, Hoyng CB. Early-onset stargardt disease: phenotypic and genotypic characteristics. Ophthalmology 2014; 122:335-44. [PMID: 25444351 DOI: 10.1016/j.ophtha.2014.08.032] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/16/2014] [Accepted: 08/14/2014] [Indexed: 10/24/2022] Open
Abstract
OBJECTIVE To describe the phenotype and genotype of patients with early-onset Stargardt disease. DESIGN Retrospective cohort study. PARTICIPANTS Fifty-one Stargardt patients with age at onset ≤10 years. METHODS We reviewed patient medical records for age at onset, medical history, initial symptoms, best-corrected visual acuity (BCVA), ophthalmoscopy, fundus photography, fundus autofluorescence (FAF), fluorescein angiography (FA), spectral-domain optical coherence tomography (SD-OCT), and full-field electroretinography (ffERG). The ABCA4 gene was screened for mutations. MAIN OUTCOME MEASURES Age at onset, BCVA, fundus appearance, FAF, FA, SD-OCT, ffERG, and presence of ABCA4 mutations. RESULTS The mean age at onset was 7.2 years (range, 1-10). The median times to develop BCVA of 20/32, 20/80, 20/200, and 20/500 were 3, 5, 12, and 23 years, respectively. Initial ophthalmoscopy in 41 patients revealed either no abnormalities or foveal retinal pigment epithelium (RPE) changes in 10 and 9 patients, respectively; the other 22 patients had foveal atrophy, atrophic RPE lesions, and/or irregular yellow-white fundus flecks. On FA, there was a "dark choroid" in 21 out of 29 patients. In 14 out of 50 patients, foveal atrophy occurred before flecks developed. On FAF, there was centrifugal expansion of disseminated atrophic spots, which progressed to the eventual profound chorioretinal atrophy. Spectral-domain OCT revealed early photoreceptor damage followed by atrophy of the outer retina, RPE, and choroid. On ffERG in 26 patients, 15 had normal amplitudes, and 11 had reduced photopic and/or scotopic amplitudes at their first visit. We found no correlation between ffERG abnormalities and the rate of vision loss. Thirteen out of 25 patients had progressive ffERG abnormalities. Finally, genetic screening of 44 patients revealed ≥2 ABCA4 mutations in 37 patients and single heterozygous mutations in 7. CONCLUSIONS In early-onset Stargardt, initial ophthalmoscopy can reveal no abnormalities or minor retinal abnormalities. Yellow-white flecks can be preceded by foveal atrophy and may be visible only on FAF. Although ffERG is insufficient for predicting the rate of vision loss, abnormalities can develop. Over time, visual acuity declines rapidly in parallel with progressive retinal degeneration, resulting in profound chorioretinal atrophy. Thus, early-onset Stargardt lies at the severe end of the spectrum of ABCA4-associated retinal phenotypes.
Collapse
Affiliation(s)
- Stanley Lambertus
- Department of Ophthalmology, Radboud university medical center, Nijmegen, The Netherlands
| | - Ramon A C van Huet
- Department of Ophthalmology, Radboud university medical center, Nijmegen, The Netherlands
| | - Nathalie M Bax
- Department of Ophthalmology, Radboud university medical center, Nijmegen, The Netherlands
| | - Lies H Hoefsloot
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Radboud university medical center, Nijmegen, The Netherlands; Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - B Jeroen Klevering
- Department of Ophthalmology, Radboud university medical center, Nijmegen, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud university medical center, Nijmegen, The Netherlands.
