101
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Utz VM, Chappelow AV, Marino MJ, Beight CD, Sturgill-Short GM, Pauer GJT, Crowe S, Hagstrom SA, Traboulsi EI. Identification of three ABCA4 sequence variations exclusive to African American patients in a cohort of patients with Stargardt disease. Am J Ophthalmol 2013; 156:1220-1227.e2. [PMID: 24011517 DOI: 10.1016/j.ajo.2013.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 07/10/2013] [Accepted: 07/11/2013] [Indexed: 11/18/2022]
Abstract
PURPOSE To describe the clinical and molecular findings in ten unrelated African American patients with Stargardt disease. DESIGN Retrospective, observational case series. METHODS We reviewed the clinical histories, examinations, and genotypes of 85 patients with molecular diagnoses of Stargardt disease. Three ABCA4 sequence variations identified exclusively in African Americans were evaluated in 300 African American controls and by in silico analysis. RESULTS ABCA4 sequence changes were identified in 85 patients from 80 families, of which 11 patients identified themselves as African American. Of these 11 patients, 10 unrelated patients shared 1 of 3 ABCA4 sequence variations: c.3602T>G (p.L1201R); c.3899G>A (p.R1300Q); or c.6320G>A (p.R2107H). The minor allele frequencies in the African American control population for each variation were 7.5%, 6.3%, and 2%, respectively. This is comparable to the allele frequency in African Americans in the Exome Variant Server. In contrast, the allele frequency of all three of these variations was less than or equal to 0.05% in European Americans. Although both c.3602T>G and c.3899G>A have been reported as likely disease-causing variations, one of our control patients was homozygous for each variant, suggesting that these are nonpathogenic. In contrast, the absence of c.6320G>A in the control population in the homozygous state, combined with the results of bioinformatics analysis, support its pathogenicity. CONCLUSIONS Three ABCA4 sequence variations were identified exclusively in 10 unrelated African American patients: p.L1201R and p.R1300Q likely represent nonpathogenic sequence variants, whereas the p.R2107H substitution appears to be pathogenic. Characterization of population-specific disease alleles may have important implications for the development of genetic screening algorithms.
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102
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Fujinami K, Zernant J, Chana RK, Wright GA, Tsunoda K, Ozawa Y, Tsubota K, Webster AR, Moore AT, Allikmets R, Michaelides M. ABCA4 gene screening by next-generation sequencing in a British cohort. Invest Ophthalmol Vis Sci 2013; 54:6662-74. [PMID: 23982839 DOI: 10.1167/iovs.13-12570] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE We applied a recently reported next-generation sequencing (NGS) strategy for screening the ABCA4 gene in a British cohort with ABCA4-associated disease and report novel mutations. METHODS We identified 79 patients with a clinical diagnosis of ABCA4-associated disease who had a single variant identified by the ABCA4 microarray. Comprehensive phenotypic data were obtained, and the NGS strategy was applied to identify the second allele by means of sequencing the entire coding region and adjacent intronic sequences of the ABCA4 gene. Identified variants were confirmed by Sanger sequencing and assessed for pathogenicity by in silico analysis. RESULTS Of the 42 variants detected by prescreening with the microarray, in silico analysis suggested that 34, found in 66 subjects, were disease-causing and 8, found in 13 subjects, were benign variants. We detected 42 variants by NGS, of which 39 were classified as disease-causing. Of these 39 variants, 31 were novel, including 16 missense, 7 splice-site-altering, 4 nonsense, 1 in-frame deletion, and 3 frameshift variants. Two or more disease-causing variants were confirmed in 37 (47%) of 79 patients, one disease-causing variant in 36 (46%) subjects, and no disease-causing variant in 6 (7%) individuals. CONCLUSIONS Application of the NGS platform for ABCA4 screening enabled detection of the second disease-associated allele in approximately half of the patients in a British cohort where one mutation had been detected with the arrayed primer extension (APEX) array. The time- and cost-efficient NGS strategy is useful in screening large cohorts, which will be increasingly valuable with the advent of ABCA4-directed therapies.
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Affiliation(s)
- Kaoru Fujinami
- Laboratory of Visual Physiology, National Institute of Sensory Organs, National Tokyo Medical Center, Tokyo, Japan
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El Matri L, Ouechtati F, Chebil A, Largueche L, Abdelhak S. Clinical polymorphism of stargardt disease in a large consanguineous tunisian family; implications for nosology. J Ophthalmic Vis Res 2013; 8:341-50. [PMID: 24653822 PMCID: PMC3957041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 07/20/2013] [Indexed: 11/12/2022] Open
Abstract
PURPOSE To describe the polymorphic expression of Stargardt disease in a large Tunisian family with clinical intra- and interfamilial variation of the condition. METHODS Twelve subjects from two related families with autosomal recessive Stargardt disease were enrolled. A detailed clinical examination including visual acuity and visual field measurement, fundus photography, fluorescein angiography, electroretinography (ERG) and color vision testing was performed for all subjects. RESULTS The youngest child from family A manifested typical Stargardt disease while her two brothers presented with Stargardt disease-fundus flavimaculatus (STGD-FFM) and her two sisters demonstrated a peculiar phenotype overlapping Stargardt disease and cone-rod dystrophy; their phenotypic manifestation corresponded well with ERG groups I, II and III, respectively. This uncommon occurrence of an age-related decline in ERG amplitude and worsening of fundus changes is suggestive of a grading pattern in Stargardt disease. Their two cousins in family B, displayed the STGD-FFM phenotype. Despite clinically similar STGD-FFM patterns in both families, age of onset and progression of the phenotype in family B differed from family A. CONCLUSION This is the first report on phenotypic variation of Stargardt disease in a large Tunisian family. Regarding phenotype and severity of visual symptoms, family A demonstrated Stargardt disease at various stages of progression. In addition, STGD-FFM appeared to be an independent clinical entity in family B. These findings imply that further parameters are required to classify Stargardt's disease.
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Affiliation(s)
- Leila El Matri
- Department of Ophthalmology, Hedi Rais Institute of Ophthalmology, Tunis, Tunisia,Ocular Genetics Research Unit (UR17/04), Hedi Rais Institute of Ophthalmology, Tunis, Tunisia,Leila El Matri, MD. Hedi Rais Institute of Ophthalmology, Boulevard 9 Avril 1006 Bab Saadoun, Tunis , Tunisia; Tel: +216 71 573604, Fax: +216 71 575956; e-mail: L
| | - Farah Ouechtati
- Ocular Genetics Research Unit (UR17/04), Hedi Rais Institute of Ophthalmology, Tunis, Tunisia,Molecular Investigation of Genetic Orphan Diseases Unit, Institut Pasteur, Tunis, Tunisia
| | - Ahmed Chebil
- Department of Ophthalmology, Hedi Rais Institute of Ophthalmology, Tunis, Tunisia,Ocular Genetics Research Unit (UR17/04), Hedi Rais Institute of Ophthalmology, Tunis, Tunisia
| | - Leila Largueche
- Department of Ophthalmology, Hedi Rais Institute of Ophthalmology, Tunis, Tunisia,Ocular Genetics Research Unit (UR17/04), Hedi Rais Institute of Ophthalmology, Tunis, Tunisia
| | - Sonia Abdelhak
- Molecular Investigation of Genetic Orphan Diseases Unit, Institut Pasteur, Tunis, Tunisia
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104
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Gemenetzi M, Lotery AJ. Phenotype/genotype correlation in a case series of Stargardt's patients identifies novel mutations in the ABCA4 gene. Eye (Lond) 2013; 27:1316-9. [PMID: 23949494 DOI: 10.1038/eye.2013.176] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/16/2013] [Indexed: 11/09/2022] Open
Abstract
PURPOSE To investigate phenotypic variability in terms of best-corrected visual acuity (BCVA) in patients with Stargardt disease (STGD) and confirmed ABCA4 mutations. METHODS Entire coding region analysis of the ABCA4 gene by direct sequencing of seven patients with clinical findings of STGD seen in the Retina Clinics of Southampton Eye Unit between 2002 and 2011.Phenotypic variables recorded were BCVA, fluorescein angiographic appearance, electrophysiology, and visual fields. RESULTS All patients had heterozygous amino acid-changing variants (missense mutations) in the ABCA4 gene. A splice sequence change was found in a 30-year-old patient with severly affected vision. Two novel sequence changes were identified: a missense mutation in a mildly affected 44-year-old patient and a frameshift mutation in a severly affected 34-year-old patient. CONCLUSION The identified ABCA4 mutations were compatible with the resulting phenotypes in terms of BCVA. Higher BCVAs were recorded in patients with missense mutations. Sequence changes, predicted to have more deleterious effect on protein function, resulted in a more severe phenotype. This case series of STGD patients demonstrates novel genotype/phenotype correlations, which may be useful to counselling of patients. This information may prove useful in selection of candidates for clinical trials in ABCA4 disease.
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Affiliation(s)
- M Gemenetzi
- Southampton Eye Unit, Southampton General Hospital, Southampton, UK
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105
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Fujinami K, Sergouniotis PI, Davidson AE, Mackay DS, Tsunoda K, Tsubota K, Robson AG, Holder GE, Moore AT, Michaelides M, Webster AR. The clinical effect of homozygous ABCA4 alleles in 18 patients. Ophthalmology 2013; 120:2324-31. [PMID: 23769331 DOI: 10.1016/j.ophtha.2013.04.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 04/17/2013] [Accepted: 04/17/2013] [Indexed: 10/26/2022] Open
Abstract
PURPOSE To describe the phenotypic presentation of a cohort of individuals with homozygous disease-associated ABCA4 variants. DESIGN Retrospective case series. PARTICIPANTS Eighteen affected individuals from 13 families ascertained from a total cohort of 214 families with ABCA4-related retinal disease presenting to a single center. METHODS A detailed history was obtained, and color fundus photography, autofluorescence (AF) imaging, optical coherence tomography (OCT), and electrophysiologic assessment were performed. Phenotypes based on ophthalmoscopy, AF, and electrophysiology were assigned using previously reported characteristics. ABCA4 mutation detection was performed using the ABCR400 microarray (Asper Biotech, Tartu, Estonia) and high-throughput DNA sequencing, with direct sequencing used to assess segregation. MAIN OUTCOME MEASURES Detailed clinical, electrophysiologic, and molecular genetic findings. RESULTS Eleven disease-associated homozygous ABCA4 alleles were identified, including 1 frame shift, 2 stops, 1 intronic variant causing splice-site alteration, 2 complex missense variants, and 5 missense variants: p.Glu905fsX916, p.Arg1300X, p.Gln2220X, c.4253+4 C>T, p.Leu541Pro and p.Ala1038Val (homozygosity for complex allele), p.Val931Met and p.Arg1705Gln (complex allele), p.Arg212Cys, p.Cys1488Arg, p.Arg1640Trp, p.Gly1961Glu, and p.Leu2027Phe. Eight of these 11 homozygous alleles have not been reported previously. Six of 7 patients with homozygous null alleles had early-onset (<10 years) disease, with all 7 having a severe phenotype. Two patients with homozygous missense variants (p.Leu541Pro and p.Ala1038Val [complex], and p.Arg1640Trp) presented with a severe phenotype. Three patients with homozygous p.Gly1961Glu had adult-onset disease and a mild phenotype. One patient with homozygous p.Leu2027Phe showed a spared fovea and preserved visual acuity. CONCLUSIONS The phenotypes represented in patients identified as homozygous for presumed disease-associated ABCA4 variants gives insight into the effect of individual alleles. Null alleles have severe functional effects, and certain missense variants are similar to nulls, suggesting complete abrogation of protein function. The common alleles identified, p.Gly1961Glu and p. Leu2027Phe, both have a mild structural and functional effect on the adult retina; the latter is associated with relatively retained photoreceptor architecture and function at the fovea.
