1
|
Owete AC, Ionin R, Huryn LA, Cukras CA, Blain D, Agather AR, Hufnagel RB, Brooks BP, Nwanyanwu K, Zein WM. Seeing in Color: Inclusion and Characterization of Hereditary Eye Disease in African Americans. Transl Vis Sci Technol 2024; 13:4. [PMID: 39226063 PMCID: PMC11373706 DOI: 10.1167/tvst.13.9.4] [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: 09/04/2024] Open
Abstract
Purpose Hereditary eye diseases (HEDs) are individually rare but affect millions globally. The era of molecular genetics has ushered major advances in the study of these disorders; however, the inclusivity and population diversity of this research is unknown. Questions on the accuracy and applicability of these findings in diverse populations, especially African American patients, came up consistently during counselling sessions. This also raised the possibility of missed opportunities for broader understanding of these rare diseases. We conducted a literature review to measure the representation of African Americans in genomic research surrounding nine HEDs. Methods A detailed literature search using a predetermined set of search terms for each of nine HED categories was performed across PubMed, Embase, Web of Science, and Scopus focusing on studies published between Jan 1990 and July 2021. Predetermined inclusion criteria were applied to filter the sources. Results We identified 46 studies clearly reporting HED characterization in African Americans. Analysis of these inclusive studies revealed unique findings demonstrating the known usefulness of including diverse cohorts in genomics research. Conclusions HED characterization in diverse participants, specifically African Americans, is identified as a knowledge gap area. Genomic research is more applicable to patients when conducted in populations that share their ancestral background. Greater inclusion of African Americans in ophthalmic genetics research is a scientific imperative and a needed step in the pursuit of the best possible patient care for populations of all ancestries. Translational Relevance This work reveals gaps in genomic research in African Americans with HEDs.
Collapse
Affiliation(s)
- Agnes C Owete
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institute of Health, Bethesda, MD, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Raisa Ionin
- National Institutes of Health Library, National Institutes of Health, Bethesda, MD, USA
| | - Laryssa A Huryn
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institute of Health, Bethesda, MD, USA
| | - Catherine A Cukras
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institute of Health, Bethesda, MD, USA
| | - Delphine Blain
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institute of Health, Bethesda, MD, USA
| | - Aime R Agather
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institute of Health, Bethesda, MD, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institute of Health, Bethesda, MD, USA
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institute of Health, Bethesda, MD, USA
| | - Kristen Nwanyanwu
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT, USA
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institute of Health, Bethesda, MD, USA
| |
Collapse
|
2
|
Scortecci JF, Garces FA, Mahto JK, Molday LL, Van Petegem F, Molday RS. Structural and functional characterization of the nucleotide-binding domains of ABCA4 and their role in Stargardt disease. J Biol Chem 2024; 300:107666. [PMID: 39128720 DOI: 10.1016/j.jbc.2024.107666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/29/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024] Open
Abstract
ABCA4 is an ATP-binding cassette (ABC) transporter that prevents the buildup of toxic retinoid compounds by facilitating the transport of N-retinylidene-phosphatidylethanolamine across membranes of rod and cone photoreceptor cells. Over 1500 missense mutations in ABCA4, many in the nucleotide-binding domains (NBDs), have been genetically linked to Stargardt disease. Here, we show by cryo-EM that ABCA4 is converted from an open outward conformation to a closed conformation upon the binding of adenylyl-imidodiphosphate. Structural information and biochemical studies were used to further define the role of the NBDs in the functional properties of ABCA4 and the mechanisms by which mutations lead to the loss in activity. We show that ATPase activity in both NBDs is required for the functional activity of ABCA4. Mutations in Walker A asparagine residues cause a severe reduction in substrate-activated ATPase activity due to the loss in polar interactions with residues within the D-loops of the opposing NBD. The structural basis for how disease mutations in other NBD residues, including the R1108C, R2077W, R2107H, and L2027F, affect the structure and function of ABCA4 is described. Collectively, our studies provide insight into the structure and function of ABCA4 and mechanisms underlying Stargardt disease.
Collapse
Affiliation(s)
- Jessica Fernandes Scortecci
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fabian A Garces
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jai K Mahto
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laurie L Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Filip Van Petegem
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert S Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
3
|
Goto K, Koyanagi Y, Akiyama M, Murakami Y, Fukushima M, Fujiwara K, Iijima H, Yamaguchi M, Endo M, Hashimoto K, Ishizu M, Hirakata T, Mizobuchi K, Takayama M, Ota J, Sajiki AF, Kominami T, Ushida H, Fujita K, Kaneko H, Ueno S, Hayashi T, Terao C, Hotta Y, Murakami A, Kuniyoshi K, Kusaka S, Wada Y, Abe T, Nakazawa T, Ikeda Y, Momozawa Y, Sonoda KH, Nishiguchi KM. Disease-specific variant interpretation highlighted the genetic findings in 2325 Japanese patients with retinitis pigmentosa and allied diseases. J Med Genet 2024; 61:613-620. [PMID: 38499336 DOI: 10.1136/jmg-2023-109750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/02/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND As gene-specific therapy for inherited retinal dystrophy (IRD) advances, unified variant interpretation across institutes is becoming increasingly important. This study aims to update the genetic findings of 86 retinitis pigmentosa (RP)-related genes in a large number of Japanese patients with RP by applying the standardised variant interpretation guidelines for Japanese patients with IRD (J-IRD-VI guidelines) built upon the American College of Medical Genetics and Genomics and the Association for Molecular Pathology rules, and assess the contribution of these genes in RP-allied diseases. METHODS We assessed 2325 probands with RP (n=2155, including n=1204 sequenced previously with the same sequencing panel) and allied diseases (n=170, newly analysed), including Usher syndrome, Leber congenital amaurosis and cone-rod dystrophy (CRD). Target sequencing using a panel of 86 genes was performed. The variants were interpreted according to the J-IRD-VI guidelines. RESULTS A total of 3564 variants were detected, of which 524 variants were interpreted as pathogenic or likely pathogenic. Among these 524 variants, 280 (53.4%) had been either undetected or interpreted as variants of unknown significance or benign variants in our earlier study of 1204 patients with RP. This led to a genetic diagnostic rate in 38.6% of patients with RP, with EYS accounting for 46.7% of the genetically solved patients, showing a 9% increase in diagnostic rate from our earlier study. The genetic diagnostic rate for patients with CRD was 28.2%, with RP-related genes significantly contributing over other allied diseases. CONCLUSION A large-scale genetic analysis using the J-IRD-VI guidelines highlighted the population-specific genetic findings for Japanese patients with IRD; these findings serve as a foundation for the clinical application of gene-specific therapies.