| |
Collapse
|
87
|
Fujinami K, Zernant J, Chana RK, Wright GA, Tsunoda K, Ozawa Y, Tsubota K, Robson AG, Holder GE, Allikmets R, Michaelides M, Moore AT. Clinical and molecular characteristics of childhood-onset Stargardt disease. Ophthalmology 2014; 122:326-34. [PMID: 25312043 PMCID: PMC4459618 DOI: 10.1016/j.ophtha.2014.08.012] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/21/2014] [Accepted: 08/04/2014] [Indexed: 11/25/2022] Open
Abstract
Purpose To describe the clinical and molecular characteristics of patients with childhood-onset Stargardt disease (STGD). Design Retrospective case series. Participants Forty-two patients who were diagnosed with STGD in childhood at a single institution between January 2001 and January 2012. Methods A detailed history and a comprehensive ophthalmic examination were undertaken, including color fundus photography, autofluorescence imaging, spectral-domain optical coherence tomography (SD-OCT), and pattern and full-field electroretinograms. The entire coding region and splice sites of ABCA4 were screened using a next-generation, sequencing-based strategy. The molecular genetic findings of childhood-onset STGD patients were compared with those of adult-onset patients. Main Outcome Measures Clinical, imaging, electrophysiologic, and molecular genetic findings. Results The median ages of onset and the median age at baseline examination were 8.5 (range, 3–16) and 12.0 years (range, 7-16), respectively. The median baseline logarithm of the minimum angle of resolution visual acuity was 0.74. At baseline, 26 of 39 patients (67%) with available photographs had macular atrophy with macular/peripheral flecks; 11 (28%) had macular atrophy without flecks; 1 (2.5%) had numerous flecks without macular atrophy; and 1 (2.5%) had a normal fundus appearance. Flecks were not identified at baseline in 12 patients (31%). SD-OCT detected foveal outer retinal disruption in all 21 patients with available images. Electrophysiologic assessment demonstrated retinal dysfunction confined to the macula in 9 patients (36%), macular and generalized cone dysfunction in 1 subject (4%), and macular and generalized cone and rod dysfunction in 15 individuals (60%). At least 1 disease-causing ABCA4 variant was identified in 38 patients (90%), including 13 novel variants; ≥2 variants were identified in 34 patients (81%). Patients with childhood-onset STGD more frequently harbored 2 deleterious variants (18% vs 5%) compared with patients with adult-onset STGD. Conclusions Childhood-onset STGD is associated with severe visual loss, early morphologic changes, and often generalized retinal dysfunction, despite often having less severe fundus abnormalities on examination. One third of children do not have flecks at presentation. The relatively high proportion of deleterious ABCA4 variants supports the hypothesis that earlier onset disease is often owing to more severe variants in ABCA4 than those found in adult-onset disease.
Collapse
Affiliation(s)
- Kaoru Fujinami
- Laboratory of Visual Physiology, National Institute of Sensory Organs, National Hospital Organization, Tokyo Medical Center, Tokyo, Japan; Department of Ophthalmology, Keio University, School of Medicine, Tokyo, Japan; UCL Institute of Ophthalmology, London, UK; Moorfields Eye Hospital, City Road, London, UK
| | - Jana Zernant
- Department of Ophthalmology, Columbia University, New York, New York
| | - Ravinder K Chana
- UCL Institute of Ophthalmology, London, UK; Moorfields Eye Hospital, City Road, London, UK
| | - Genevieve A Wright
- UCL Institute of Ophthalmology, London, UK; Moorfields Eye Hospital, City Road, London, UK
| | - Kazushige Tsunoda
- Laboratory of Visual Physiology, National Institute of Sensory Organs, National Hospital Organization, Tokyo Medical Center, Tokyo, Japan
| | - Yoko Ozawa
- Department of Ophthalmology, Keio University, School of Medicine, Tokyo, Japan
| | - Kazuo Tsubota
- Department of Ophthalmology, Keio University, School of Medicine, Tokyo, Japan
| | - Anthony G Robson
- UCL Institute of Ophthalmology, London, UK; Moorfields Eye Hospital, City Road, London, UK
| | - Graham E Holder
- UCL Institute of Ophthalmology, London, UK; Moorfields Eye Hospital, City Road, London, UK
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, New York; Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Michel Michaelides
- UCL Institute of Ophthalmology, London, UK; Moorfields Eye Hospital, City Road, London, UK.
| | - Anthony T Moore
- UCL Institute of Ophthalmology, London, UK; Moorfields Eye Hospital, City Road, London, UK.