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Affiliation(s)
- Kaoru Fujinami
- UCL Institute of Ophthalmology, London, United Kingdom; Moorfields Eye Hospital, London, United Kingdom; National Institute of Sensory Organs, National Tokyo Medical Center, Tokyo, Japan; Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
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106
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Riveiro-Alvarez R, Lopez-Martinez MA, Zernant J, Aguirre-Lamban J, Cantalapiedra D, Avila-Fernandez A, Gimenez A, Lopez-Molina MI, Garcia-Sandoval B, Blanco-Kelly F, Corton M, Tatu S, Fernandez-San Jose P, Trujillo-Tiebas MJ, Ramos C, Allikmets R, Ayuso C. Outcome of ABCA4 disease-associated alleles in autosomal recessive retinal dystrophies: retrospective analysis in 420 Spanish families. Ophthalmology 2013; 120:2332-7. [PMID: 23755871 DOI: 10.1016/j.ophtha.2013.04.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/03/2013] [Accepted: 04/03/2013] [Indexed: 10/26/2022] Open
Abstract
OBJECTIVE To provide a comprehensive overview of all detected mutations in the ABCA4 gene in Spanish families with autosomal recessive retinal disorders, including Stargardt's disease (arSTGD), cone-rod dystrophy (arCRD), and retinitis pigmentosa (arRP), and to assess genotype-phenotype correlation and disease progression in 10 years by considering the type of variants and age at onset. DESIGN Case series. PARTICIPANTS A total of 420 unrelated Spanish families: 259 arSTGD, 86 arCRD, and 75 arRP. METHODS Spanish families were analyzed through a combination of ABCR400 genotyping microarray, denaturing high-performance liquid chromatography, and high-resolution melting scanning. Direct sequencing was used as a confirmation technique for the identified variants. Screening by multiple ligation probe analysis was used to detect possible large deletions or insertions in the ABCA4 gene. Selected families were analyzed further by next generation sequencing. MAIN OUTCOME MEASURES DNA sequence variants, mutation detection rates, haplotypes, age at onset, central or peripheral vision loss, and night blindness. RESULTS Overall, we detected 70.5% and 36.6% of all expected ABCA4 mutations in arSTGD and arCRD patient cohorts, respectively. In the fraction of the cohort where the ABCA4 gene was sequenced completely, the detection rates reached 73.6% for arSTGD and 66.7% for arCRD. However, the frequency of possibly pathogenic ABCA4 alleles in arRP families was only slightly higher than that in the general population. Moreover, in some families, mutations in other known arRP genes segregated with the disease phenotype. CONCLUSIONS An increasing understanding of causal ABCA4 alleles in arSTGD and arCRD facilitates disease diagnosis and prognosis and also is paramount in selecting patients for emerging clinical trials of therapeutic interventions. Because ABCA4-associated diseases are evolving retinal dystrophies, assessment of age at onset, accurate clinical diagnosis, and genetic testing are crucial. We suggest that ABCA4 mutations may be associated with a retinitis pigmentosa-like phenotype often as a consequence of severe (null) mutations, in cases of long-term, advanced disease, or both. Patients with classical arRP phenotypes, especially from the onset of the disease, should be screened first for mutations in known arRP genes and not ABCA4.
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Affiliation(s)
- Rosa Riveiro-Alvarez
- Department of Genetics, Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain; Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Raras, ISCIII, Madrid, Spain
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107
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Fujinami K, Lois N, Davidson AE, Mackay DS, Hogg CR, Stone EM, Tsunoda K, Tsubota K, Bunce C, Robson AG, Moore AT, Webster AR, Holder GE, Michaelides M. A longitudinal study of stargardt disease: clinical and electrophysiologic assessment, progression, and genotype correlations. Am J Ophthalmol 2013; 155:1075-1088.e13. [PMID: 23499370 DOI: 10.1016/j.ajo.2013.01.018] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 01/14/2013] [Accepted: 01/16/2013] [Indexed: 01/01/2023]
Abstract
PURPOSE To investigate the clinical and electrophysiologic natural history of Stargardt disease and correlate with the genotype. DESIGN Cohort study of 59 patients. METHODS Clinical history, examination, and electrophysiologic assessment were undertaken in a longitudinal survey. Patients were classified into 3 groups based on electrophysiologic findings, as previously published: Group 1 had dysfunction confined to the macula; Group 2 had macular and generalized cone system dysfunction; and Group 3 had macular and both generalized cone and rod system dysfunction. At baseline, there were 27 patients in Group 1, 17 in Group 2, and 15 in Group 3. Amplitude reduction of >50% in the relevant electroretinogram (ERG) component or a peak time shift of >3 ms for the 30 Hz flicker ERG or bright flash a-wave was considered clinically significant ERG deterioration. Molecular screening of ABCA4 was undertaken. RESULTS The mean age at baseline was 31.7 years, with the mean follow-up interval being 10.5 years. A total of 22% of patients from Group 1 showed ERG group transition during follow-up, with 11% progressing to Group 2 and 11% to Group 3. Forty-seven percent of patients in Group 2 progressed to Group 3. There was clinically significant ERG deterioration in 54% of all subjects: 22% of Group 1, 65% of Group 2, and 100% of Group 3. At least 1 disease-causing ABCA4 variant was identified in 47 patients. CONCLUSIONS All patients with initial rod ERG involvement demonstrated clinically significant electrophysiologic deterioration; only 20% of patients with normal full-field ERGs at baseline showed clinically significant progression. Such data assist counseling by providing more accurate prognostic information and are also highly relevant in the design, patient selection, and monitoring of potential therapeutic interventions.
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108
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Stargardt disease: towards developing a model to predict phenotype. Eur J Hum Genet 2013; 21:1173-6. [PMID: 23695285 DOI: 10.1038/ejhg.2013.92] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 04/10/2013] [Accepted: 04/16/2013] [Indexed: 11/08/2022] Open
Abstract
Stargardt disease is an ABCA4-associated retinopathy, which generally follows an autosomal recessive inheritance pattern and is a frequent cause of macular degeneration in childhood. ABCA4 displays significant allelic heterogeneity whereby different mutations can cause retinal diseases with varying severity and age of onset. A genotype-phenotype model has been proposed linking ABCA4 mutations, purported ABCA4 functional protein activity and severity of disease, as measured by degree of visual loss and the age of onset. It has, however, been difficult to verify this model statistically in observational studies, as the number of individuals sharing any particular mutation combination is typically low. Seven founder mutations have been identified in a large number of Caucasian Afrikaner patients in South Africa, making it possible to test the genotype-phenotype model. A generalised linear model was developed to predict and assess the relative pathogenic contribution of the seven mutations to the age of onset of Stargardt disease. It is shown that the pathogenicity of an individual mutation can differ significantly depending on the genetic context in which it occurs. The results reported here may be used to identify suitable candidates for inclusion in clinical trials, as well as guide the genetic counselling of affected individuals and families.
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109
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Tran-Viet KN, Powell C, Barathi V, Klemm T, Maurer-Stroh S, Limviphuvadh V, Soler V, Ho C, Yanovitch T, Schneider G, Li YJ, Nading E, Metlapally R, Saw SM, Goh L, Rozen S, Young T. Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. Am J Hum Genet 2013; 92:820-6. [PMID: 23643385 DOI: 10.1016/j.ajhg.2013.04.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/21/2013] [Accepted: 04/08/2013] [Indexed: 12/31/2022] Open
Abstract
Myopia, or near-sightedness, is an ocular refractive error of unfocused image quality in front of the retinal plane. Individuals with high-grade myopia (dioptric power greater than -6.00) are predisposed to ocular morbidities such as glaucoma, retinal detachment, and myopic maculopathy. Nonsyndromic, high-grade myopia is highly heritable, and to date multiple gene loci have been reported. We performed exome sequencing in 4 individuals from an 11-member family of European descent from the United States. Affected individuals had a mean dioptric spherical equivalent of -22.00 sphere. A premature stop codon mutation c.157C>T (p.Gln53*) cosegregating with disease was discovered within SCO2 that maps to chromosome 22q13.33. Subsequent analyses identified three additional mutations in three highly myopic unrelated individuals (c.341G>A, c.418G>A, and c.776C>T). To determine differential gene expression in a developmental mouse model, we induced myopia by applying a -15.00D lens over one eye. Messenger RNA levels of SCO2 were significantly downregulated in myopic mouse retinae. Immunohistochemistry in mouse eyes confirmed SCO2 protein localization in retina, retinal pigment epithelium, and sclera. SCO2 encodes for a copper homeostasis protein influential in mitochondrial cytochrome c oxidase activity. Copper deficiencies have been linked with photoreceptor loss and myopia with increased scleral wall elasticity. Retinal thinning has been reported with an SC02 variant. Human mutation identification with support from an induced myopic animal provides biological insights of myopic development.
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110
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Jonsson F, Burstedt MS, Sandgren O, Norberg A, Golovleva I. Novel mutations in CRB1 and ABCA4 genes cause Leber congenital amaurosis and Stargardt disease in a Swedish family. Eur J Hum Genet 2013; 21:1266-71. [PMID: 23443024 DOI: 10.1038/ejhg.2013.23] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 11/09/2022] Open
Abstract
This study aimed to identify genetic mechanisms underlying severe retinal degeneration in one large family from northern Sweden, members of which presented with early-onset autosomal recessive retinitis pigmentosa and juvenile macular dystrophy. The clinical records of affected family members were analysed retrospectively and ophthalmological and electrophysiological examinations were performed in selected cases. Mutation screening was initially performed with microarrays, interrogating known mutations in the genes associated with recessive retinitis pigmentosa, Leber congenital amaurosis and Stargardt disease. Searching for homozygous regions with putative causative disease genes was done by high-density SNP-array genotyping, followed by segregation analysis of the family members. Two distinct phenotypes of retinal dystrophy, Leber congenital amaurosis and Stargardt disease were present in the family. 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 carrier of the same mutation and a novel ABCA4 mutation c.4773+3A>G. Sequence analysis of the entire ABCA4 gene in patients with Stargardt disease revealed complex alleles with additional sequence variants, which were evaluated by bioinformatics tools. In conclusion, presence of different genetic mechanisms resulting in variable phenotype within the family is not rare and can challenge molecular geneticists, ophthalmologists and genetic counsellors.
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Affiliation(s)
- Frida Jonsson
- Department of Medical Biosciences/Medical and Clinical Genetics, University of Umeå, Umeå, Sweden
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111
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Chacón-Camacho OF, Granillo-Alvarez M, Ayala-Ramírez R, Zenteno JC. ABCA4 mutational spectrum in Mexican patients with Stargardt disease: Identification of 12 novel mutations and evidence of a founder effect for the common p.A1773V mutation. Exp Eye Res 2013; 109:77-82. [PMID: 23419329 DOI: 10.1016/j.exer.2013.02.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 01/16/2013] [Accepted: 02/04/2013] [Indexed: 01/10/2023]
Abstract
The aim of this study was to assess the mutational spectrum of the ABCA4 gene in a cohort of patients with Stargardt disease from Mexico, a previously uncharacterized population. Clinical diagnosis in each patient was supported by a complete ophthalmological assessment that included visual acuity measurement, a slit lamp examination, a fundus examination and photography, electroretinography, fluorescein angiography, and computerized visual fields testing. Molecular analysis was performed by PCR amplification and direct nucleotide sequence of the 50 exons of the ABCA4 gene in genomic DNA. A total of 31 unrelated subjects with the disease were enrolled in the study. Molecular analysis in the total group of 62 alleles allowed the identification of 46 mutant ABCA4 alleles carrying 29 different pathogenic disease-associated mutations. Two ABCA4 mutant alleles were detected in 20 of the 31 patients (64.5%), a single disease allele was identified in six (19.4%), and no mutant alleles were detected in five of the cases (16.1%). Most patients with two ABCA4 mutations (11/20, 55%) were compound heterozygotes. Twelve variants were novel ABCA4 mutations. Nucleotide substitutions were the most frequent type of variation, occurring in 26 out of 29 (89.7%) different mutations. The two most common mutations in our study were the missense changes p.A1773V and p.G818E, which were identified in eight (17%) and seven (15%) of the total 46 disease-associated alleles, respectively. Haplotype analyses of intragenic SNPs in four subjects carrying the p.A1773V mutation supported a common origin for this mutation. In conclusion, this is the first report of ABCA4 molecular screening in Latin American Stargardt disease patients. Our results expand the mutational spectrum of the disease by adding 12 novel ABCA4 pathogenic variants and support the occurrence of a founder effect for the p.A1773V mutation in the Mexican population. The identification of recurrent mutations in our cohort will direct future ABCA4 molecular screening in patients from this ethnic group.