Collapse
Affiliation(s)
- Kensuke Goto
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshito Koyanagi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masato Akiyama
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yusuke Murakami
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masatoshi Fukushima
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kohta Fujiwara
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hanae Iijima
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Mitsuyo Yamaguchi
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Mikiko Endo
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Kazuki Hashimoto
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masataka Ishizu
- Department of Ophthalmology, University of Miyazaki Faculty of Medicine, Miyazaki, Japan
| | - Toshiaki Hirakata
- Department of Ophthalmology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kei Mizobuchi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Masakazu Takayama
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Junya Ota
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ai Fujita Sajiki
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taro Kominami
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroaki Ushida
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kosuke Fujita
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroki Kaneko
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinji Ueno
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Ophthalmology, Hirosaki University Graduate School of Medicine, Hisoraki, Japan
| | - Takaaki Hayashi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Yoshihiro Hotta
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Akira Murakami
- Department of Ophthalmology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kazuki Kuniyoshi
- Department of Ophthalmology, Kindai University Faculty of Medicine, Osaka-sayama, Japan
| | - Shunji Kusaka
- Department of Ophthalmology, Kindai University Faculty of Medicine, Osaka-sayama, Japan
| | | | - Toshiaki Abe
- Division of Clinical Cell Therapy, Tohoku University Graduate School of Medicine United Centers for Advanced Research and Translational Medicine, Sendai, Japan
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yasuhiro Ikeda
- Department of Ophthalmology, University of Miyazaki Faculty of Medicine, Miyazaki, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koji M Nishiguchi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| |
Collapse
|
4
|
Genetic characteristics of 234 Italian patients with macular and cone/cone-rod dystrophy. Sci Rep 2022; 12:3774. [PMID: 35260635 PMCID: PMC8904500 DOI: 10.1038/s41598-022-07618-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/16/2022] [Indexed: 01/09/2023] Open
Abstract
Two-hundred and thirty-four Italian patients with a clinical diagnosis of macular, cone and cone-rod dystrophies (MD, CD, and CRD) were examined using next-generation sequencing (NGS) and gene sequencing panels targeting a specific set of genes, Sanger sequencing and—when necessary—multiplex ligation-dependent probe amplification (MLPA) to diagnose the molecular cause of the aforementioned diseases. When possible, segregation analysis was performed in order to confirm unsolved cases. Each patient’s retinal phenotypic characteristics were determined using focal and full-field ERGs, perimetry, spectral domain optical coherence tomography and fundus autofluorescence. We identified 236 potentially causative variants in 136 patients representing the 58.1% of the total cohort, 43 of which were unpublished. After stratifying the patients according to their clinical suspicion, the diagnostic yield was 62.5% and 53.8% for patients with MD and for those with CD/CRD, respectively. The mode of inheritance of all cases confirmed by genetic analysis was 70% autosomal recessive, 26% dominant, and 4% X-linked. The main cause (59%) of both MD and CD/CRD cases was the presence of variants in the ABCA4 gene, followed by variants in PRPH2 (9%) and BEST1 (6%). A careful morpho-functional evaluation of the phenotype, together with genetic counselling, resulted in an acceptable diagnostic yield in a large cohort of Italian patients. Our study emphasizes the role of targeted NGS to diagnose MDs, CDs, and CRDs, as well as the clinical usefulness of segregation analysis for patients with unsolved diagnosis.
Collapse
|
5
|
Molecular analysis of ABCA4 gene in an Iranian cohort with Stargardt disease. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2021.101450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
6
|
Molday RS, Garces FA, Scortecci JF, Molday LL. Structure and function of ABCA4 and its role in the visual cycle and Stargardt macular degeneration. Prog Retin Eye Res 2021; 89:101036. [PMID: 34954332 DOI: 10.1016/j.preteyeres.2021.101036] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 12/17/2022]
Abstract
ABCA4 is a member of the superfamily of ATP-binding cassette (ABC) transporters that is preferentially localized along the rim region of rod and cone photoreceptor outer segment disc membranes. It uses the energy from ATP binding and hydrolysis to transport N-retinylidene-phosphatidylethanolamine (N-Ret-PE), the Schiff base adduct of retinal and phosphatidylethanolamine, from the lumen to the cytoplasmic leaflet of disc membranes. This ensures that all-trans-retinal and excess 11-cis-retinal are efficiently cleared from photoreceptor cells thereby preventing the accumulation of toxic retinoid compounds. Loss-of-function mutations in the gene encoding ABCA4 cause autosomal recessive Stargardt macular degeneration, also known as Stargardt disease (STGD1), and related autosomal recessive retinopathies characterized by impaired central vision and an accumulation of lipofuscin and bis-retinoid compounds. High resolution structures of ABCA4 in its substrate and nucleotide free state and containing bound N-Ret-PE or ATP have been determined by cryo-electron microscopy providing insight into the molecular architecture of ABCA4 and mechanisms underlying substrate recognition and conformational changes induced by ATP binding. The expression and functional characterization of a large number of disease-causing missense ABCA4 variants have been determined. These studies have shed light into the molecular mechanisms underlying Stargardt disease and a classification that reliably predicts the effect of a specific missense mutation on the severity of the disease. They also provide a framework for developing rational therapeutic treatments for ABCA4-associated diseases.
Collapse
Affiliation(s)
- Robert S Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada; Department of Ophthalmology & Visual Sciences, University of British Columbia, Vancouver, B.C., Canada.
| | - Fabian A Garces
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
| | | | - Laurie L Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
| |
Collapse
|
7
|
Al-Khuzaei S, Broadgate S, Foster CR, Shah M, Yu J, Downes SM, Halford S. An Overview of the Genetics of ABCA4 Retinopathies, an Evolving Story. Genes (Basel) 2021; 12:1241. [PMID: 34440414 PMCID: PMC8392661 DOI: 10.3390/genes12081241] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022] Open
Abstract
Stargardt disease (STGD1) and ABCA4 retinopathies (ABCA4R) are caused by pathogenic variants in the ABCA4 gene inherited in an autosomal recessive manner. The gene encodes an importer flippase protein that prevents the build-up of vitamin A derivatives that are toxic to the RPE. Diagnosing ABCA4R is complex due to its phenotypic variability and the presence of other inherited retinal dystrophy phenocopies. ABCA4 is a large gene, comprising 50 exons; to date > 2000 variants have been described. These include missense, nonsense, splicing, structural, and deep intronic variants. Missense variants account for the majority of variants in ABCA4. However, in a significant proportion of patients with an ABCA4R phenotype, a second variant in ABCA4 is not identified. This could be due to the presence of yet unknown variants, or hypomorphic alleles being incorrectly classified as benign, or the possibility that the disease is caused by a variant in another gene. This underlines the importance of accurate genetic testing. The pathogenicity of novel variants can be predicted using in silico programs, but these rely on databases that are not ethnically diverse, thus highlighting the need for studies in differing populations. Functional studies in vitro are useful towards assessing protein function but do not directly measure the flippase activity. Obtaining an accurate molecular diagnosis is becoming increasingly more important as targeted therapeutic options become available; these include pharmacological, gene-based, and cell replacement-based therapies. The aim of this review is to provide an update on the current status of genotyping in ABCA4 and the status of the therapeutic approaches being investigated.
Collapse
Affiliation(s)
- Saoud Al-Khuzaei
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-K.); (M.S.)
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
| | - Suzanne Broadgate
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
| | | | - Mital Shah
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-K.); (M.S.)
| | - Jing Yu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
| | - Susan M. Downes
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-K.); (M.S.)