| |
Collapse
|
88
|
Sun X, Yang Q, Deng Z, Ye X. Digital inventory of Arabidopsis transcripts revealed by 61 RNA sequencing samples. PLANT PHYSIOLOGY 2014; 166:869-78. [PMID: 25118256 PMCID: PMC4213114 DOI: 10.1104/pp.114.241604] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/10/2014] [Indexed: 05/30/2023]
Abstract
Alternative splicing is an essential biological process to generate proteome diversity and phenotypic complexity. Recent improvements in RNA sequencing accuracy and computational algorithms have provided unprecedented opportunities to examine the expression levels of Arabidopsis (Arabidopsis thaliana) transcripts. In this article, we analyzed 61 RNA sequencing samples from 10 totally independent studies of Arabidopsis and calculated the transcript expression levels in different tissues, treatments, developmental stages, and varieties. These data provide a comprehensive profile of Arabidopsis transcripts with single-base resolution. We quantified the expression levels of 40,745 transcripts annotated in The Arabidopsis Information Resource 10, comprising 73% common transcripts, 15% rare transcripts, and 12% nondetectable transcripts. In addition, we investigated diverse common transcripts in detail, including ubiquitous transcripts, dominant/subordinate transcripts, and switch transcripts, in terms of their expression and transcript ratio. Interestingly, alternative splicing was the highly enriched function for the genes related to dominant/subordinate transcripts and switch transcripts. In addition, motif analysis revealed that TC motifs were enriched in dominant transcripts but not in subordinate transcripts. These motifs were found to have a strong relationship with transcription factor activity. Our results shed light on the complexity of alternative splicing and the diversity of the contributing factors.
Collapse
Affiliation(s)
- Xiaoyong Sun
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China (X.S.);Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75235 (Q.Y.);State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (Z.D.); andFruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China (X.Y.)
| | - Qiuying Yang
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China (X.S.);Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75235 (Q.Y.);State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (Z.D.); andFruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China (X.Y.)
| | - Zhiping Deng
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China (X.S.);Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75235 (Q.Y.);State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (Z.D.); andFruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China (X.Y.)
| | - Xinfu Ye
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China (X.S.);Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75235 (Q.Y.);State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China (Z.D.); andFruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China (X.Y.)
| |
Collapse
|
89
|
Bonilha VL, Rayborn ME, Bell BA, Marino MJ, Fishman GA, Hollyfield JG. Retinal Histopathology in Eyes from a Patient with Stargardt disease caused by Compound Heterozygous ABCA4 Mutations. Ophthalmic Genet 2014; 37:150-60. [DOI: 10.3109/13816810.2014.958861] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Vera L. Bonilha
- Cole Eye Institute, Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA, and
| | - Mary E. Rayborn
- Cole Eye Institute, Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA, and
| | - Brent A. Bell
- Cole Eye Institute, Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA, and
| | - Meghan J. Marino
- Cole Eye Institute, Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA, and
| | - Gerald A. Fishman
- Chicago Lighthouse for People Who Are Blind or Visually Impaired, Chicago, IL, USA
| | - Joe G. Hollyfield
- Cole Eye Institute, Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA, and
| |
Collapse
|
90
|
Zernant J, Xie YA, Ayuso C, Riveiro-Alvarez R, Lopez-Martinez MA, Simonelli F, Testa F, Gorin MB, Strom SP, Bertelsen M, Rosenberg T, Boone PM, Yuan B, Ayyagari R, Nagy PL, Tsang SH, Gouras P, Collison FT, Lupski JR, Fishman GA, Allikmets R. Analysis of the ABCA4 genomic locus in Stargardt disease. Hum Mol Genet 2014; 23:6797-806. [PMID: 25082829 DOI: 10.1093/hmg/ddu396] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Autosomal recessive Stargardt disease (STGD1, MIM 248200) is caused by mutations in the ABCA4 gene. Complete sequencing of ABCA4 in STGD patients identifies compound heterozygous or homozygous disease-associated alleles in 65-70% of patients and only one mutation in 15-20% of patients. This study was designed to find the missing disease-causing ABCA4 variation by a combination of next-generation sequencing (NGS), array-Comparative Genome Hybridization (aCGH) screening, familial segregation and in silico analyses. The entire 140 kb ABCA4 genomic locus was sequenced in 114 STGD patients with one known ABCA4 exonic mutation revealing, on average, 200 intronic variants per sample. Filtering of these data resulted in 141 candidates for new mutations. Two variants were detected in four samples, two in three samples, and 20 variants in two samples, the remaining 117 new variants were detected only once. Multimodal analysis suggested 12 new likely pathogenic intronic ABCA4 variants, some of which were specific to (isolated) ethnic groups. No copy number variation (large deletions and insertions) was detected in any patient suggesting that it is a very rare event in the ABCA4 locus. Many variants were excluded since they were not conserved in non-human primates, were frequent in African populations and, therefore, represented ancestral, and not disease-associated, variants. The sequence variability in the ABCA4 locus is extensive and the non-coding sequences do not harbor frequent mutations in STGD patients of European-American descent. Defining disease-associated alleles in the ABCA4 locus requires exceptionally well characterized large cohorts and extensive analyses by a combination of various approaches.