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Affiliation(s)
- Oscar F Chacón-Camacho
- Department of Genetics-Research Unit, Institute of Ophthalmology Conde de Valenciana, Mexico City, Mexico
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112
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Burke TR, Fishman GA, Zernant J, Schubert C, Tsang SH, Smith RT, Ayyagari R, Koenekoop RK, Umfress A, Ciccarelli ML, Baldi A, Iannaccone A, Cremers FPM, Klaver CCW, Allikmets R. Retinal phenotypes in patients homozygous for the G1961E mutation in the ABCA4 gene. Invest Ophthalmol Vis Sci 2012; 53:4458-67. [PMID: 22661473 DOI: 10.1167/iovs.11-9166] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE We evaluated the pathogenicity of the G1961E mutation in the ABCA4 gene, and present the range of retinal phenotypes associated with this mutation in homozygosity in a patient cohort with ABCA4-associated phenotypes. METHODS Patients were enrolled from the ABCA4 disease database at Columbia University or by inquiry from collaborating physicians. Only patients homozygous for the G1961E mutation were enrolled. The entire ABCA4 gene open reading frame, including all exons and flanking intronic sequences, was sequenced in all patients. Phenotype data were obtained from clinical history and examination, fundus photography, infrared imaging, fundus autofluorescence, fluorescein angiography, and spectral domain-optical coherence tomography. Additional functional data were obtained using the full-field electroretinogram, and static or kinetic perimetry. RESULTS We evaluated 12 patients homozygous for the G1961E mutation. All patients had evidence of retinal pathology consistent with the range of phenotypes observed in ABCA4 disease. The latest age of onset was recorded at 64 years, in a patient diagnosed initially with age-related macular degeneration (AMD). Of 6 patients in whom severe structural (with/without functional) fundus changes were detected, 5 had additional, heterozygous or homozygous, variants detected in the ABCA4 gene. CONCLUSIONS Homozygous G1961E mutation in ABCA4 results in a range of retinal pathology. The phenotype usually is at the milder end of the disease spectrum, with severe phenotypes linked to the presence of additional ABCA4 variants. Our report also highlights that milder, late-onset Stargardt disease may be confused with AMD.
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Affiliation(s)
- Tomas R Burke
- Department of Ophthalmology, Columbia University, New York, New York 10032, USA
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Westeneng-van Haaften SC, Boon CJF, Cremers FPM, Hoefsloot LH, den Hollander AI, Hoyng CB. Clinical and genetic characteristics of late-onset Stargardt's disease. Ophthalmology 2012; 119:1199-210. [PMID: 22449572 DOI: 10.1016/j.ophtha.2012.01.005] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 01/04/2012] [Accepted: 01/04/2012] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE To describe the genotype and phenotype of patients with a late-onset Stargardt's disease (STGD1). DESIGN Retrospective case series. PARTICIPANTS Twenty-one unrelated STGD1 patients with an age at onset of ≥45 years and ≥1 rare variant in the ABCA4 gene. METHODS Ophthalmologic examination, including best-corrected visual acuity (VA), Amsler grid testing, fundus photography, fluorescein angiography (FA), spectral-domain optical coherence tomography (OCT), fundus autofluorescence (FAF) imaging, full-field electroretinography (ERG), multifocal ERG, and central visual field testing. Analysis of the ABCA4 gene was performed using microarray analysis, sequencing, and multiplex ligation-dependent probe amplification. In addition, the PRPH2 and CFH genes were sequenced. MAIN OUTCOME MEASURES Age at onset, VA, fundus appearance, FA, FAF, and OCT findings; ABCA4 mutations; and genotype-phenotype correlation. RESULTS The mean age at onset was 55 years (range, 45-72 years). Seven patients were diagnosed without visual symptoms (age range, 45-83 years). The VA was ≥20/40 in 24 eyes of 14 patients (59%) owing to foveal sparing. On ophthalmoscopy, late-onset STGD1 showed flavimaculatus flecks (15 patients), small flecks surrounding mottled foveal changes (3 patients), extensive chorioretinal atrophy (2 patients), or small yellowish spots in the macula (1 patient). The fundus flecks showed increased autofluorescence on FAF. The choroidal background fluorescence on FA was obscured in 16 patients (80%). We found a single heterozygous ABCA4 variant in 11 patients (52%), 2 compound heterozygous variants in 8 patients (38%), and a homozygous variant in 2 patients (10%). No PRPH2 or CFH mutations were detected. CONCLUSIONS Late-onset STGD1 is at the mild end of the spectrum of retinal dystrophies caused by ABCA4 mutations. The VA is frequently preserved in late-onset STGD1 patients owing to foveal sparing. This phenotype may be caused by 1 or 2 ABCA4 variants. The differential diagnosis between late-onset STGD1 and age-related macular degeneration may be challenging. A thorough clinical and genetic analysis makes a distinction possible, which is important for clinical and genetic counseling. FINANCIAL DISCLOSURE(S) The authors have no proprietary or commercial interest in any of the materials discussed in this article.
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114
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Roberts LJ, Nossek CA, Greenberg LJ, Ramesar RS. Stargardt macular dystrophy: common ABCA4 mutations in South Africa--establishment of a rapid genetic test and relating risk to patients. Mol Vis 2012; 18:280-9. [PMID: 22328824 PMCID: PMC3275638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 01/28/2012] [Indexed: 10/26/2022] Open
Abstract
PURPOSE Based on the previous indications of founder ATP-binding cassette sub-family A member 4 gene (ABCA4) mutations in a South African subpopulation, the purpose was to devise a mechanism for identifying common disease-causing mutations in subjects with ABCA4-associated retinopathies (AARs). Facilitating patient access to this data and determining the frequencies of the mutations in the South African population would enhance the current molecular diagnostic service offered. METHODS The majority of subjects in this study were of Caucasian ancestry and affected with Stargardt macular dystrophy. The initial cohort consisted of DNA samples from 181 patients, and was screened using the ABCR400 chip. An assay was then designed to screen a secondary cohort of 72 patients for seven of the most commonly occurring ABCA4 mutations in this population. A total of 269 control individuals were also screened for the seven ABCA4 mutations. RESULTS Microarray screening results from a cohort of 181 patients affected with AARs revealed that seven ABCA4 mutations (p.Arg152*, c.768G>T, p.Arg602Trp, p.Gly863Ala, p.Cys1490Tyr, c.5461-10T>C, and p.Leu2027Phe) occurred at a relatively high frequency. The newly designed genetic assay identified two of the seven disease-associated mutations in 28/72 patients in a secondary patient cohort. In the control cohort, 12/269 individuals were found to be heterozygotes, resulting in an estimated background frequency of these mutations in this particular population of 4.46 per 100 individuals. CONCLUSIONS The relatively high detection rate of seven ABCA4 mutations in the primary patient cohort led to the design and subsequent utility of a multiplex assay. This assay can be used as a viable screening tool and to reduce costs and laboratory time. The estimated background frequency of the seven ABCA4 mutations, together with the improved diagnostic service, could be used by counselors to facilitate clinical and genetic management of South African families with AARs.
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115
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Littink KW, den Hollander AI, Cremers FPM, Collin RWJ. The power of homozygosity mapping: discovery of new genetic defects in patients with retinal dystrophy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 723:345-51. [PMID: 22183352 DOI: 10.1007/978-1-4614-0631-0_45] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Karin W Littink
- The Rotterdam Eye Hospital, 70030, 3000 LM, Rotterdam, The Netherlands
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116
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Zernant J, Schubert C, Im KM, Burke T, Brown CM, Fishman GA, Tsang SH, Gouras P, Dean M, Allikmets R. Analysis of the ABCA4 gene by next-generation sequencing. Invest Ophthalmol Vis Sci 2011; 52:8479-87. [PMID: 21911583 DOI: 10.1167/iovs.11-8182] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
PURPOSE To find all possible disease-associated variants in coding sequences of the ABCA4 gene in a large cohort of patients diagnosed with ABCA4-associated diseases. METHODS One hundred sixty-eight patients who had been clinically diagnosed with Stargardt disease, cone-rod dystrophy, and other ABCA4-associated phenotypes were prescreened for mutations in ABCA4 with the ABCA4 microarray, resulting in finding 1 of 2 expected mutations in 111 patients and 0 of 2 mutations in 57 patients. The next-generation sequencing (NGS) strategy was applied to these patients to sequence the entire coding region and the splice sites of the ABCA4 gene. Identified new variants were confirmed or rejected by Sanger sequencing and analyzed for possible pathogenicity by in silico programs and, where possible, by segregation analyses. RESULTS Sequencing was successful in 159 of 168 patients and identified the second disease-associated allele in 49 of 103 (~48%) of patients with one previously identified mutation. Among those with no mutations, both disease-associated alleles were detected in 4 of 56 patients, and one mutation was detected in 10 of 56 patients. The authors detected a total of 57 previously unknown, possibly pathogenic, variants: 29 missense, 4 nonsense, 9 small deletions and 15 splice-site-altering variants. Of these, 55 variants were deemed pathogenic by a combination of predictive methods and segregation analyses. CONCLUSIONS Many mutations in the coding sequences of the ABCA4 gene are still unknown, and many possibly reside in noncoding regions of the ABCA4 locus. Although the ABCA4 array remains a good first-pass screening option, the NGS platform is a time- and cost-efficient tool for screening large cohorts.
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Affiliation(s)
- Jana Zernant
- Department of Ophthalmology, Columbia University, New York, New York 10032, USA
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117
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Abstract
Since the discovery of the ABCA4 gene as the cause of autosomal recessive Stargardt disease/fundus flavimaculatus much has been written of the phenotypic variability in ABCA4 retinopathy. In this review the authors discuss the findings seen on examination and the disease features detected using various clinical tests. Important differential diagnoses are presented and unusual presentations of ABCA4 disease highlighted.