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
| |
Collapse
|
8
|
Xiao Q, Lauschke VM. The prevalence, genetic complexity and population-specific founder effects of human autosomal recessive disorders. NPJ Genom Med 2021; 6:41. [PMID: 34078906 PMCID: PMC8172936 DOI: 10.1038/s41525-021-00203-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/05/2021] [Indexed: 11/13/2022] Open
Abstract
Autosomal recessive (AR) disorders pose a significant burden for public health. However, despite their clinical importance, epidemiology and molecular genetics of many AR diseases remain poorly characterized. Here, we analyzed the genetic variability of 508 genes associated with AR disorders based on sequencing data from 141,456 individuals across seven ethnogeographic groups by integrating variants with documented pathogenicity from ClinVar, with stringent functionality predictions for variants with unknown pathogenicity. We first validated our model using 85 diseases for which population-specific prevalence data were available and found that our estimates strongly correlated with the respective clinically observed disease frequencies (r = 0.68; p < 0.0001). We found striking differences in population-specific disease prevalence with 101 AR diseases (27%) being limited to specific populations, while an additional 305 diseases (68%) differed more than tenfold across major ethnogeographic groups. Furthermore, by analyzing genetic AR disease complexity, we confirm founder effects for cystic fibrosis and Stargardt disease, and provide strong evidences for >25 additional population-specific founder mutations. The presented analyses reveal the molecular genetics of AR diseases with unprecedented resolution and provide insights into epidemiology, complexity, and population-specific founder effects. These data can serve as a powerful resource for clinical geneticists to inform population-adjusted genetic screening programs, particularly in otherwise understudied ethnogeographic groups.
Collapse
Affiliation(s)
- Qingyang Xiao
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
9
|
Tomkiewicz TZ, Suárez-Herrera N, Cremers FPM, Collin RWJ, Garanto A. Antisense Oligonucleotide-Based Rescue of Aberrant Splicing Defects Caused by 15 Pathogenic Variants in ABCA4. Int J Mol Sci 2021; 22:ijms22094621. [PMID: 33924840 PMCID: PMC8124656 DOI: 10.3390/ijms22094621] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/16/2022] Open
Abstract
The discovery of novel intronic variants in the ABCA4 locus has contributed significantly to solving the missing heritability in Stargardt disease (STGD1). The increasing number of variants affecting pre-mRNA splicing makes ABCA4 a suitable candidate for antisense oligonucleotide (AON)-based splicing modulation therapies. In this study, AON-based splicing modulation was assessed for 15 recently described intronic variants (three near-exon and 12 deep-intronic variants). In total, 26 AONs were designed and tested in vitro using a midigene-based splice system. Overall, partial or complete splicing correction was observed for two variants causing exon elongation and all variants causing pseudoexon inclusion. Together, our results confirm the high potential of AONs for the development of future RNA therapies to correct splicing defects causing STGD1.
Collapse
Affiliation(s)
- Tomasz Z. Tomkiewicz
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands; (T.Z.T.); (N.S.-H.); (F.P.M.C.); (R.W.J.C.)
| | - Nuria Suárez-Herrera
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands; (T.Z.T.); (N.S.-H.); (F.P.M.C.); (R.W.J.C.)
| | - Frans P. M. Cremers
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands; (T.Z.T.); (N.S.-H.); (F.P.M.C.); (R.W.J.C.)
| | - Rob W. J. Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands; (T.Z.T.); (N.S.-H.); (F.P.M.C.); (R.W.J.C.)
| | - Alejandro Garanto
- Departments of Pediatrics and Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands
- Correspondence:
| |
Collapse
|
10
|
Camp DA, Gemayel MC, Ciulla TA. Understanding the genetic pathology of Stargardt disease: a review of current findings and challenges. Expert Opin Orphan Drugs 2021. [DOI: 10.1080/21678707.2021.1898373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- David A. Camp
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michael C. Gemayel
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Thomas A. Ciulla
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, USA
- Retina Service, Midwest Eye Institute, Indianapolis, IN, USA
| |
Collapse
|
11
|
Ma DJ, Lee HS, Kim K, Choi S, Jang I, Cho SH, Yoon CK, Lee EK, Yu HG. Whole-exome sequencing in 168 Korean patients with inherited retinal degeneration. BMC Med Genomics 2021; 14:74. [PMID: 33691693 PMCID: PMC7945660 DOI: 10.1186/s12920-021-00874-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/13/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND To date, no genetic analysis of inherited retinal disease (IRD) using whole-exome sequencing (WES) has been conducted in a large-scale Korean cohort. The aim of this study was to characterise the genetic profile of IRD patients in Korea using WES. METHODS We performed comprehensive molecular testing in 168 unrelated Korean IRD patients using WES. The potential pathogenicity of candidate variants was assessed using the American College of Medical Genetics and Genomics and the Association for Molecular Pathology variant interpretation guidelines, in silico prediction tools, published literature, and compatibility with known phenotypes or inheritance patterns. RESULTS Causative variants were detected in 86/168 (51.2%) IRD patients, including 58/107 (54.2%) with retinitis pigmentosa, 7/15 (46.7%) with cone and cone-rod dystrophy, 2/3 (66.6%) with Usher syndrome, 1/2 (50.0%) with congenital stationary night blindness, 2/2 (100.0%) with Leber congenital amaurosis, 1/1 (100.0%) with Bietti crystalline dystrophy, 1/1 (100.0%) with Joubert syndrome, 9/10 (90.0%) with Stargardt macular dystrophy, 1/10 (10.0%) with vitelliform macular dystrophy, 1/11 (9.1%) with other forms of macular dystrophy, and 3/4 (75.0%) with choroideraemia. USH2A, ABCA4, and EYS were the most common causative genes associated with IRD. For retinitis pigmentosa, variants of USH2A and EYS were the most common causative gene mutations. CONCLUSIONS This study demonstrated the distribution of causative genetic mutations in Korean IRD patients. The data will serve as a reference for future genetic screening and development of treatment modalities for Korean IRD patients.
Collapse
Affiliation(s)
- Dae Joong Ma
- Retinal Degeneration Research Lab, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Ophthalmology, Hallym University Kangnam Sacred Heart Hospital, Seoul, Republic of Korea
| | - Hyun-Seob Lee
- Genomics Core Facility, Translational Research Institute, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kwangsoo Kim
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seongmin Choi
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Insoon Jang
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seo-Ho Cho
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Chang Ki Yoon
- Retinal Degeneration Research Lab, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Ophthalmology, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Eun Kyoung Lee
- Retinal Degeneration Research Lab, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Ophthalmology, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Hyeong Gon Yu
- Retinal Degeneration Research Lab, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
- Department of Ophthalmology, College of Medicine, Seoul National University, Seoul, Republic of Korea.
| |
Collapse
|
12
|
Liu F, Lee J, Chen J. Molecular structures of the eukaryotic retinal importer ABCA4. eLife 2021; 10:63524. [PMID: 33605212 PMCID: PMC7932691 DOI: 10.7554/elife.63524] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/18/2021] [Indexed: 12/20/2022] Open
Abstract
The ATP-binding cassette (ABC) transporter family contains thousands of members with diverse functions. Movement of the substrate, powered by ATP hydrolysis, can be outward (export) or inward (import). ABCA4 is a eukaryotic importer transporting retinal to the cytosol to enter the visual cycle. It also removes toxic retinoids from the disc lumen. Mutations in ABCA4 cause impaired vision or blindness. Despite decades of clinical, biochemical, and animal model studies, the molecular mechanism of ABCA4 is unknown. Here, we report the structures of human ABCA4 in two conformations. In the absence of ATP, ABCA4 adopts an outward-facing conformation, poised to recruit substrate. The presence of ATP induces large conformational changes that could lead to substrate release. These structures provide a molecular basis to understand many disease-causing mutations and a rational guide for new experiments to uncover how ABCA4 recruits, flips, and releases retinoids.