Collapse
Affiliation(s)
| | | | - Carmen Ayuso
- Department of Genetics, Instituto de Investigacion Sanitaria-University Hospital Fundacion Jimenez Diaz, UAM (IIS-FJD), Madrid, Spain Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics, Instituto de Investigacion Sanitaria-University Hospital Fundacion Jimenez Diaz, UAM (IIS-FJD), Madrid, Spain Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Miguel-Angel Lopez-Martinez
- Department of Genetics, Instituto de Investigacion Sanitaria-University Hospital Fundacion Jimenez Diaz, UAM (IIS-FJD), Madrid, Spain Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Second University of Naples, Naples, Italy
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Second University of Naples, Naples, Italy
| | - Michael B Gorin
- Department of Ophthalmology Department of Human Genetics, Jules Stein Eye Institute and
| | - Samuel P Strom
- Department of Ophthalmology Department of Human Genetics, Jules Stein Eye Institute and Department of Pathology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Mette Bertelsen
- Kennedy Center Eye Clinic, Glostrup Hospital, Glostrup, Denmark
| | | | - Philip M Boone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Radha Ayyagari
- Department of Ophthalmology, University of California San Diego, La Jolla, CA, USA and
| | - Peter L Nagy
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Stephen H Tsang
- Department of Ophthalmology and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | | | - Frederick T Collison
- The Pangere Center for Hereditary Retinal Diseases, The Chicago Lighthouse for People Who are Blind or Visually Impaired, Chicago, IL, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Gerald A Fishman
- The Pangere Center for Hereditary Retinal Diseases, The Chicago Lighthouse for People Who are Blind or Visually Impaired, Chicago, IL, USA
| | - Rando Allikmets
- Department of Ophthalmology and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| |
Collapse
|
91
|
Siemiatkowska AM, Collin RWJ, den Hollander AI, Cremers FPM. Genomic approaches for the discovery of genes mutated in inherited retinal degeneration. Cold Spring Harb Perspect Med 2014; 4:a017137. [PMID: 24939053 PMCID: PMC4109577 DOI: 10.1101/cshperspect.a017137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In view of their high degree of genetic heterogeneity, inherited retinal diseases (IRDs) pose a significant challenge for identifying novel genetic causes. Thus far, more than 200 genes have been found to be mutated in IRDs, which together contain causal variants in >80% of the cases. Accurate genetic diagnostics is particularly important for isolated cases, in which X-linked and de novo autosomal dominant variants are not uncommon. In addition, new gene- or mutation-specific therapies are emerging, underlining the importance of identifying causative mutations in each individual. Sanger sequencing of selected genes followed by cost-effective targeted next-generation sequencing (NGS) can identify defects in known IRD-associated genes in the majority of the cases. Exome NGS in combination with genetic linkage or homozygosity mapping studies can aid the identification of the remaining causal genes. As these are thought to be mutated in <1% of the cases, validation through functional modeling in, for example, zebrafish and/or replication through the genotyping of large patient cohorts is required. In the near future, whole genome NGS in combination with transcriptome NGS may reveal mutations that are currently hidden in the noncoding regions of the human genome.