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Affiliation(s)
- Tomas R Burke
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University, 160 Fort Washington Avenue, New York, NY, 10032, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University, 160 Fort Washington Avenue, New York, NY, 10032, USA
- Department of Pathology and Cell Biology, Bernard and Shirlee Brown Glaucoma Laboratory, Edward S. Harkness Eye Institute, Columbia University, 160 Fort Washington Avenue, New York, NY, 10032, USA
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Ma L, Kaufman Y, Zhang J, Washington I. C20-D3-vitamin A slows lipofuscin accumulation and electrophysiological retinal degeneration in a mouse model of Stargardt disease. J Biol Chem 2010; 286:7966-7974. [PMID: 21156790 DOI: 10.1074/jbc.m110.178657] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Stargardt disease, also known as juvenile macular degeneration, occurs in approximately one in 10,000 people and results from genetic defects in the ABCA4 gene. The disease is characterized by premature accumulation of lipofuscin in the retinal pigment epithelium (RPE) of the eye and by vision loss. No cure or treatment is available. Although lipofuscin is considered a hallmark of Stargardt disease, its mechanism of formation and its role in disease pathogenesis are poorly understood. In this work we investigated the effects of long-term administration of deuterium-enriched vitamin A, C20-D(3)-vitamin A, on RPE lipofuscin deposition and eye function in a mouse model of Stargardt's disease. Results support the notion that lipofuscin forms partly as a result of the aberrant reactivity of vitamin A through the formation of vitamin A dimers, provide evidence that preventing vitamin A dimerization may slow disease related, retinal physiological changes and perhaps vision loss and suggest that administration of C20-D(3)-vitamin A may be a potential clinical strategy to ameliorate clinical symptoms resulting from ABCA4 genetic defects.
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Affiliation(s)
- Li Ma
- From the Department of Ophthalmology, Columbia University Medical Center, New York, New York 10032
| | - Yardana Kaufman
- From the Department of Ophthalmology, Columbia University Medical Center, New York, New York 10032
| | - Junhua Zhang
- From the Department of Ophthalmology, Columbia University Medical Center, New York, New York 10032
| | - Ilyas Washington
- From the Department of Ophthalmology, Columbia University Medical Center, New York, New York 10032.
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Hinzpeter A, Aissat A, Sondo E, Costa C, Arous N, Gameiro C, Martin N, Tarze A, Weiss L, de Becdelièvre A, Costes B, Goossens M, Galietta LJ, Girodon E, Fanen P. Alternative splicing at a NAGNAG acceptor site as a novel phenotype modifier. PLoS Genet 2010; 6. [PMID: 20949073 PMCID: PMC2951375 DOI: 10.1371/journal.pgen.1001153] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 09/09/2010] [Indexed: 11/18/2022] Open
Abstract
Approximately 30% of alleles causing genetic disorders generate premature termination codons (PTCs), which are usually associated with severe phenotypes. However, bypassing the deleterious stop codon can lead to a mild disease outcome. Splicing at NAGNAG tandem splice sites has been reported to result in insertion or deletion (indel) of three nucleotides. We identified such a mechanism as the origin of the mild to asymptomatic phenotype observed in cystic fibrosis patients homozygous for the E831X mutation (2623G>T) in the CFTR gene. Analyses performed on nasal epithelial cell mRNA detected three distinct isoforms, a considerably more complex situation than expected for a single nucleotide substitution. Structure-function studies and in silico analyses provided the first experimental evidence of an indel of a stop codon by alternative splicing at a NAGNAG acceptor site. In addition to contributing to proteome plasticity, alternative splicing at a NAGNAG tandem site can thus remove a disease-causing UAG stop codon. This molecular study reveals a naturally occurring mechanism where the effect of either modifier genes or epigenetic factors could be suspected. This finding is of importance for genetic counseling as well as for deciding appropriate therapeutic strategies. Mild disease outcomes associated with premature termination codons can result from at least three different mechanisms, but none of these mechanisms explain the mild phenotype observed in some patients. Subtle differences in alternative transcripts have recently been reported at NAGNAG tandem acceptor motifs, which can be detected in 30% of human genes. We provide the first experimental evidence of premature termination codon removal by alternative splicing at a NAGNAG acceptor splice site. Our study emphasizes the biological significance of such alternative splicing in the context of disease-causing mutations and defines a new phenotype-modifying mechanism that buffers nonsense mutations.
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Affiliation(s)
| | - Abdel Aissat
- INSERM, Unité U955, Créteil, France
- Université Paris-Est, Faculté de Médecine, UMR-S 955, Créteil, France
| | - Elvira Sondo
- Laboratorio di Genetica Molecolare, Istituto G. Gaslini, Genova, Italy
| | - Catherine Costa
- INSERM, Unité U955, Créteil, France
- AP-HP, Groupe Henri-Mondor Albert-Chenevier, Service de Biochimie-Génétique, Créteil, France
| | | | - Christine Gameiro
- AP-HP, Groupe Henri-Mondor Albert-Chenevier, Service de Biochimie-Génétique, Créteil, France
| | | | - Agathe Tarze
- INSERM, Unité U955, Créteil, France
- Université Paris-Est, Faculté de Médecine, UMR-S 955, Créteil, France
| | - Laurence Weiss
- Service de Pédiatrie I, Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Alix de Becdelièvre
- INSERM, Unité U955, Créteil, France
- Université Paris-Est, Faculté de Médecine, UMR-S 955, Créteil, France
- AP-HP, Groupe Henri-Mondor Albert-Chenevier, Service de Biochimie-Génétique, Créteil, France
| | - Bruno Costes
- Université Paris-Est, Faculté de Médecine, UMR-S 955, Créteil, France
| | - Michel Goossens
- INSERM, Unité U955, Créteil, France
- Université Paris-Est, Faculté de Médecine, UMR-S 955, Créteil, France
- AP-HP, Groupe Henri-Mondor Albert-Chenevier, Service de Biochimie-Génétique, Créteil, France
| | - Luis J. Galietta
- Laboratorio di Genetica Molecolare, Istituto G. Gaslini, Genova, Italy
| | - Emmanuelle Girodon
- INSERM, Unité U955, Créteil, France
- AP-HP, Groupe Henri-Mondor Albert-Chenevier, Service de Biochimie-Génétique, Créteil, France
| | - Pascale Fanen
- INSERM, Unité U955, Créteil, France
- Université Paris-Est, Faculté de Médecine, UMR-S 955, Créteil, France
- AP-HP, Groupe Henri-Mondor Albert-Chenevier, Service de Biochimie-Génétique, Créteil, France
- * E-mail:
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Schindler EI, Nylen EL, Ko AC, Affatigato LM, Heggen AC, Wang K, Sheffield VC, Stone EM. Deducing the pathogenic contribution of recessive ABCA4 alleles in an outbred population. Hum Mol Genet 2010; 19:3693-701. [PMID: 20647261 PMCID: PMC2935854 DOI: 10.1093/hmg/ddq284] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Accurate prediction of the pathogenic effects of specific genotypes is important for the design and execution of clinical trials as well as for meaningful counseling of individual patients. However, for many autosomal recessive diseases, it can be difficult to deduce the relative pathogenic contribution of individual alleles because relatively few affected individuals share the same two disease-causing variations. In this study, we used multiple regression analysis to estimate the pathogenicity of specific alleles of ABCA4 in patients with retinal phenotypes ranging from Stargardt disease to retinitis pigmentosa. This analysis revealed quantitative allelic effects on two aspects of the visual phenotype, visual acuity (P < 10−3) and visual field (P < 10−7). Discordance between visual acuity and visual field in individual patients suggests the existence of at least two non-ABCA4 modifying factors. The findings of this study will facilitate the discovery of factors that modify ABCA4 disease and will also aid in the optimal selection of subjects for clinical trials of new therapies.
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Affiliation(s)
- Emily I Schindler
- Howard Hughes Medical Institute, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA 52242, USA
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121
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Molday RS, Zhang K. Defective lipid transport and biosynthesis in recessive and dominant Stargardt macular degeneration. Prog Lipid Res 2010; 49:476-92. [PMID: 20633576 DOI: 10.1016/j.plipres.2010.07.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Stargardt disease is a common inherited macular degeneration characterized by a significant loss in central vision in the first or second decade of life, bilateral atrophic changes in the central retina associated with degeneration of photoreceptors and underlying retinal pigment epithelial cells, and the presence of yellow flecks extending from the macula. Autosomal recessive Stargardt disease, the most common macular dystrophy, is caused by mutations in the gene encoding ABCA4, a photoreceptor ATP binding cassette (ABC) transporter. Biochemical studies together with analysis of abca4 knockout mice and Stargardt patients have implicated ABCA4 as a lipid transporter that facilitates the removal of potentially toxic retinal compounds from photoreceptors following photoexcitation. An autosomal dominant form of Stargardt disease also known as Stargardt-like dystrophy is caused by mutations in a gene encoding ELOVL4, an enzyme that catalyzes the elongation of very long-chain fatty acids in photoreceptors and other tissues. This review focuses on the molecular characterization of ABCA4 and ELOVL4 and their role in photoreceptor cell biology and the pathogenesis of Stargardt disease.
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Affiliation(s)
- Robert S Molday
- Department of Biochemistry and Molecular Biology, Centre of Macular Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada.
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Tsai KW, Chan WC, Hsu CN, Lin WC. Sequence features involved in the mechanism of 3' splice junction wobbling. BMC Mol Biol 2010; 11:34. [PMID: 20459675 PMCID: PMC2875228 DOI: 10.1186/1471-2199-11-34] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 05/07/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alternative splicing is an important mechanism mediating the diversified functions of genes in multicellular organisms, and such event occurs in around 40-60% of human genes. Recently, a new splice-junction wobbling mechanism was proposed that subtle modifications exist in mRNA maturation by alternatively choosing at 5'- GTNGT and 3'- NAGNAG, which created single amino acid insertion and deletion isoforms. RESULTS By browsing the Alternative Splicing Database information, we observed that most 3' alternative splice site choices occur within six nucleotides of the dominant splice site and the incidence significantly decreases further away from the dominant acceptor site. Although a lower frequency of alternative splicing occurs within the intronic region (alternative splicing at the proximal AG) than in the exonic region (alternative splicing at the distal AG), alternative AG sites located within the intronic region show stronger potential as the acceptor. These observations revealed that the choice of 3' splice sites during 3' splicing junction wobbling could depend on the distance between the duplicated AG and the branch point site (BPS). Further mutagenesis experiments demonstrated that the distance of AG-to-AG and BPS-to-AG can greatly influence 3' splice site selection. Knocking down a known alternative splicing regulator, hSlu7, failed to affect wobble splicing choices. CONCLUSION Our results implied that nucleotide distance between proximal and distal AG sites has an important regulatory function. In this study, we showed that occurrence of 3' wobble splicing occurs in a distance-dependent manner and that most of this wobble splicing is probably caused by steric hindrance from a factor bound at the neighboring tandem motif sequence.
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Affiliation(s)
- Kuo-Wang Tsai
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
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123
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Sinha R, Lenser T, Jahn N, Gausmann U, Friedel S, Szafranski K, Huse K, Rosenstiel P, Hampe J, Schuster S, Hiller M, Backofen R, Platzer M. TassDB2 - A comprehensive database of subtle alternative splicing events. BMC Bioinformatics 2010; 11:216. [PMID: 20429909 PMCID: PMC2878309 DOI: 10.1186/1471-2105-11-216] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 04/29/2010] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Subtle alternative splicing events involving tandem splice sites separated by a short (2-12 nucleotides) distance are frequent and evolutionarily widespread in eukaryotes, and a major contributor to the complexity of transcriptomes and proteomes. However, these events have been either omitted altogether in databases on alternative splicing, or only the cases of experimentally confirmed alternative splicing have been reported. Thus, a database which covers all confirmed cases of subtle alternative splicing as well as the numerous putative tandem splice sites (which might be confirmed once more transcript data becomes available), and allows to search for tandem splice sites with specific features and download the results, is a valuable resource for targeted experimental studies and large-scale bioinformatics analyses of tandem splice sites. Towards this goal we recently set up TassDB (Tandem Splice Site DataBase, version 1), which stores data about alternative splicing events at tandem splice sites separated by 3 nt in eight species. DESCRIPTION We have substantially revised and extended TassDB. The currently available version 2 contains extensive information about tandem splice sites separated by 2-12 nt for the human and mouse transcriptomes including data on the conservation of the tandem motifs in five vertebrates. TassDB2 offers a user-friendly interface to search for specific genes or for genes containing tandem splice sites with specific features as well as the possibility to download result datasets. For example, users can search for cases of alternative splicing where the proportion of EST/mRNA evidence supporting the minor isoform exceeds a specific threshold, or where the difference in splice site scores is specified by the user. The predicted impact of each event on the protein is also reported, along with information about being a putative target for the nonsense-mediated decay (NMD) pathway. Links are provided to the UCSC genome browser and other external resources. CONCLUSION TassDB2, available via http://www.tassdb.info, provides comprehensive resources for researchers interested in both targeted experimental studies and large-scale bioinformatics analyses of short distance tandem splice sites.