Collapse
Affiliation(s)
- Fangyu Liu
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, United States.,Tri-Institutional Training Program in Chemical Biology, New York, United States
| | - James Lee
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, United States
| | - Jue Chen
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| |
Collapse
|
13
|
Sun Z, Yang L, Li H, Zou X, Wang L, Wu S, Zhu T, Wei X, Zhong Y, Sui R. Clinical and genetic analysis of the ABCA4 gene associated retinal dystrophy in a large Chinese cohort. Exp Eye Res 2020; 202:108389. [PMID: 33301772 DOI: 10.1016/j.exer.2020.108389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 12/31/2022]
Abstract
ABCA4 gene associated retinal dystrophies (ABCA4-RD) are a group of inherited eye diseases caused by ABCA4 gene mutations, including Stargardt disease, cone-rod dystrophy and retinitis pigmentosa. With the development of next-generation sequencing (NGS), numerous clinical and genetic studies on ABCA4-RD have been performed, and the genotype and phenotype spectra have been elucidated. However, most of the studies focused on the Caucasian population and limited studies of large Chinese ABCA4-RD cohorts were reported. In this study, we summarized the phenotypic and genotypic characteristics of 129 Chinese patients with ABCA4-RD. We found a mutation spectrum of Chinese patients which is considerably different from that of the Caucasian population and identified 35 novel ABCA4 mutations. We also reported some rare and special cases, such as, pedigrees with patients in two generations, patients diagnosed with cone-rod dystrophy or retinitis pigmentosa, patients with subretinal fibrosis and patients with preserved foveal structure. At the same time, we focused on the correlation between the genotypes and phenotypes. By the comprehensive analysis of multiple clinical examinations and the application of multiple regression analysis, we proved that patients with two "null" variants had a younger onset age and reached legal blindness earlier than patients with two "none-null" variants. Patients with one or more "none-null" variants tended to have better visual acuity and presented with milder fundus autofluorescence changes and more preserved rod functions on the full-field electroretinography than patients with two "null" variants. Furthermore, most patients with the p.(Phe2188Ser) variant shared a mild phenotype with a low fundus autofluorescence signal limited to the fovea and with normal full-field electroretinography responses. Our findings expand the variant spectrum of the ABCA4 gene and enhance the knowledge of Chinese patients with ABCA4-RD.
Collapse
Affiliation(s)
- Zixi Sun
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lizhu Yang
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China; Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization, Tokyo Medical Center, Tokyo, 152-8902, Japan; Department of Ophthalmology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Hui Li
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xuan Zou
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lei Wang
- Beijing Mei'ermu Hospital, Beijing, China
| | - Shijing Wu
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Tian Zhu
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xing Wei
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yong Zhong
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| |
Collapse
|
14
|
Curtis SB, Molday LL, Garces FA, Molday RS. Functional analysis and classification of homozygous and hypomorphic ABCA4 variants associated with Stargardt macular degeneration. Hum Mutat 2020; 41:1944-1956. [PMID: 32845050 DOI: 10.1002/humu.24100] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]
Abstract
Stargardt macular degeneration (Stargardt disease 1 [STGD1]) is caused by mutations in the gene encoding ABCA4, an ATP-binding cassette protein that transports N-retinylidene-phosphatidylethanolamine (N-Ret-PE) across photoreceptor membranes. Reduced ABCA4 activity results in retinoid accumulation leading to photoreceptor degeneration. The disease onset and severity vary from severe loss in visual acuity in the first decade to mild visual impairment late in life. We determined the effect of 22 disease-causing missense mutations on the expression and ATPase activity of ABCA4 in the absence and presence of N-Ret-PE. Three classes were identified that correlated with the disease onset in homozygous STGD1 individuals: Class 1 exhibited reduced ABCA4 expression and ATPase activity that was not stimulated by N-Ret-PE; individuals homozygous for these variants had an early disease onset (≤13 years); Class 2 showed reduced ATPase activity with limited stimulation by N-Ret-PE; these correlated with moderate disease onset (14-40 years); and Class 3 displayed high expression and ATPase activity that was strongly activated by N-Ret-PE; these were associated with late disease onset (>40 years). On the basis of our results, we introduce a functionality index for gauging the effect of missense mutations on STGD1 severity. Our studies support the mild phenotype exhibited by the p.Gly863Ala, p.Asn1868Ile, and p.Gly863Ala/p.Asn1868Ile variants.
Collapse
Affiliation(s)
- Susan B Curtis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fabian A Garces
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
15
|
Novel variants associated with Stargardt disease in Chinese patients. Gene 2020; 754:144890. [DOI: 10.1016/j.gene.2020.144890] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 12/11/2022]
|
16
|
Abstract
We report the molecular basis of the largest Tunisian cohort with inherited retinal dystrophies (IRD) reported to date, identify disease-causing pathogenic variants and describe genotype-phenotype correlations. A subset of 26 families from a cohort of 73 families with clinical diagnosis of autosomal recessive IRD (AR-IRD) excluding Usher syndrome was analyzed by whole exome sequencing and autozygosity mapping. Causative pathogenic variants were identified in 50 families (68.4%), 42% of which were novel. The most prevalent pathogenic variants were observed in ABCA4 (14%) and RPE65, CRB1 and CERKL (8% each). 26 variants (8 novel and 18 known) in 19 genes were identified in 26 families (14 missense substitutions, 5 deletions, 4 nonsense pathogenic variants and 3 splice site variants), with further allelic heterogeneity arising from different pathogenic variants in the same gene. The most common phenotype in our cohort is retinitis pigmentosa (23%) and cone rod dystrophy (23%) followed by Leber congenital amaurosis (19.2%). We report the association of new disease phenotypes. This research was carried out in Tunisian patients with IRD in order to delineate the genetic population architecture.
Collapse
|
17
|
Cremers FPM, Lee W, Collin RWJ, Allikmets R. Clinical spectrum, genetic complexity and therapeutic approaches for retinal disease caused by ABCA4 mutations. Prog Retin Eye Res 2020; 79:100861. [PMID: 32278709 PMCID: PMC7544654 DOI: 10.1016/j.preteyeres.2020.100861] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 12/18/2022]
Abstract
The ABCA4 protein (then called a “rim protein”) was first
identified in 1978 in the rims and incisures of rod photoreceptors. The
corresponding gene, ABCA4, was cloned in 1997, and variants
were identified as the cause of autosomal recessive Stargardt disease (STGD1).
Over the next two decades, variation in ABCA4 has been
attributed to phenotypes other than the classically defined STGD1 or fundus
flavimaculatus, ranging from early onset and fast progressing cone-rod dystrophy
and retinitis pigmentosa-like phenotypes to very late onset cases of mostly mild
disease sometimes resembling, and confused with, age-related macular
degeneration. Similarly, analysis of the ABCA4 locus uncovered
a trove of genetic information, including >1200 disease-causing mutations
of varying severity, and of all types – missense, nonsense, small
deletions/insertions, and splicing affecting variants, of which many are located
deep-intronic. Altogether, this has greatly expanded our understanding of
complexity not only of the diseases caused by ABCA4 mutations,
but of all Mendelian diseases in general. This review provides an in depth
assessment of the cumulative knowledge of ABCA4-associated retinopathy –
clinical manifestations, genetic complexity, pathophysiology as well as current
and proposed therapeutic approaches.