Collapse
Affiliation(s)
- Anna M Siemiatkowska
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| |
Collapse
|
92
|
Computational evidence of NAGNAG alternative splicing in human large intergenic noncoding RNA. BIOMED RESEARCH INTERNATIONAL 2014; 2014:736798. [PMID: 24995327 PMCID: PMC4068082 DOI: 10.1155/2014/736798] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/08/2014] [Accepted: 05/21/2014] [Indexed: 11/23/2022]
Abstract
NAGNAG alternative splicing plays an essential role in biological processes and represents a highly adaptable system for posttranslational regulation of gene function. NAGNAG alternative splicing impacts a myriad of biological processes. Previous studies of NAGNAG largely focused on messenger RNA. To the best of our knowledge, this is the first study testing the hypothesis that NAGNAG alternative splicing is also operative in large intergenic noncoding RNA (lincRNA). The RNA-seq data sets from recent deep sequencing studies were queried to test our hypothesis. NAGNAG alternative splicing of human lincRNA was identified while querying two independent RNA-seq data sets. Within these datasets, 31 NAGNAG alternative splicing sites were identified in lincRNA. Notably, most exons of lincRNA containing NAGNAG acceptors were longer than those from protein-coding genes. Furthermore, presence of CAG coding appeared to participate in the splice site selection. Finally, expression of the isoforms of NAGNAG lincRNA exhibited tissue specificity. Together, this study improves our understanding of the NAGNAG alternative splicing in lincRNA.
Collapse
|
93
|
Roosing S, Thiadens AAHJ, Hoyng CB, Klaver CCW, den Hollander AI, Cremers FPM. Causes and consequences of inherited cone disorders. Prog Retin Eye Res 2014; 42:1-26. [PMID: 24857951 DOI: 10.1016/j.preteyeres.2014.05.001] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 04/29/2014] [Accepted: 05/06/2014] [Indexed: 11/18/2022]
Abstract
Hereditary cone disorders (CDs) are characterized by defects of the cone photoreceptors or retinal pigment epithelium underlying the macula, and include achromatopsia (ACHM), cone dystrophy (COD), cone-rod dystrophy (CRD), color vision impairment, Stargardt disease (STGD) and other maculopathies. Forty-two genes have been implicated in non-syndromic inherited CDs. Mutations in the 5 genes implicated in ACHM explain ∼93% of the cases. On the contrary, only 21% of CRDs (17 genes) and 25% of CODs (8 genes) have been elucidated. The fact that the large majority of COD and CRD-associated genes are yet to be discovered hints towards the existence of unknown cone-specific or cone-sensitive processes. The ACHM-associated genes encode proteins that fulfill crucial roles in the cone phototransduction cascade, which is the most frequently compromised (10 genes) process in CDs. Another 7 CD-associated proteins are required for transport processes towards or through the connecting cilium. The remaining CD-associated proteins are involved in cell membrane morphogenesis and maintenance, synaptic transduction, and the retinoid cycle. Further novel genes are likely to be identified in the near future by combining large-scale DNA sequencing and transcriptomics technologies. For 31 of 42 CD-associated genes, mammalian models are available, 14 of which have successfully been used for gene augmentation studies. However, gene augmentation for CDs should ideally be developed in large mammalian models with cone-rich areas, which are currently available for only 11 CD genes. Future research will aim to elucidate the remaining causative genes, identify the molecular mechanisms of CD, and develop novel therapies aimed at preventing vision loss in individuals with CD in the future.