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Affiliation(s)
- Rileen Sinha
- Bioinformatics group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Thorsten Lenser
- Bio Systems Analysis Group, Friedrich Schiller University Jena, Ernst-Abbe-Platz 1-4, D-07743 Jena, Germany
| | - Niels Jahn
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Ulrike Gausmann
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Swetlana Friedel
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Systems Biology/Bioinformatics, Beutenbergstrasse. 11a, 07745 Jena, Germany
| | - Karol Szafranski
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Klaus Huse
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Schittenhelmstrasse, 12, 24105 Kiel, Germany
| | - Jochen Hampe
- Department of General Internal Medicine, University Hospital Schleswig-Holstein, Campus Kiel, Schittenhelmstrasse, 12, 24105 Kiel, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Michael Hiller
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Rolf Backofen
- Bioinformatics group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Freiburg Initiative for Systems Biology (FRISYS), University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
- Centre for Biological Signalling Studies (bioss), University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany
| | - Matthias Platzer
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
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ABC transporters in ophthalmic disease. Methods Mol Biol 2010. [PMID: 20419437 DOI: 10.1007/978-1-60761-700-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
ABC transporters have been implicated in a variety of human diseases. The ABCR gene and its protein have been linked to Stargardt's disease, fundus flavimaculatus, cone-rod dystrophy, retinitis pigmentosa, and age-related macular degeneration. The genetic and molecular pathways involved in the pathogenesis of ABCR-related ophthalmic conditions will be explored. Future diagnostic and therapeutic objectives for these diseases will also be discussed.
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125
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Berger W, Kloeckener-Gruissem B, Neidhardt J. The molecular basis of human retinal and vitreoretinal diseases. Prog Retin Eye Res 2010; 29:335-75. [PMID: 20362068 DOI: 10.1016/j.preteyeres.2010.03.004] [Citation(s) in RCA: 394] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
During the last two to three decades, a large body of work has revealed the molecular basis of many human disorders, including retinal and vitreoretinal degenerations and dysfunctions. Although belonging to the group of orphan diseases, they affect probably more than two million people worldwide. Most excitingly, treatment of a particular form of congenital retinal degeneration is now possible. A major advantage for treatment is the unique structure and accessibility of the eye and its different components, including the vitreous and retina. Knowledge of the many different eye diseases affecting retinal structure and function (night and colour blindness, retinitis pigmentosa, cone and cone rod dystrophies, photoreceptor dysfunctions, as well as vitreoretinal traits) is critical for future therapeutic development. We have attempted to present a comprehensive picture of these disorders, including biological, clinical, genetic and molecular information. The structural organization of the review leads the reader through non-syndromic and syndromic forms of (i) rod dominated diseases, (ii) cone dominated diseases, (iii) generalized retinal degenerations and (iv) vitreoretinal disorders, caused by mutations in more than 165 genes. Clinical variability and genetic heterogeneity have an important impact on genetic testing and counselling of affected families. As phenotypes do not always correlate with the respective genotypes, it is of utmost importance that clinicians, geneticists, counsellors, diagnostic laboratories and basic researchers understand the relationships between phenotypic manifestations and specific genes, as well as mutations and pathophysiologic mechanisms. We discuss future perspectives.
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Affiliation(s)
- Wolfgang Berger
- Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Schorenstrasse 16, CH-8603 Schwerzenbach, Switzerland.
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Ernest PJ, Boon CJ, Klevering BJ, Hoefsloot LH, Hoyng CB. Outcome of ABCA4 microarray screening in routine clinical practice. Mol Vis 2009; 15:2841-7. [PMID: 20029649 PMCID: PMC2796636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 12/09/2009] [Indexed: 11/01/2022] Open
Abstract
PURPOSE To retrospectively analyze the clinical characteristics of patients who were screened for mutations with the ATP-binding cassette transporter gene ABCA4 (ABCA4) microarray in a routine clinical DNA diagnostics setting. METHODS We performed a retrospective analysis of the medical charts of 65 patients who underwent an ABCA4 microarray screening between the years 2002 and 2006. An additional denaturing gradient gel electrophoresis (DGGE) was performed in these patients if less than two mutations were found with the microarray. We included all patients who were suspected of autosomal recessive Stargardt disease (STGD1), autosomal recessive cone-rod dystrophy (arCRD), or autosomal recessive retinitis pigmentosa at the time of microarray request. After a retrospective analysis of the clinical characteristics, the patients who were suspected of STGD1 were categorized as having either a typical or atypical form of STGD1, according to the age at onset, fundus appearance, fluorescein angiography, and electroretinography. The occurrence of typical clinical features for STGD1 was compared between patients with different numbers of discovered mutations. RESULTS Of the 44 patients who were suspected of STGD1, 26 patients (59%) had sufficient data available for a classification in either typical (six patients; 23%) or atypical (20 patients; 77%) STGD1. In the suspected STGD1 group, 59% of all expected pathogenic alleles were found with the ABCA4 microarray. DGGE led to the finding of 12 more mutations, resulting in an overall detection rate of 73%. Thirty-one percent of patients with two or three discovered ABCA4 mutations met all typical STGD1 criteria. An age at onset younger than 25 years and a dark choroid on fluorescein angiography were the most predictive clinical features to find ABCA4 mutations in patients suspected of STGD1. In 18 patients suspected of arCRD, microarray screening detected 22% of the possible pathogenic alleles. CONCLUSIONS In addition to confirmation of the diagnosis in typical STGD1, ABCA4 microarray screening is usually requested in daily clinical practice to strengthen the diagnosis when the disease is atypical. This study supports the view that the efficiency and accuracy of ABCA4 microarray screening are directly dependent upon the clinical features of the patients who are screened.
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Affiliation(s)
- Paul J.G. Ernest
- Department of Ophthalmology, University Hospital Maastricht, Maastricht, The Netherlands,Department of Epidemiology, Maastricht University, Maastricht, The Netherlands
| | - Camiel J.F. Boon
- Department of Ophthalmology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - B. Jeroen Klevering
- Department of Ophthalmology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Lies H. Hoefsloot
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Carel B. Hoyng
- Department of Ophthalmology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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127
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Mellough CB, Steel DHW, Lako M. Genetic basis of inherited macular dystrophies and implications for stem cell therapy. Stem Cells 2009; 27:2833-45. [PMID: 19551904 PMCID: PMC2962903 DOI: 10.1002/stem.159] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2009] [Accepted: 06/11/2009] [Indexed: 12/25/2022]
Abstract
Untreatable hereditary macular dystrophy (HMD) presents a major burden to society in terms of the resulting patient disability and the cost to the healthcare provision system. HMD results in central vision loss in humans sufficiently severe for blind registration, and key issues in the development of therapeutic strategies to target these conditions are greater understanding of the causes of photoreceptor loss and the development of restorative procedures. More effective and precise analytical techniques coupled to the development of transgenic models of disease have led to a prolific growth in the identification and our understanding of the genetic mutations that underly HMD. Recent successes in driving differentiation of pluripotent cells towards specific somatic lineages have led to the development of more efficient protocols that can yield enriched populations of a desired phenotype. Retinal pigmented epithelial cells and photoreceptors derived from these are some of the most promising cells that may soon be used in the treatment of specific HMD, especially since rapid developments in the field of induced pluripotency have now set the stage for the production of patient-derived stem cells that overcome the ethical and methodological issues surrounding the use of embryonic derivatives. In this review we highlight a selection of HMD which appear suitable candidates for combinatorial restorative therapy, focusing specifically on where those photoreceptor loss occurs. This technology, along with increased genetic screening, opens up an entirely new pathway to restore vision in patients affected by HMD.
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Affiliation(s)
- Carla B Mellough
- Institute of Human Genetics andInternational Centre for LifeNewcastle Upon Tyne, United Kingdom
| | - David HW Steel
- Sunderland Eye InfirmaryQueen Alexandra Road, Sunderland, Tyne and Wear, United Kingdom
| | - Majlinda Lako
- North East Stem Cell Institute, Newcastle University, International Centre for LifeNewcastle Upon Tyne, United Kingdom
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Xi Q, Li L, Traboulsi EI, Wang QK. Novel ABCA4 compound heterozygous mutations cause severe progressive autosomal recessive cone-rod dystrophy presenting as Stargardt disease. Mol Vis 2009; 15:638-45. [PMID: 19352439 PMCID: PMC2665199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2009] [Accepted: 03/21/2009] [Indexed: 11/26/2022] Open
Abstract
PURPOSE To identify the gene causing a severe form of progressive autosomal recessive cone-rod dystrophy presenting as Stargardt disease and to characterize clinical features in a large American family. METHODS We characterized an American family who had an unusual retinal dystrophy with clinical features of Stargardt disease and severe progressive cone-rod dystrophy. Family members underwent complete ocular examinations with evaluation of visual acuity, visual fields, fundus examination, fluorescein angiography, and electroretinography. Genome-wide linkage analysis of the family was performed using 408 microsatellite markers spanning the entire human genome. Direct DNA sequence analysis was used for mutational analysis of the ABCA4 gene in all exons and exon-intron boundary regions and for testing cosegregation of the mutations with the disease in the family. DNA sequence analysis was used to determine the presence of the mutations in 200 unrelated controls. RESULTS The proband presented with a clinical phenotype that was initially compatible with Stargardt disease, only to progress to a severe cone-rod dystrophy over the course of a few years. The disease-causing gene in the family was linked to the ABCA4 locus on chromosomal 1p22. One novel mutation, c.655A>T, was identified in exon 6 and another novel splicing mutation, c.5312+3A>T, was identified in intron 37 of ABCA4. The mutations were not present in 200 controls. The two affected sisters in this pedigree were compound heterozygotes for the mutations. Unaffected family members either did not carry either or had only one of the two mutations. CONCLUSIONS We have identified two novel ABCA4 mutations, c.655A>T and c.5312+3A>T. When present as a compound heterozygous state, the mutations cause a phenotype of retinal dystrophy that initially manifests as Stargardt disease and slowly progresses to a severe cone-rod dystrophy. These results expand the wide range of clinical manifestations of ABCA4 mutations.