Collapse
Affiliation(s)
- Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, PO Box 9104, 6500 HE, Nijmegen, the Netherlands.
| | - Winston Lee
- Department of Ophthalmology, Columbia University, New York, NY, 10032, USA; Department of Genetics & Development, Columbia University, New York, NY, 10032, USA
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, PO Box 9104, 6500 HE, Nijmegen, the Netherlands
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY, 10032, USA; Department of Pathology & Cell Biology, Columbia University, New York, NY, 10032, USA.
| |
Collapse
|
18
|
Joo K, Seong MW, Park KH, Park SS, Woo SJ. Genotypic profile and phenotype correlations of ABCA4-associated retinopathy in Koreans. Mol Vis 2019; 25:679-690. [PMID: 31814693 PMCID: PMC6857773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/10/2019] [Indexed: 11/29/2022] Open
Abstract
PURPOSE This study was conducted to analyze the clinical features associated with the pathogenic variants of ABCA4 in Korean patients with inherited retinal dystrophies (IRDs). METHODS We enrolled patients with IRDs who visited a tertiary referral hospital and identified the pathogenic variants of ABCA4 through targeted gene panel sequencing and whole exome sequencing. We analyzed the clinical characteristics and phenotypic spectrum according to genotype. RESULTS Eleven patients (from nine families) with IRDs and pathogenic variants in ABCA4 were included. Eight patients (from seven families) with Stargardt disease (STGD), two (from one family) with cone-rod dystrophy (CRD), and one with early-onset retinitis pigmentosa (RP) were included. Two heterozygous mutations were identified in eight families, and one variant was found in a patient with fundus flavimaculatus. Two variants, p.Gln294Ter and p.Gln636Lys, were associated with severe phenotypes, such as early-onset RP and CRD. Four novel pathogenic variants, p.Gln636Lys, p.Ile1114del, p.Thr1117Ala, and p.Asn1588Tyr, were identified. p.Gln294Ter, p.Leu1157Ter, and p.Lys2049ArgfsTer12 were repeatedly detected in Koreans with ABCA4-associated retinal diseases (ABCA4-RD). CONCLUSIONS Various pathogenic variants of ABCA4, including four novel variants, were identified, and ABCA4-RD exhibited various phenotypes and disease severities in a Korean IRD cohort. These findings will be useful for understanding the clinical features of ABCA4-RD and ethnicity-specific variants in East Asians.
Collapse
Affiliation(s)
- Kwangsic Joo
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| |
Collapse
|
19
|
Hu FY, Li JK, Gao FJ, Qi YH, Xu P, Zhang YJ, Wang DD, Wang LS, Li W, Wang M, Chen F, Shen SM, Xu GZ, Zhang SH, Chang Q, Wu JH. ABCA4 Gene Screening in a Chinese Cohort With Stargardt Disease: Identification of 37 Novel Variants. Front Genet 2019; 10:773. [PMID: 31543898 PMCID: PMC6739639 DOI: 10.3389/fgene.2019.00773] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 07/22/2019] [Indexed: 11/13/2022] Open
Abstract
Purpose: To clarify the mutation spectrum and frequency of ABCA4 in a Chinese cohort with Stargardt disease (STGD1). Methods: A total of 153 subjects, comprising 25 families (25 probands and their family members) and 71 sporadic cases, were recruited for the analysis of ABCA4 variants. All probands with STGD1 underwent a comprehensive ophthalmologic examination. Overall, 792 genes involved in common inherited eye diseases were screened for variants by panel-based next-generation sequencing (NGS). Variants were filtered and analyzed to evaluate possible pathogenicity. Results: The total variant detection rate of at least one ABCA4 mutant allele was 84.3% (129/153): two or three disease-associated variants in 86 subjects (56.2%), one mutant allele in 43 subjects (28.1%), and no variants in 24 subjects (15.7%). Ninety-six variants were identified in the total cohort, which included 62 missense (64%), 15 splicing (16%), 11 frameshift (12%), 6 nonsense (6%), and 2 small insertion or deletion (2%) variants. Thirty-seven novel variants were found, including a de novo variant, c.4561delA. The most prevalent variant was c.101_106delCTTTAT (10.5%), followed by c.2894A > G (6.5%) and c.6563T > C (4.6%), in STGD1 patients from eastern China. Conclusion: Thirty-seven novel variants were detected using panel-based NGS, including one de novo variant, further extending the mutation spectrum of ABCA4. The common variants in a population from eastern China with STGD1 were also identified.
Collapse
Affiliation(s)
- Fang-Yuan Hu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Jian-Kang Li
- BGI-Shenzhen, Shenzhen, China.,Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Feng-Juan Gao
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Yu-He Qi
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Ping Xu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Yong-Jin Zhang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Dan-Dan Wang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Lu-Sheng Wang
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Wei Li
- BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Min Wang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Shenzhen Engineering Laboratory for Birth Defects Screening, BGI-Shenzhen, Shenzhen, China
| | | | - Ge-Zhi Xu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Sheng-Hai Zhang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Qing Chang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Ji-Hong Wu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| |
Collapse
|
20
|
Abstract
PURPOSE To describe an unusual manifestation of hyperreflective deposits in the subretinal space in a group of patients with clinically and genetically confirmed Stargardt disease. METHODS Retrospective review of color fundus, autofluorescence, infrared reflectance, red-free images, and spectral domain optical coherence tomography in 296 clinically diagnosed and genetically confirmed (2 expected disease-causing mutations in ABCA4) patients with Stargardt disease. Full-field electroretinogram (ffERG), medical history, and genotype data (in silico predictions) were further analyzed from the selected cohort. RESULTS Eight of 296 patients (2.7%) were found to exhibit small crystalline deposits that were detectable on certain imaging modalities, such as color, infrared reflectance and red-free images, but not autofluorescence. The deposits were most prevalent in the superior region of the macula, and spectral domain optical coherence tomography revealed their presence in the subretinal space. All patients presented with these findings at a notably advanced disease stage with abnormal ffERG and a high proportion of highly deleterious ABCA4 alleles. CONCLUSION Hyperreflective subretinal deposits may be a manifestation of advanced ABCA4 disease, particularly in regions susceptible to disease-related changes, such as lipofuscin accumulation.
Collapse
|
21
|
Garanto A, Duijkers L, Tomkiewicz TZ, Collin RWJ. Antisense Oligonucleotide Screening to Optimize the Rescue of the Splicing Defect Caused by the Recurrent Deep-Intronic ABCA4 Variant c.4539+2001G>A in Stargardt Disease. Genes (Basel) 2019; 10:genes10060452. [PMID: 31197102 PMCID: PMC6628380 DOI: 10.3390/genes10060452] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/04/2019] [Accepted: 06/11/2019] [Indexed: 12/17/2022] Open
Abstract
Deep-sequencing of the ABCA4 locus has revealed that ~10% of autosomal recessive Stargardt disease (STGD1) cases are caused by deep-intronic mutations. One of the most recurrent deep-intronic variants in the Belgian and Dutch STGD1 population is the c.4539+2001G>A mutation. This variant introduces a 345-nt pseudoexon to the ABCA4 mRNA transcript in a retina-specific manner. Antisense oligonucleotides (AONs) are short sequences of RNA that can modulate splicing. In this work, we designed 26 different AONs to perform a thorough screening to identify the most effective AONs to correct splicing defects associated with c.4539+2001G>A. All AONs were tested in patient-derived induced pluripotent stem cells (iPSCs) that were differentiated to photoreceptor precursor cells (PPCs). AON efficacy was assessed through RNA analysis and was based on correction efficacy, and AONs were grouped and their properties assessed. We (a) identified nine AONs with significant correction efficacies (>50%), (b) confirmed that a single nucleotide mismatch was sufficient to significantly decrease AON efficacy, and (c) found potential correlations between efficacy and some of the parameters analyzed. Overall, our results show that AON-based splicing modulation holds great potential for treating Stargardt disease caused by splicing defects in ABCA4.