Collapse
Affiliation(s)
- Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology Erasmus Medical Centre, 3000 CA, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Centre, 3000 CA, Rotterdam, The Netherlands
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, PO Box 9101, 6500 HB, Nijmegen, The Netherlands; Department of Ophthalmology, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
| |
Collapse
|
94
|
Bertelsen M, Zernant J, Larsen M, Duno M, Allikmets R, Rosenberg T. Generalized choriocapillaris dystrophy, a distinct phenotype in the spectrum of ABCA4-associated retinopathies. Invest Ophthalmol Vis Sci 2014; 55:2766-76. [PMID: 24713488 DOI: 10.1167/iovs.13-13391] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE We describe a particular form of autosomal recessive generalized choriocapillaris dystrophy phenotype associated with ABCA4 mutations. METHODS A cohort of 30 patients with identified ABCA4 mutations and a distinct phenotype was studied. A retrospective review of history, fundus photographs, electroretinography, visual field testing, dark adaptometry, and optical coherence tomography was performed. Genetic analyses were performed by ABCA4 microarray analysis, high resolution melting, and/or next generation sequencing of all protein-coding sequences of the ABCA4 gene. RESULTS The earliest recorded manifestation of ABCA4-associated disease was a central bull's eye type of macular dystrophy that progressed to chorioretinal atrophy of the macula with coarse rounded hyperpigmentations and expanding involvement of the periphery. The mean age at first presentation was 10.3 years, the longest follow-up was 61 years. All patients had two ABCA4 mutations identified, confirming the molecular genetic diagnosis of an ABCA4-associated disease. Most patients harbored at least one mutation classified as "severe," the most common of which was the p.N965S variant that had been found previously at a high frequency among patients with ABCA4-associated retinal dystrophies in Denmark. CONCLUSIONS Generalized choriocapillaris dystrophy is a progressive ABCA4-associated phenotype characterized by early-onset macular dystrophy that disperses and expands to widespread end-stage chorioretinal atrophy with profound visual loss. All cases in this study were confirmed as harboring two ABCA4 mutations. Most of the ABCA4 mutations were classified as "severe" explaining the early onset, panretinal degeneration, and fast progression of the disease.
Collapse
Affiliation(s)
- Mette Bertelsen
- Department of Ophthalmology, Glostrup Hospital, Glostrup, Denmark
| | | | | | | | | | | |
Collapse
|
95
|
Saksens NT, Fleckenstein M, Schmitz-Valckenberg S, Holz FG, den Hollander AI, Keunen JE, Boon CJ, Hoyng CB. Macular dystrophies mimicking age-related macular degeneration. Prog Retin Eye Res 2014; 39:23-57. [PMID: 24291520 DOI: 10.1016/j.preteyeres.2013.11.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/15/2013] [Accepted: 11/18/2013] [Indexed: 01/30/2023]
|
96
|
Miraldi Utz V, Coussa RG, Marino MJ, Chappelow AV, Pauer GJ, Hagstrom SA, Traboulsi EI. Predictors of visual acuity and genotype-phenotype correlates in a cohort of patients with Stargardt disease. Br J Ophthalmol 2014; 98:513-8. [DOI: 10.1136/bjophthalmol-2013-304270] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
97
|
Sutherland JE, Day MA. Advantages and disadvantages of molecular testing in ophthalmology. EXPERT REVIEW OF OPHTHALMOLOGY 2014. [DOI: 10.1586/eop.11.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
98
|
Kjellström U. Association between genotype and phenotype in families with mutations in the ABCA4 gene. Mol Vis 2014; 20:89-104. [PMID: 24453473 PMCID: PMC3892680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 01/03/2014] [Indexed: 10/25/2022] Open
Abstract
PURPOSE To investigate the genotype and phenotype in families with adenosine triphosphate-binding cassette, sub-family A, member 4 (ABCA4)-associated retinal degeneration. METHODS Three families with at least one family member with known homozygous or compound heterozygote mutations in the ABCA4 gene were studied. The investigations included full field electroretinography (ff-ERG), multifocal ERG (mERG), Goldmann visual fields, optical coherence tomography (OCT), and standard ophthalmological examination. Microarray (Asper) was used for ABCA4 genotyping. RESULTS In family 1, the proband (age 23) was homozygote for the c768 G>T mutation. She was diagnosed with cone rod dystrophy (CRD) while her aunt (age 69) was compound heterozygote for the c768 G>T and c2894 A>G mutations and had autosomal recessive retinitis pigmentosa (arRP). The father (age 61) and the mother (age 60) of the proband were asymptomatic carriers of the c768 G>T