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Affiliation(s)
- Quansheng Xi
- Center for Cardiovascular Genetics and Department of Molecular Cardiology, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH
| | - Lin Li
- Center for Cardiovascular Genetics and Department of Molecular Cardiology, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH
| | | | - Qing Kenneth Wang
- Center for Cardiovascular Genetics and Department of Molecular Cardiology, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH,Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
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Maia-Lopes S, Aguirre-Lamban J, Castelo-Branco M, Riveiro-Alvarez R, Ayuso C, Silva ED. ABCA4 mutations in Portuguese Stargardt patients: identification of new mutations and their phenotypic analysis. Mol Vis 2009; 15:584-91. [PMID: 19365591 PMCID: PMC2660377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 03/09/2009] [Indexed: 11/29/2022] Open
Abstract
PURPOSE To resolve the spectrum of causative retina-specific ATP-binding cassette transporter gene (ABCA4) gene mutations in Portuguese Stargardt (STGD) patients and compare allele frequencies obtained in this cohort with those of previous population surveys. METHODS Using a microarray technique (ABCR400 gene chip), we screened all previously reported ABCA4 gene mutations in the genomic DNA of 27 patients from 21 unrelated Stargardt families whose phenotypes had been clinically evaluated using psychophysics and electrophysiological measurements. Furthermore, we performed denaturing high performance liquid chromatography whenever one or both mutant alleles failed to be detected using the ABCR gene chip. RESULTS A total of 36 mutant alleles (out of the 54 tested) were identified in STGD patients, resulting in a detection rate of 67%. Two mutant alleles were present in 12 out of 21 STGD families (57%), whereas in four out of 21 (19%) of the families, only one mutant allele was found. We report the presence of 22 putative pathogenic alterations, including two sequence changes not found in other populations, c.2T>C (p.Met1Thr) and c.4036_4037delAC (p.Thr1346fs), and two novel disease-associated variants, c.400C>T (p.Gln134X) and c.4720G>T (p.Glu1574X). The great majority of the mutations were missense (72.7%). Seven frameshift variants (19.4%), three nonsense mutations (8.3%), and one splicing sequence change (2.7%) were also found in STGD chromosomes. The most prevalent pathologic variant was the missense mutation p.Leu11Pro. Present in 19% of the families, this mutation represents a quite high prevalence in comparison to other European populations. In addition, 23 polymorphisms were also identified, including four novel intronic sequence variants. CONCLUSIONS To our knowledge, this study represents the first report of ABCA4 mutations in Portuguese STGD patients and provides further evidence of different mutation frequency across populations. Phenotypic characterization of novel putative mutations was addressed.
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Affiliation(s)
- Susana Maia-Lopes
- Visual Neuroscience Laboratory, IBILI, Faculty of Medicine, Coimbra, Portugal
| | - Jana Aguirre-Lamban
- Genetics Department, Fundacíon Jiménez Díaz and CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | | | - Rosa Riveiro-Alvarez
- Genetics Department, Fundacíon Jiménez Díaz and CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Carmen Ayuso
- Genetics Department, Fundacíon Jiménez Díaz and CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Eduardo Duarte Silva
- Visual Neuroscience Laboratory, IBILI, Faculty of Medicine, Coimbra, Portugal,Centre for Hereditary Eye Diseases, Department of Ophthalmology, University Hospital Coimbra, Coimbra, Portugal
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130
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Passerini I, Sodi A, Giambene B, Mariottini A, Menchini U, Torricelli F. Novel mutations in of the ABCR gene in Italian patients with Stargardt disease. Eye (Lond) 2009; 24:158-64. [PMID: 19265867 DOI: 10.1038/eye.2009.35] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Stargardt disease (STGD) is the most prevalent juvenile macular dystrophy, and it has been associated with mutations in the ABCR gene, encoding a photoreceptor-specific transport protein. In this study, we determined the mutation spectrum in the ABCR gene in a group of Italian STGD patients. METHODS The DNA samples of 71 Italian patients (from 62 independent pedigrees), affected with autosomal recessive STGD, were analysed for mutations in all 50 exons of the ABCR gene by the DHPLC approach (with optimization of the DHPLC conditions for mutation analysis) and direct sequencing techniques. RESULTS In our group of STGD patients, 71 mutations were identified in 68 patients with a detection rate of 95.7%. Forty-three mutations had been already reported in the literature, whereas 28 mutations had not been previously described and were not detected in 150 unaffected control individuals of Italian origin. Missense mutations represented the most frequent finding (59.2%); G1961E was the most common mutation and it was associated with phenotypes in various degrees of severity. CONCLUSIONS Some novel mutations in the ABCR gene were reported in a group of Italian STGD patients confirming the extensive allelic heterogeneity of this gene-probably related to the vast number of exons that favours rearrangements in the DNA sequence.
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Affiliation(s)
- I Passerini
- Department of Genetic Diagnosis, Careggi Universitary Hospital, Florence, Italy.
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131
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Hozoji M, Kimura Y, Kioka N, Ueda K. Formation of two intramolecular disulfide bonds is necessary for ApoA-I-dependent cholesterol efflux mediated by ABCA1. J Biol Chem 2009; 284:11293-300. [PMID: 19258317 DOI: 10.1074/jbc.m900580200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ABCA1 plays a major role in cholesterol homeostasis and high density lipoprotein (HDL) metabolism. ABCA1 contains disulfide bond(s) between its N- and C-terminal halves, but it remains unclear whether disulfide bond formation is important for the functions of ABCA1 and which cysteines are involved in disulfide bond formation. To answer these questions, we constructed >30 ABCA1 mutants in which 16 extracellular domain (ECD) cysteines were replaced with serines and examined disulfide bond formation, apoA-I binding, and HDL formation in these mutants. From the single cysteine replacements, two cysteines (Cys(75) and Cys(309)) in ECD1 were found to be essential for apoA-I binding. In contrast, in ECD2, only Cys(1477) was found to be essential for HDL formation, and no single cysteine replacement impaired apoA-I binding. The concurrent replacement of two cysteines, Cys(1463) and Cys(1465), impaired apoA-I binding and HDL formation, suggesting that four of five extracellular cysteines (Cys(75), Cys(309), Cys(1463), Cys(1465), and Cys(1477)) are involved in these functions of ABCA1. Trypsin digestion experiments suggested that one disulfide bond is not sufficient and that two intramolecular disulfide bonds (between Cys(75) and Cys(309) in ECD1 and either Cys(1463) or Cys(1465) and Cys(1477) in ECD2) are required for ABCA1 to be fully functional.
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Affiliation(s)
- Masako Hozoji
- Laboratory of Cellular Biochemistry, Division of Applied Life Sciences, Kyoto University Graduate School of Agriculture, Kyoto, Japan
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132
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The role of the photoreceptor ABC transporter ABCA4 in lipid transport and Stargardt macular degeneration. Biochim Biophys Acta Mol Cell Biol Lipids 2009; 1791:573-83. [PMID: 19230850 DOI: 10.1016/j.bbalip.2009.02.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 02/04/2009] [Accepted: 02/05/2009] [Indexed: 12/26/2022]
Abstract
ABCA4 is a member of the ABCA subfamily of ATP binding cassette (ABC) transporters that is expressed in rod and cone photoreceptors of the vertebrate retina. ABCA4, also known as the Rim protein and ABCR, is a large 2,273 amino acid glycoprotein organized as two tandem halves, each containing a single membrane spanning segment followed sequentially by a large exocytoplasmic domain, a multispanning membrane domain and a nucleotide binding domain. Over 500 mutations in the gene encoding ABCA4 are associated with a spectrum of related autosomal recessive retinal degenerative diseases including Stargardt macular degeneration, cone-rod dystrophy and a subset of retinitis pigmentosa. Biochemical studies on the purified ABCA4 together with analysis of abca4 knockout mice and patients with Stargardt disease have implicated ABCA4 as a retinylidene-phosphatidylethanolamine transporter that facilitates the removal of potentially reactive retinal derivatives from photoreceptors following photoexcitation. Knowledge of the genetic and molecular basis for ABCA4 related retinal degenerative diseases is being used to develop rationale therapeutic treatments for this set of disorders.
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133
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Lv J, Yang Y, Yin H, Chu F, Wang H, Zhang W, Zhang Y, Jin Y. Molecular determinants and evolutionary dynamics of wobble splicing. Mol Biol Evol 2009; 26:1081-92. [PMID: 19221008 PMCID: PMC2668829 DOI: 10.1093/molbev/msp023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Alternative splicing at tandem splice sites (wobble splicing) is widespread in many species, but the mechanisms specifying the tandem sites remain poorly understood. Here, we used synaptotagmin I as a model to analyze the phylogeny of wobble splicing spanning more than 300 My of insect evolution. Phylogenetic analysis indicated that the occurrence of species-specific wobble splicing was related to synonymous variation at tandem splice sites. Further mutagenesis experiments demonstrated that wobble splicing could be lost by artificially induced synonymous point mutations due to destruction of splice acceptor sites. In contrast, wobble splicing could not be correctly restored through mimicking an ancestral tandem acceptor by artificial synonymous mutation in in vivo splicing assays, which suggests that artificial tandem splice sites might be incompatible with normal wobble splicing. Moreover, combining comparative genomics with hybrid minigene analysis revealed that alternative splicing has evolved from the 3′ tandem donor to the 5′ tandem acceptor in Culex pipiens, as a result of an evolutionary shift of cis element sequences from 3′ to 5′ splice sites. These data collectively suggest that the selection of tandem splice sites might not simply be an accident of history but rather in large part the result of coevolution between splice site and cis element sequences as a basis for wobble splicing. An evolutionary model of wobble splicing is proposed.
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Affiliation(s)
- Jianning Lv
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Zijingang Campus, Hangzhou, Zhejiang, China
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134
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Kremer H, Cremers FPM. Positional cloning of deafness genes. Methods Mol Biol 2009; 493:215-238. [PMID: 18839350 DOI: 10.1007/978-1-59745-523-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The identification of the majority of the known causative genes involved in nonsyndromic sensorineural hearing loss (NSHL) started with linkage analysis as part of a positional cloning procedure. The human and mouse genome projects in combination with technical developments on genotyping, transcriptomics, proteomics, and the creation of animal models have greatly enhanced the speed of disease gene identification. In the present chapter, we first discuss the possibilities for exclusion of known NSHL loci and genes. Subsequently, methods are described to determine the genomic regions that contain the genetic defects. These include linkage analysis with genotyping and statistical evaluation and the determination of copy number variations. In the case of a large genomic region, candidate genes are selected and prioritized using gene expression analysis, protein network data, and phenotypes of animal models. A number of algorithms are described to automate the process of candidate gene selection. The novel high-throughput sequencing techniques might make gene selection and prioritization unnecessary in the near future. Once genetic variants are identified, questions on pathogenicity need to be addressed, which is the topic of the last section of this chapter.
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Affiliation(s)
- Hannie Kremer
- Department of Otorhinolaryngology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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135
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Zhong M, Molday LL, Molday RS. Role of the C terminus of the photoreceptor ABCA4 transporter in protein folding, function, and retinal degenerative diseases. J Biol Chem 2008; 284:3640-9. [PMID: 19056738 DOI: 10.1074/jbc.m806580200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ABCA4 is an ATP-binding cassette transporter that is expressed in rod and cone photoreceptor cells and implicated in the removal of retinal derivatives from outer segments following photoexcitation. Mutations in the ABCA4 gene are responsible for a number of related retinal degenerative diseases, including Stargardt macular degeneration, cone-rod dystrophy, retinitis pigmentosa, and age-related macular degeneration. In order to determine the role of the C terminus of ABCA4 in protein structure and function and understand mechanisms by which C-terminal mutations cause retinal degenerative diseases, we have expressed and purified a series of deletion and substitution mutants of ABCA4 and ABCA1 in HEK 293T cells for analysis of their cellular localization and biochemical properties. Removal of the C-terminal 30 amino acids of ABCA4, including a conserved VFVNFA motif, resulted in a loss in N-retinylidene-phosphatidylethanolamine substrate binding, ATP photoaffinity labeling, and retinal-stimulated ATPase activity. This mutant was also retained in the endoplasmic reticulum of cells. Replacement of the VFVNFA motif with alanine residues also resulted in loss in function and cellular mislocalization. In contrast, C-terminal deletion mutants that retain the VFVNFA motif were functionally active and localized to intracellular vesicles similar to wild-type ABCA4. Our studies indicated that the VFVNFA motif is required for the proper folding of ABCA4 into a functionally active protein. This motif also contributes to the efficient folding of ABCA1 into an active protein. Our results provide a molecular based rationale for the disease phenotype displayed by individuals with mutations in the C terminus of ABCA4.