Collapse
Affiliation(s)
- Alejandro Garanto
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
| | - Lonneke Duijkers
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
| | - Tomasz Z Tomkiewicz
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
| | - Rob W J Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
| |
Collapse
|
22
|
Allikmets R, Zernant J, Lee W. Penetrance of the ABCA4 p.Asn1868Ile Allele in Stargardt Disease. Invest Ophthalmol Vis Sci 2019; 59:5564-5565. [PMID: 30480703 PMCID: PMC6735614 DOI: 10.1167/iovs.18-25579] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Rando Allikmets
- Departments of Ophthalmology, Columbia University, New York, New York, United States.,Pathology & Cell Biology, Columbia University, New York, New York, United States
| | - Jana Zernant
- Departments of Ophthalmology, Columbia University, New York, New York, United States
| | - Winston Lee
- Departments of Ophthalmology, Columbia University, New York, New York, United States
| |
Collapse
|
23
|
A case-control collapsing analysis identifies retinal dystrophy genes associated with ophthalmic disease in patients with no pathogenic ABCA4 variants. Genet Med 2019; 21:2336-2344. [PMID: 30926958 DOI: 10.1038/s41436-019-0495-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 03/12/2019] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Variants in the ABCA4 gene are causal for a variety of retinal dystrophy phenotypes, including Stargardt disease (STGD1). However, 15% of patients who present with symptoms compatible with STGD1/ABCA4 disease do not have identifiable causal ABCA4 variants. We hypothesized that a case-control collapsing analysis in ABCA4-negative patients with compatible symptoms would provide an objective measure to identify additional disease genes. METHODS We performed a genome-wide enrichment analysis of "qualifying variants"-ultrarare variants predicted to impact protein function-in protein-coding genes in 79 unrelated cases and 9028 unrelated controls. RESULTS Despite modest sample size, two known retinal dystrophy genes, PRPH2 and CRX, achieved study-wide significance (p < 1.33 × 10-6) under a dominant disease model, and eight additional known retinal dystrophy genes achieved nominal significance (p < 0.05). Across these ten genes, the excess of qualifying variants explained up to 36.8% of affected individuals. Furthermore, under a recessive model, the cone-rod dystrophy gene CERKL approached study-wide significance. CONCLUSION Our results indicate that case-control collapsing analyses can efficiently identify pathogenic variants in genes in non-ABCA4 retinal dystrophies. The genome-wide collapsing analysis framework is an objective discovery method particularly suitable in settings with overlapping disease phenotypes.
Collapse
|
24
|
|
25
|
|
26
|
Bryant L, Lozynska O, Maguire AM, Aleman TS, Bennett J. Prescreening whole exome sequencing results from patients with retinal degeneration for variants in genes associated with retinal degeneration. Clin Ophthalmol 2017; 12:49-63. [PMID: 29343940 PMCID: PMC5749571 DOI: 10.2147/opth.s147684] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background Accurate clinical diagnosis and prognosis of retinal degeneration can be aided by the identification of the disease-causing genetic variant. It can confirm the clinical diagnosis as well as inform the clinician of the risk for potential involvement of other organs such as kidneys. It also aids in genetic counseling for affected individuals who want to have a child. Finally, knowledge of disease-causing variants informs laboratory investigators involved in translational research. With the advent of next-generation sequencing, identifying pathogenic mutations is becoming easier, especially the identification of novel pathogenic variants. Methods We used whole exome sequencing on a cohort of 69 patients with various forms of retinal degeneration and in whom screens for previously identified disease-causing variants had been inconclusive. All potential pathogenic variants were verified by Sanger sequencing and, when possible, segregation analysis of immediate relatives. Potential variants were identified by using a semi-masked approach in which rare variants in candidate genes were identified without knowledge of the clinical diagnosis (beyond "retinal degeneration") or inheritance pattern. After the initial list of genes was prioritized, genetic diagnosis and inheritance pattern were taken into account. Results We identified the likely pathogenic variants in 64% of the subjects. Seven percent had a single heterozygous mutation identified that would cause recessive disease and 13% had no obviously pathogenic variants and no family members available to perform segregation analysis. Eleven subjects are good candidates for novel gene discovery. Two de novo mutations were identified that resulted in dominant retinal degeneration. Conclusion Whole exome sequencing allows for thorough genetic analysis of candidate genes as well as novel gene discovery. It allows for an unbiased analysis of genetic variants to reduce the chance that the pathogenic mutation will be missed due to incomplete or inaccurate family history or analysis at the early stage of a syndromic form of retinal degeneration.
Collapse
Affiliation(s)
- Laura Bryant
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), FM Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Olga Lozynska
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), FM Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Albert M Maguire
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), FM Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tomas S Aleman
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), FM Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jean Bennett
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), FM Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
27
|
Edwards TL. Discovery of Māori and Polynesian phototransduction pathway founder mutation: what is the gene and what does it mean? Clin Exp Ophthalmol 2017; 45:854-856. [PMID: 29271598 DOI: 10.1111/ceo.13080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas L Edwards
- Centre for Eye Research Australia, Melbourne, Victoria, Australia.,Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia.,Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, UK
| |
Collapse
|
28
|
Qi YH, Gao FJ, Hu FY, Zhang SH, Chen JY, Huang WJ, Tian GH, Wang M, Gan DK, Wu JH, Xu GZ. Next-Generation Sequencing-Aided Rapid Molecular Diagnosis of Occult Macular Dystrophy in a Chinese Family. Front Genet 2017; 8:107. [PMID: 28890726 PMCID: PMC5574873 DOI: 10.3389/fgene.2017.00107] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/02/2017] [Indexed: 11/15/2022] Open
Abstract
Purpose: To show early, rapid and accurate molecular diagnosis of occult macular dystrophy (OMD) in a four-generation Chinese family with inherited macular dystrophy. Methods: In the current study, we comprehensively screened 130 genes involved in common inherited non-syndromic eye diseases with next-generation sequencing-based target capture sequencing of the proband of a four-generation Chinese family that has suffered from maculopathy without a definitive diagnosis for over 10 years. Variants were filtered and analyzed to identify possible disease-causing variants before validation by Sanger sequencing. Results: Two heterozygous mutations—RP1L1 c.133 C > T (p.Arg45Trp), which is a hot spot for OMD, and ABCA4 c.6119 G > A (p.Arg2040Gln), which was identified in Stargardt’s disease were found in three patients, but neither of the mutations was found in the unaffected individuals in the same family, who are phenotypically normal or in the normal control volunteers. Conclusion: These results cannot only confirm the diagnosis of OMD in the proband, but also provide presymptomatic diagnosis of the proband’s children before the onset of visual acuity impairment and guidance regarding the prognosis and management of these patients. Heterozygous mutations of RP1L1 c.133 C > T (p.Arg45Trp) and ABCA4 c.6119 G > A (p.Arg2040Gln) are likely responsible for OMD. Our results further extend our current understanding of the genetic basis of OMD, and emphasize the importance of molecular diagnosis and genetic counseling for OMD.