mutation. In family 2, the proband (age 25) was homozygote for the c5917del. She was diagnosed with CRD. Her father and two sisters were compound heterozygote for the c5917del and c5882 G>A mutations. The eldest sister (age 23) suffered from Stargardt disease (STGD) while the youngest sister (age 12) and their father (age 48) had no visual complaints. Anyhow, their ERG measurements indicated changes corresponding to STGD. The mother (age 42), (heterozygote for the c5917 delG mutation) and the youngest child (age 9; heterozygote for the c5882 G>A mutation) had a normal phenotype. In family 3, the proband (age 43) was compound heterozygote for c768 G>T and c3113 C>T and had been diagnosed with STGD. Her son (age 12), who was homozygote for the c768 G>T mutation, had wider scotomas with earlier onset (age 6), ff-ERG cone responses in the lower range of normality, and reduced mERG. At the moment, he is classified as having STGD but may progress to CRD. The father (age 45) was asymptomatic and heterozygote for the c768 G>T mutation. The patients with progressive disorders (CRD or arRP) had prolonged implicit times for the 30 Hz flicker ff-ERG and the mERG. All patients with two mutations in the ABCA4 gene demonstrated attenuation of retinal thickness on the OCT macular map. CONCLUSIONS This study confirms that ABCA4 mutations lead to a spectrum of retinal degenerations ranging from STGD to CRD or arRP. At the time of diagnosis, it is not possible to predict the severity of the condition only from genotyping. Our results suggest that prolongation of implicit times for the ff-ERG and/or mERG seem to be associated with progressive conditions such as CRD and arRP. Since ABCA4 mutations are common in the general population, different family members can harbor various combinations of mutations resulting in diverse phenotype and prognosis in the same family, further emphasizing the importance of a combination of genetic and electrophysiological tests at the first visit and follow-up.
Collapse
|
99
|
Shi Y, Sha G, Sun X. Genome-wide study of NAGNAG alternative splicing in Arabidopsis. PLANTA 2014; 239:127-138. [PMID: 24097263 DOI: 10.1007/s00425-013-1965-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 09/23/2013] [Indexed: 06/02/2023]
Abstract
NAGNAG alternative splicing is one type of alternative splicing in mammals and plants. There are two opposite arguments regarding the mechanism of this NAGNAG event, i.e. whether splice variation is controllable by the cell or is just biological noise. In this paper, we systematically investigated NAGNAG acceptors in Arabidopsis thaliana using both cDNA/EST and RNA-Seq data. We identified 9,473 NAGNAG motifs, including 529 cDNA/EST-confirmed NAGNAG acceptors. A nomenclature tree for this type of alternative splicing was defined based on the cDNA/EST validation, location in the exon, sequence and expression level. Low expression of some NAGNAG motifs was observed in various tissues or pathogen-infected samples, indicating the existence of background splicing. Tissue-specific or treatment-specific differences in the dynamic profiles suggest that some NAGNAG acceptors are highly regulated.
Collapse
Affiliation(s)
- Yanjing Shi
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, Shandong, People's Republic of China
| | | | | |
Collapse
|
100
|
Jonsson F, Burstedt MS, Sandgren O, Norberg A, Golovleva I. Genetic heterogeneity and clinical outcome in a Swedish family with retinal degeneration caused by mutations in CRB1 and ABCA4 genes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 801:177-83. [PMID: 24664696 DOI: 10.1007/978-1-4614-3209-8_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Genetic mechanisms underlying severe retinal dystrophy in a large Swedish family presenting two distinct phenotypes, Leber congenital amaurosis and Stargardt disease were investigated. In the family, four patients with Leber congenital amaurosis were homozygous for a novel c.2557C>T (p.Q853X) mutation in the CRB1 gene, while of two cases with Stargardt disease, one was homozygous for c.5461-10T>C in the ABCA4 gene and another was a compound heterozygous for c.5461-10T>C and a novel ABCA4 mutation c.4773+3 A>G. Sequence analysis of the entire ABCA4 gene in patients with Stargardt disease revealed complex alleles with additional sequence variants.Our results provide evidence of genetic complexity causative of different clinical features present in the same family, which is an obvious challenge for ophthalmologists, molecular geneticists and genetic counsellors.
Collapse
Affiliation(s)
- Frida Jonsson
- Department of Medical Biosciences/Medical and Clinical Genetics, University Hospital of Umeå, SE 901 85, Umeå, Sweden,
| | | | | | | | | |
Collapse
|