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Affiliation(s)
- Ming Zhong
- Department of Biochemistry and Molecular Biology, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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136
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Sherwin JC, Hewitt AW, Ruddle JB, Mackey DA. Genetic isolates in ophthalmic diseases. Ophthalmic Genet 2008; 29:149-61. [PMID: 19005985 DOI: 10.1080/13816810802334341] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In recent years, noteworthy gains have been made in unravelling the genetic contribution to some complex ocular diseases, principally age-related macular degeneration. Yet, a relatively poor understanding of the genetic aetiology for many other heritable blinding diseases, such as glaucoma, keratoconus and myopia, remains. Genetic isolates, populations with varying degrees of geographical or cultural seclusion, provide an effective means for investigating the molecular mechanisms involved in human diseases. This is particularly true for rare diseases in which founded alleles can be rapidly driven to a high frequency due to restriction of gene flow in the population. Recent success in complex gene mapping has resulted from the widened linkage disequilibrium (LD) in the genome of genetically isolated populations. An improved understanding of the predisposing genetic risk factors allows for enhanced screening modalities and paves the foundations for the translation of genomic technology into the clinic. This review focuses on the role population isolates have had in the investigation of genes underlying complex eye diseases and discusses their likely usefulness given the expansion of large-scale case-control association studies.
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Affiliation(s)
- Justin C Sherwin
- Department of Ophthalmology, Centre for Eye Research Australia, University of Melbourne, elbourne, Australia
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137
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Riveiro-Alvarez R, Aguirre-Lamban J, Lopez-Martinez MA, Trujillo-Tiebas MJ, Cantalapiedra D, Vallespin E, Avila-Fernandez A, Ramos C, Ayuso C. Frequency of ABCA4 mutations in 278 Spanish controls: an insight into the prevalence of autosomal recessive Stargardt disease. Br J Ophthalmol 2008; 93:1359-64. [PMID: 18977788 PMCID: PMC2743849 DOI: 10.1136/bjo.2008.148155] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Aim: To determine the carrier frequency of ABCA4 mutations in order to achieve an insight into the prevalence of autosomal recessive Stargardt disease (arSTGD) in the Spanish population. Methods: arSTGD patients (n = 133) were analysed using ABCR400 microarray and sequencing. Control subjects were analysed by two different strategies: 200 individuals were screened for the p.Arg1129Leu mutation by denaturing-HPLC and sequencing; 78 individuals were tested for variants with the microarray and sequencing. Results: For the first strategy in control subjects, the p.Arg1129Leu variant was found in two heterozygous individuals, which would mean a carrier frequency for any variant of ∼6.0% and a calculated arSTGD prevalence of 1:1000. For the second strategy, carrier frequency was 6.4% and therefore an estimated prevalence of the disease of 1:870. Conclusion: Calculated prevalence of arSTGD based on the ABCA4 carrier frequency could be considerably higher than previous estimation. This discrepancy between observed (genotypic) and estimated (phenotypic) prevalence could be due to the existence of non-pathological or low penetrance alleles, which may result in late-onset arSTGD or may be implicated in age-related macular degeneration. This situation should be regarded with especial care when genetic counselling is given and further follow-up of these patients should be recommended.
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Kong J, Kim SR, Binley K, Pata I, Doi K, Mannik J, Zernant-Rajang J, Kan O, Iqball S, Naylor S, Sparrow JR, Gouras P, Allikmets R. Correction of the disease phenotype in the mouse model of Stargardt disease by lentiviral gene therapy. Gene Ther 2008; 15:1311-20. [PMID: 18463687 DOI: 10.1038/gt.2008.78] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Autosomal recessive Stargardt disease (STGD1) is a macular dystrophy caused by mutations in the ABCA4 (ABCR) gene. The disease phenotype that is most recognized in STGD1 patients, and also in the Abca4-/- mouse (a disease model), is lipofuscin accumulation in retinal pigment epithelium. Here, we tested whether delivery of the normal (wt) human ABCA4 gene to the subretinal space of the Abca4 -/- mice via lentiviral vectors would correct the disease phenotype; that is, reduce accumulation of the lipofuscin pigment A2E. Equine infectious anemia virus (EIAV)-derived lentiviral vectors were constructed expressing either the human ABCA4 gene or the LacZ reporter gene under the control of the constitutive (CMV) or photoreceptor-specific (Rho) promoters. Abca4-/- mice were injected subretinally with 1 microl ( approximately 5.0 x 10(5) TU) of each EIAV vector in one eye at postnatal days 4 and 5. An injection of saline, an EIAV-null vector, or an uninjected contralateral eye served as a control. Mice were killed at various times after injection to determine photoreceptor (PR) transduction efficiency and A2E concentrations. EIAV-LacZ vectors transduced from 5 to 20% of the PRs in the injected area in mice. Most importantly, a single subretinal injection of EIAV-CMV-ABCA4 to Abca4-/- mouse eyes substantially reduced disease-associated A2E accumulation compared to untreated and mock-treated control eyes. Treated eyes of Abca4-/- mice accumulated 8-12 pmol per eye (s.d.=2.7) of A2E 1 year after treatment, amounts comparable to wt controls, whereas mock-treated or untreated eyes had 3-5 times more A2E (27-39 pmol per eye, s.d.=1.5; P=0.001-0.005). Although extrapolation to humans requires caution, the high transduction efficiency of both rod and cone photoreceptors and the statistically significant reduction of A2E accumulation in the mouse model of STGD1 suggest that lentiviral gene therapy is a potentially efficient tool for treating ABCA4-associated diseases.
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Affiliation(s)
- J Kong
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA
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139
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ATP-binding cassette transporter ABCA4: molecular properties and role in vision and macular degeneration. J Bioenerg Biomembr 2008; 39:507-17. [PMID: 17994272 DOI: 10.1007/s10863-007-9118-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
ABCA4, also known as ABCR or the rim protein, is a member of the ABCA subfamily of ATP binding cassette (ABC) transporters expressed in vertebrate rod and cone photoreceptor cells and localized to outer segment disk membranes. ABCA4 is organized in two tandem halves, each consisting of a transmembrane segment followed successively by a large exocytoplasmic domain, a multispanning membrane domain, and a nucleotide-binding domain. Over 400 mutations in ABCA4 have been linked to Stargardt macular degeneration and related retinal degenerative diseases that cause severe vision loss in affected individuals. Direct binding studies and ATPase activation measurements have identified N-retinylidene-phosphatidylethanolamine, a product generated from the photobleaching of rhodopsin, as the substrate for ABCA4. Mice deficient in ABCA4 accumulate phosphatidylethanolamine, all-trans retinal, and N-retinylidene-phosphatidylethanolamine in photoreceptors and the diretinal pyridinium compound A2E in retinal pigment epithelial cells. On the basis of these studies, ABCA4 is proposed to actively transport or flip N-retinylidene-phosphatidylethanolamine from the lumen to the cytoplasmic side of disc membranes following the photobleaching of rhodopsin. This transport activity insures that retinoids do not accumulate in disc membranes. Disease-linked mutations in ABCA4 that result in diminished transport activity lead to an accumulation of all-trans retinal and N-retinylidene-PE in disc membranes which react to produce A2E precursors. A2E progressively accumulates as lipofuscin deposits in retinal pigment epithelial cells as a result of phagocytosis of outer segment discs. A2E and photo-oxidation products cause RPE cell death and consequently photoreceptor degeneration resulting in a loss in vision in individuals with Stargardt macular degeneration and other retinal degenerative diseases associated with mutations in ABCA4.
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140
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Hiller M, Platzer M. Widespread and subtle: alternative splicing at short-distance tandem sites. Trends Genet 2008; 24:246-55. [PMID: 18394746 DOI: 10.1016/j.tig.2008.03.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 03/05/2008] [Accepted: 03/06/2008] [Indexed: 12/11/2022]
Abstract
Alternative splicing at donor or acceptor sites located just a few nucleotides apart is widespread in many species. It results in subtle changes in the transcripts and often in the encoded proteins. Several of these tandem splice events contribute to the repertoire of functionally different proteins, whereas many are neutral or deleterious. Remarkably, some of the functional events are differentially spliced in tissues or developmental stages, whereas others exhibit constant splicing ratios, indicating that function is not always associated with differential splicing. Stochastic splice site selection seems to play a major role in these processes. Here, we review recent progress in understanding functional and evolutionary aspects as well as the mechanism of splicing at short-distance tandem sites.
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Affiliation(s)
- Michael Hiller
- Bioinformatics Group, Albert-Ludwigs-University Freiburg, 79110 Freiburg, Germany.
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141
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Abstract
Stargardt's disease is an autosomal recessive form of juvenile macular degeneration. The clinical presentation, relevant ancillary tests, and classic histologic features will be reviewed. The role of genetic mutations in the pathophysiology of Stargardt's disease will also be explored. Stargardt's disease is caused by mutations in the ABCR (ABCA4) gene on chromosome 1. Mutations in this gene have also been attributed to some cases of cone-rod dystrophy, retinitis pigmentosa, and age-related macular degeneration. The genetic and molecular pathways that produce Stargardt's disease will be discussed. Future diagnostic and therapeutic objectives for this visually disabling condition will also be presented.
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Affiliation(s)
- Corey Westerfeld
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
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142
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ABCA4 gene analysis in patients with autosomal recessive cone and cone rod dystrophies. Eur J Hum Genet 2008; 16:812-9. [PMID: 18285826 DOI: 10.1038/ejhg.2008.23] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The ATP-binding cassette (ABC) transporters constitute a family of large membrane proteins, which transport a variety of substrates across membranes. The ABCA4 protein is expressed in photoreceptors and possibly functions as a transporter for N-retinylidene-phosphatidylethanolamine (N-retinylidene-PE), the Schiff base adduct of all-trans-retinal with PE. Mutations in the ABCA4 gene have been initially associated with autosomal recessive Stargardt disease. Subsequent studies have shown that mutations in ABCA4 can also cause a variety of other retinal dystrophies including cone rod dystrophy and retinitis pigmentosa. To determine the prevalence and mutation spectrum of ABCA4 gene mutations in non-Stargardt phenotypes, we have screened 64 unrelated patients with autosomal recessive cone (arCD) and cone rod dystrophy (arCRD) applying the Asper Ophthalmics ABCR400 microarray followed by DNA sequencing of all coding exons of the ABCA4 gene in subjects with single heterozygous mutations. Disease-associated ABCA4 alleles were identified in 20 of 64 patients with arCD or arCRD. In four of 64 patients (6%) only one mutant ABCA4 allele was detected and in 16 patients (25%), mutations on both ABCA4 alleles were identified. Based on these data we estimate a prevalence of 31% for ABCA4 mutations in arCD and arCRD, supporting the concept that the ABCA4 gene is a major locus for various types of degenerative retinal diseases with abnormalities in cone or both cone and rod function.