Collapse
Affiliation(s)
- Yu-He Qi
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan UniversityShanghai, China
| | - Feng-Juan Gao
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan UniversityShanghai, China
| | - Fang-Yuan Hu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan UniversityShanghai, China
| | - Sheng-Hai Zhang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan UniversityShanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai MunicipalityShanghai, China.,Key Laboratory of Myopia, Ministry of HealthShanghai, China
| | - Jun-Yi Chen
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan UniversityShanghai, China
| | - Wan-Jing Huang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan UniversityShanghai, China
| | - Guo-Hong Tian
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan UniversityShanghai, China
| | - Min Wang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan UniversityShanghai, China
| | - De-Kang Gan
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan UniversityShanghai, China
| | - Ji-Hong Wu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan UniversityShanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai MunicipalityShanghai, China.,Key Laboratory of Myopia, Ministry of HealthShanghai, China
| | - Ge-Zhi Xu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan UniversityShanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai MunicipalityShanghai, China.,Key Laboratory of Myopia, Ministry of HealthShanghai, China
| |
Collapse
|
29
|
Schulz HL, Grassmann F, Kellner U, Spital G, Rüther K, Jägle H, Hufendiek K, Rating P, Huchzermeyer C, Baier MJ, Weber BHF, Stöhr H. Mutation Spectrum of the ABCA4 Gene in 335 Stargardt Disease Patients From a Multicenter German Cohort-Impact of Selected Deep Intronic Variants and Common SNPs. Invest Ophthalmol Vis Sci 2017; 58:394-403. [PMID: 28118664 PMCID: PMC5270621 DOI: 10.1167/iovs.16-19936] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Purpose Stargardt disease (STGD1) is an autosomal recessive retinopathy, caused by mutations in the retina-specific ATP-binding cassette transporter (ABCA4) gene. To establish the mutational spectrum and to assess effects of selected deep intronic and common genetic variants on disease, we performed a comprehensive sequence analysis in a large cohort of German STGD1 patients. Methods DNA samples of 335 STGD1 patients were analyzed for ABCA4 mutations in its 50 coding exons and adjacent intronic sequences by resequencing array technology or next generation sequencing (NGS). Parts of intron 30 and 36 were screened by Sanger chain-terminating dideoxynucleotide sequencing. An in vitro splicing assay was used to test selected variants for their splicing behavior. By logistic regression analysis we assessed the association of common ABCA4 alleles while a multivariate logistic regression model calculated a genetic risk score (GRS). Results Our analysis identified 148 pathogenic or likely pathogenic mutations, of which 48 constitute so far unpublished ABCA4-associated disease alleles. Four rare deep intronic variants were found once in 472 alleles analyzed. In addition, we identified six risk-modulating common variants. Genetic risk score estimates suggest that defined common ABCA4 variants influence disease risk in carriers of a single pathogenic ABCA4 allele. Conclusions Our study adds to the mutational spectrum of the ABCA4 gene. Moreover, in our cohort, deep intronic variants in intron 30 and 36 likely play no or only a minor role in disease pathology. Of note, our findings demonstrate a possible modifying effect of common sequence variants on ABCA4-associated disease.
Collapse
Affiliation(s)
- Heidi L Schulz
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Felix Grassmann
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Ulrich Kellner
- Rare Retinal Disease Center, AugenZentrum Siegburg, MVZ ADTC Siegburg GmbH, Siegburg, Germany 3RetinaScience, Bonn, Germany
| | - Georg Spital
- Department of Ophthalmology, St. Franziskus-Hospital, Münster, Germany
| | | | - Herbert Jägle
- Department of Ophthalmology, University Hospital Regensburg, Regensburg, Germany
| | | | - Philipp Rating
- Department of Ophthalmology, University Hospital Essen, Essen, Germany
| | - Cord Huchzermeyer
- Department of Ophthalmology, University Hospital Erlangen, Erlangen, Germany
| | - Maria J Baier
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Heidi Stöhr
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| |
Collapse
|
30
|
Lee W, Schuerch K, Xie Y, Zernant J, Tsang SH, Sparrow JR, Allikmets R. Simultaneous Expression of ABCA4 and GPR143 Mutations: A Complex Phenotypic Manifestation. Invest Ophthalmol Vis Sci 2017; 57:3409-15. [PMID: 27367509 PMCID: PMC4961055 DOI: 10.1167/iovs.16-19621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Purpose To describe the complex, overlapping phenotype expressed in a two generation family harboring pathogenic mutations in the ABCA4 and GPR143 genes. Methods Clinical evaluation of a two generation family included quantitative autofluorescence imaging (qAF, 488-nm excitation) using a modified confocal scanning laser ophthalmoscope equipped with an internal fluorescent reference to account for varying laser power detector sensitivity, spectral-domain optical coherence tomography, and full-field ERG testing. Complete sequencing of the ABCA4 and GPR143 genes was carried out in each individual. Results Affected individuals presented with bull's eye lesions and qAF levels above the 95% confidence interval for healthy eyes; full-field ERG revealed no generalized rod dysfunction but mild implicit time delays in cone responses. Complete sequencing of the ABCA4 gene revealed two disease-causing mutations, p.L541P and p.G1961E; and mutational phase was confirmed in each unaffected parent. Further examination in the affected patients revealed a peripheral “mud-splattered” pattern of hypopigmented RPE after which sequencing of GPR143 revealed a novel missense variant, p.Y157C. The GPR143 variant segregated from the father who did not exhibit any indications of retinal disease with the exception of an abnormal near-infrared autofluorescence (NIR-AF) signal distribution in the macula. Conclusions An individual carrying both ABCA4 and GPR143 disease-causing mutations can express a complex, overlapping phenotype associated with both Stargardt disease and X-linked ocular albinism (OA1). The absence of OA1-related disease changes (with the exception of NIR-AF changes associated with melanin distribution) in the father may be indicative of mild expressivity or variable gene penetrance.
Collapse
Affiliation(s)
- Winston Lee
- Department of Ophthalmology, Columbia University, New York, New York, United States
| | - Kaspar Schuerch
- Department of Ophthalmology, Columbia University, New York, New York, United States
| | - Yajing Xie
- Department of Ophthalmology, Columbia University, New York, New York, United States
| | - Jana Zernant
- Department of Ophthalmology, Columbia University, New York, New York, United States
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University, New York, New York, United States 2Department of Pathology & Cell Biology, Columbia University, New York, New York, United States
| | - Janet R Sparrow
- Department of Ophthalmology, Columbia University, New York, New York, United States 2Department of Pathology & Cell Biology, Columbia University, New York, New York, United States
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, New York, United States 2Department of Pathology & Cell Biology, Columbia University, New York, New York, United States
| |
Collapse
|
31
|
Aukrust I, Jansson RW, Bredrup C, Rusaas HE, Berland S, Jørgensen A, Haug MG, Rødahl E, Houge G, Knappskog PM. The intronic ABCA4 c.5461-10T>C variant, frequently seen in patients with Stargardt disease, causes splice defects and reduced ABCA4 protein level. Acta Ophthalmol 2017; 95:240-246. [PMID: 27775217 DOI: 10.1111/aos.13273] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/27/2016] [Indexed: 12/23/2022]
Abstract
PURPOSE Despite being the third most common ABCA4 variant observed in patients with Stargardt disease, the functional effect of the intronic ABCA4 variant c.5461-10T>C is unknown. The purpose of this study was to investigate the molecular effect of this variant. METHODS Fibroblast samples from patients carrying the ABCA4 variant c.5461-10T>C were analysed by isolating total RNA, followed by real-time polymerase chain reaction (RT-PCR) using specific primers spanning the variant. For detection of ABCA4 protein, fibroblast samples were lysed and analysed by SDS-PAGE followed by immunoblotting using a monoclonal ABCA4 antibody. RESULTS The ABCA4 variant c.5461-10T>C causes a splicing defect resulting in the reduction of full-length mRNA in fibroblasts from patients and the presence of alternatively spliced mRNAs where exon 39-40 is skipped. A reduced level of full-length ABCA4 protein is observed compared to controls not carrying the variant. CONCLUSIONS This study describes the functional effect and the molecular mechanism of the pathogenic ABCA4 variant c.5461-10T>C. The variant is functionally important as it leads to splicing defects and a reduced level of ABCA4 protein.