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143
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Tsai KW, Tarn WY, Lin WC. Wobble splicing reveals the role of the branch point sequence-to-NAGNAG region in 3' tandem splice site selection. Mol Cell Biol 2007; 27:5835-48. [PMID: 17562859 PMCID: PMC1952111 DOI: 10.1128/mcb.00363-07] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Alternative splicing involving the 3' tandem splice site NAGNAG sequence may play a role in the structure-function diversity of proteins. However, how 3' tandem splice site utilization is determined is not well understood. We previously demonstrated that 3' NAGNAG-based wobble splicing occurs mostly in a tissue- and developmental stage-independent manner. Bioinformatic analysis reveals that the nucleotide preceding the AG dinucleotide may influence 3' splice site utilization; this is also supported by an in vivo splicing assay. Moreover, we found that the intron sequence plays an important role in 3' splice site selection for NAGNAG wobble splicing. Mutations of the region between the branch site and the NAGNAG 3' splice site, indeed, affected the ratio of the distal/proximal AG selection. Finally, we found that single nucleotide polymorphisms around the NAGNAG motif could affect the splice site choice, which may lead to a change in mRNA patterns and influence protein function. We conclude that the NAGNAG motif and its upstream region to the branch point sequence are required for 3' tandem splice site selection.
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Affiliation(s)
- Kuo-Wang Tsai
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China
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144
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Hiller M, Szafranski K, Backofen R, Platzer M. Alternative splicing at NAGNAG acceptors: simply noise or noise and more? PLoS Genet 2006; 2:e207; author reply e208. [PMID: 17121470 PMCID: PMC1657060 DOI: 10.1371/journal.pgen.0020207] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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145
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Hiller M, Nikolajewa S, Huse K, Szafranski K, Rosenstiel P, Schuster S, Backofen R, Platzer M. TassDB: a database of alternative tandem splice sites. Nucleic Acids Res 2006; 35:D188-92. [PMID: 17142241 PMCID: PMC1669710 DOI: 10.1093/nar/gkl762] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Subtle alternative splice events at tandem splice sites are frequent in eukaryotes and substantially increase the complexity of transcriptomes and proteomes. We have developed a relational database, TassDB (TAndem Splice Site DataBase), which stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. These splice events are of subtle nature since they mostly result in the insertion/deletion of a single amino acid or the substitution of one amino acid by two others. Currently, TassDB contains 114 554 tandem splice sites of eight species, 5209 of which have EST/mRNA evidence for alternative splicing. In addition, human SNPs that affect NAGNAG acceptors are annotated. The database provides a user-friendly interface to search for specific genes or for genes containing tandem splice sites with specific features as well as the possibility to download large datasets. This database should facilitate further experimental studies and large-scale bioinformatics analyses of tandem splice sites. The database is available at .
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Affiliation(s)
- Michael Hiller
- To whom correspondence should be addressed. Tel: +49 761 203 8254; Fax: +49 761 203 7462;
| | - Swetlana Nikolajewa
- Department of Bioinformatics, Friedrich-Schiller-University JenaErnst-Abbe-Platz 2, 07743 Jena, Germany
| | - Klaus Huse
- Genome Analysis, Leibniz Institute for Age Research—Fritz Lipmann InstituteBeutenbergstrasse 11, 07745 Jena, Germany
| | - Karol Szafranski
- Genome Analysis, Leibniz Institute for Age Research—Fritz Lipmann InstituteBeutenbergstrasse 11, 07745 Jena, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University KielSchittenhelmstrasse, 12, 24105 Kiel, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich-Schiller-University JenaErnst-Abbe-Platz 2, 07743 Jena, Germany
| | | | - Matthias Platzer
- Genome Analysis, Leibniz Institute for Age Research—Fritz Lipmann InstituteBeutenbergstrasse 11, 07745 Jena, Germany
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146
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Stenirri S, Battistella S, Fermo I, Manitto MP, Martina E, Brancato R, Ferrari M, Cremonesi L. De novo deletion removes a conserved motif in the C-terminus of ABCA4 and results in cone-rod dystrophy. Clin Chem Lab Med 2006; 44:533-7. [PMID: 16681420 DOI: 10.1515/cclm.2006.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Mutations in the retina-specific ABC transporter (ABCA4) gene are associated with different types of macular degeneration, including Stargardt disease, cone-rod dystrophy, Fundus flavimaculatus, Retinitis pigmentosa and probably age-related macular degeneration. METHODS Screening for mutations in the ABCA4 gene was performed using denaturing high-performance liquid chromatography and direct sequencing. RESULTS We describe the identification of a new de novo 44-bp deletion in an Italian patient affected by cone-rod dystrophy. The mutation, located in intron 48 of the ABCA4 gene, is predicted to cause exon 49 skipping, resulting in loss of the C-terminus of the ABCA4 protein. Interestingly, exon 49 also codes for a highly conserved VFVNFA motif, which has been demonstrated to be essential for the activity of ABCA1, another gene of the ABC transporter family. The presence of CT repeats at the breakpoints might have facilitated the generation of the deletion through a slippage mispairing mechanism. CONCLUSIONS The new 6730-16del44 deletion is the first de novo mutation associated with cone-rod dystrophy and may contribute to a better understanding of the role of ABCA4 mutations in macular dystrophies.
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Affiliation(s)
- Stefania Stenirri
- Unit of Genomics for Diagnosis of Human Pathologies, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
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147
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Ducroq D, Shalev S, Habib A, Munnich A, Kaplan J, Rozet JM. Three different ABCA4 mutations in the same large family with several consanguineous loops affected with autosomal recessive cone–rod dystrophy. Eur J Hum Genet 2006; 14:1269-73. [PMID: 16896346 DOI: 10.1038/sj.ejhg.5201691] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A large multiplex family presumably affected with autosomal recessive cone-rod dystrophy (CRD) was ascertained from Israel. In this family of Christian Arab ancestry with six consanguineous loops, linkage analysis failed to identify homozygosity in all six nuclear families at any of the three arCORD loci hitherto reported. However, homozygosity was found at the CORD3 locus for two nuclear families and the segregation of three distinct haplotypes at this locus in the whole pedigree suggested the alteration of the ABCA4 gene. This hypothesis was confirmed by the identification of three distinct mutations. Subsequently, with regard to the wide spectrum of autosomal recessive retinal dystrophies related to ABCA4 mutations, the natural history of the disease was revisited in all patients. Although the diagnosis of CRD was confirmed in 8/9 patients, the last one, aged of 34, displayed typical signs of Stargardt disease without extension to the peripheral retina. The results of this study emphasize the pitfalls of homozygosity mapping in highly inbred families when the heterozygote carrier frequency is particularly high in the general population.
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Affiliation(s)
- Dominique Ducroq
- Unite de Recherches sur les Handicaps Génétiques de l'Enfants, Hôpital Necker-Enfants Malades, INSERM 393, 149 rue de Sèvres, 75743 Paris Cedex 15, France
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148
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Fukui T, Fujikado T, Tsujikawa M, Okada M, Yamamoto S, Tano Y. Null ABCA4 gene mutations found in Japanese patients with panretinal degeneration. Jpn J Ophthalmol 2006; 50:179-81. [PMID: 16604398 DOI: 10.1007/s10384-005-0279-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2004] [Accepted: 05/27/2005] [Indexed: 11/24/2022]
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149
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Kaminski WE, Piehler A, Wenzel JJ. ABC A-subfamily transporters: Structure, function and disease. Biochim Biophys Acta Mol Basis Dis 2006; 1762:510-24. [PMID: 16540294 DOI: 10.1016/j.bbadis.2006.01.011] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Revised: 01/30/2006] [Accepted: 01/31/2006] [Indexed: 12/01/2022]
Abstract
ABC transporters constitute a family of evolutionarily highly conserved multispan proteins that mediate the translocation of defined substrates across membrane barriers. Evidence has accumulated during the past years to suggest that a subgroup of 12 structurally related "full-size" transporters, referred to as ABC A-subfamily transporters, mediates the transport of a variety of physiologic lipid compounds. The emerging importance of ABC A-transporters in human disease is reflected by the fact that as yet four members of this protein family (ABCA1, ABCA3, ABCR/ABCA4, ABCA12) have been causatively linked to completely unrelated groups of monogenetic disorders including familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies and congenital keratinization disorders. Although the biological function of the remaining 8 ABC A-transporters currently awaits clarification, they represent promising candidate genes for a presumably equally heterogenous group of Mendelian diseases associated with perturbed cellular lipid transport. This review summarizes our current knowledge on the role of ABC A-subfamily transporters in physiology and disease and explores clinical entities which may be potentially associated with dysfunctional members of this gene subfamily.
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Affiliation(s)
- Wolfgang E Kaminski
- Institute for Clinical Chemistry, Faculty for Clinical Medicine Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany.
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150
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Hiller M, Huse K, Szafranski K, Jahn N, Hampe J, Schreiber S, Backofen R, Platzer M. Single-nucleotide polymorphisms in NAGNAG acceptors are highly predictive for variations of alternative splicing. Am J Hum Genet 2006; 78:291-302. [PMID: 16400609 PMCID: PMC1380236 DOI: 10.1086/500151] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 11/22/2005] [Indexed: 01/16/2023] Open
Abstract
Aberrant or modified splicing patterns of genes are causative for many human diseases. Therefore, the identification of genetic variations that cause changes in the splicing pattern of a gene is important. Elsewhere, we described the widespread occurrence of alternative splicing at NAGNAG acceptors. Here, we report a genomewide screen for single-nucleotide polymorphisms (SNPs) that affect such tandem acceptors. From 121 SNPs identified, we extracted 64 SNPs that most likely affect alternative NAGNAG splicing. We demonstrate that the NAGNAG motif is necessary and sufficient for this type of alternative splicing. The evolutionarily young NAGNAG alleles, as determined by the comparison with the chimpanzee genome, exhibit the same biases toward intron phase 1 and single-amino acid insertion/deletions that were already observed for all human NAGNAG acceptors. Since 28% of the NAGNAG SNPs occur in known disease genes, they represent preferable candidates for a more-detailed functional analysis, especially since the splice relevance for some of the coding SNPs is overlooked. Against the background of a general lack of methods for identifying splice-relevant SNPs, the presented approach is highly effective in the prediction of polymorphisms that are causal for variations in alternative splicing.
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Affiliation(s)
- Michael Hiller
- Institute of Computer Science, Chair for Bioinformatics, Friedrich-Schiller-University Jena, and Genome Analysis, Leibniz Institute for Age Research–Fritz Lipmann Institute, Jena, Germany; and Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Klaus Huse
- Institute of Computer Science, Chair for Bioinformatics, Friedrich-Schiller-University Jena, and Genome Analysis, Leibniz Institute for Age Research–Fritz Lipmann Institute, Jena, Germany; and Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Karol Szafranski
- Institute of Computer Science, Chair for Bioinformatics, Friedrich-Schiller-University Jena, and Genome Analysis, Leibniz Institute for Age Research–Fritz Lipmann Institute, Jena, Germany; and Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Niels Jahn
- Institute of Computer Science, Chair for Bioinformatics, Friedrich-Schiller-University Jena, and Genome Analysis, Leibniz Institute for Age Research–Fritz Lipmann Institute, Jena, Germany; and Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Jochen Hampe
- Institute of Computer Science, Chair for Bioinformatics, Friedrich-Schiller-University Jena, and Genome Analysis, Leibniz Institute for Age Research–Fritz Lipmann Institute, Jena, Germany; and Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Stefan Schreiber
- Institute of Computer Science, Chair for Bioinformatics, Friedrich-Schiller-University Jena, and Genome Analysis, Leibniz Institute for Age Research–Fritz Lipmann Institute, Jena, Germany; and Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Rolf Backofen
- Institute of Computer Science, Chair for Bioinformatics, Friedrich-Schiller-University Jena, and Genome Analysis, Leibniz Institute for Age Research–Fritz Lipmann Institute, Jena, Germany; and Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Matthias Platzer
- Institute of Computer Science, Chair for Bioinformatics, Friedrich-Schiller-University Jena, and Genome Analysis, Leibniz Institute for Age Research–Fritz Lipmann Institute, Jena, Germany; and Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
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