Collapse
Affiliation(s)
- Ingvild Aukrust
- Center for Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen Norway
| | - Ragnhild W. Jansson
- Department of Ophthalmology; Haukeland University Hospital; Bergen Norway
- Department of Clinical Medicine; University of Bergen; Bergen Norway
| | - Cecilie Bredrup
- Department of Ophthalmology; Haukeland University Hospital; Bergen Norway
| | - Hilde E. Rusaas
- Center for Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen Norway
| | - Siren Berland
- Center for Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen Norway
| | - Agnete Jørgensen
- Division of Child and Adolescent Health; Medical Genetics Department; University Hospital of North Norway; Tromsø Norway
| | - Marte G. Haug
- Department of Pathology and Medical Genetics; St. Olav's University Hospital; Trondheim Norway
| | - Eyvind Rødahl
- Department of Ophthalmology; Haukeland University Hospital; Bergen Norway
- Department of Clinical Medicine; University of Bergen; Bergen Norway
| | - Gunnar Houge
- Center for Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen Norway
| | - Per M. Knappskog
- Center for Medical Genetics and Molecular Medicine; Haukeland University Hospital; Bergen Norway
- Department of Clinical Science; University of Bergen; Bergen Norway
| |
Collapse
|
32
|
Zernant J, Lee W, Collison FT, Fishman GA, Sergeev YV, Schuerch K, Sparrow JR, Tsang SH, Allikmets R. Frequent hypomorphic alleles account for a significant fraction of ABCA4 disease and distinguish it from age-related macular degeneration. J Med Genet 2017; 54:404-412. [PMID: 28446513 DOI: 10.1136/jmedgenet-2017-104540] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/28/2017] [Accepted: 03/07/2017] [Indexed: 12/24/2022]
Abstract
BACKGROUND Variation in the ABCA4 gene is causal for, or associated with, a wide range of phenotypes from early onset Mendelian retinal dystrophies to late-onset complex disorders such as age-related macular degeneration (AMD). Despite substantial progress in determining the causal genetic variation, even complete sequencing of the entire open reading frame and splice sites of ABCA4 identifies biallelic mutations in only 60%-70% of cases; 20%-25% remain with one mutation and no mutations are found in 10%-15% of cases with clinically confirmed ABCA4 disease. This study was designed to identify missing causal variants specifically in monoallelic cases of ABCA4 disease. METHODS Direct sequencing and analysis were performed in a large familial ABCA4 disease cohort of predominately European descent (n=643). Patient phenotypes were assessed from clinical and retinal imaging data. RESULTS We determined that a hypomorphic ABCA4 variant c.5603A>T (p.Asn1868Ile), previously considered benign due to high minor allele frequency (MAF) (~7%) in the general population, accounts for 10% of the disease, >50% of the missing causal alleles in monoallelic cases, ~80% of late-onset cases and distinguishes ABCA4 disease from AMD. It results in a distinct clinical phenotype characterised by late-onset of symptoms (4th decade) and foveal sparing (85%). Intragenic modifying effects involving this variant and another, c.2588G>C (p.Gly863Ala) allele, were also identified. CONCLUSIONS These findings substantiate the causality of frequent missense variants and their phenotypic outcomes as a significant contribution to ABCA4 disease, particularly the late-onset phenotype, and its clinical variation. They also suggest a significant revision of diagnostic screening and assessment of ABCA4 variation in aetiology of retinal diseases.
Collapse
Affiliation(s)
- Jana Zernant
- Department of Ophthalmology, Columbia University, New York, New York, USA
| | - Winston Lee
- Department of Ophthalmology, Columbia University, New York, New York, USA
| | - Frederick T Collison
- The Pangere Center for Hereditary Retinal Diseases, The Chicago Lighthouse, Chicago, Illinois, USA
| | - Gerald A Fishman
- The Pangere Center for Hereditary Retinal Diseases, The Chicago Lighthouse, Chicago, Illinois, USA
| | - Yuri V Sergeev
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kaspar Schuerch
- Department of Ophthalmology, Columbia University, New York, New York, USA
| | - Janet R Sparrow
- Department of Ophthalmology, Columbia University, New York, New York, USA.,Department of Pathology & Cell Biology, Columbia University, New York, New York, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University, New York, New York, USA.,Department of Pathology & Cell Biology, Columbia University, New York, New York, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, New York, USA.,Department of Pathology & Cell Biology, Columbia University, New York, New York, USA
| |
Collapse
|
33
|
Lee W, Schuerch K, Zernant J, Collison FT, Bearelly S, Fishman GA, Tsang SH, Sparrow JR, Allikmets R. Genotypic spectrum and phenotype correlations of ABCA4-associated disease in patients of south Asian descent. Eur J Hum Genet 2017; 25:735-743. [PMID: 28327576 DOI: 10.1038/ejhg.2017.13] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/12/2016] [Accepted: 01/11/2017] [Indexed: 11/09/2022] Open
Abstract
Variants in the ABCA4 gene are the most common cause of juvenile-onset blindness affecting close to 1 in 10 000 people worldwide. Disease severity varies largely according to genotype, which can be specific to ethnic and racial groups. Here we investigate the spectrum of ABCA4 variation and its phenotypic expression in 38 patients of South Asian descent, notably from India, Pakistan, Bangladesh and Sri Lanka. Sequencing of all exons and flanking intronic sequences of ABCA4 revealed disease-causing variants in all patients: 3 in 2.6%, 2 in 81.6% and 1 in 15.8%. Altogether, 36 distinct variants were identified, including 9 previously not described. The most frequent variant c.5882G>A, p.(G1961E) was found in half the patients, the highest ever reported in a single study cohort. The South Asian founder variant c.859-9T>C was identified along with other founder variants ascribed to Danish, Chinese, Mexican and African patients. Patients carrying c.5882G>A, p.(G1961E) exhibited a consistently confined disease phenotype, normal quantitative autofluorescence (qAF) levels and preserved full-field ERG (ffERG) while c.859-9T>C resulted in widespread disease, significantly elevated qAF and reduced to non-detectable ffERG. South Asian patients present with a relatively unique ABCA4 profile comprised of various ethnic founder variants resulting in two or three major retinal phenotypes.
Collapse
Affiliation(s)
- Winston Lee
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Kaspar Schuerch
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Jana Zernant
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Frederick T Collison
- The Pangere Center for Inherited Retinal Diseases, The Chicago Lighthouse, Chicago, IL, USA
| | | | - Gerald A Fishman
- The Pangere Center for Inherited Retinal Diseases, The Chicago Lighthouse, Chicago, IL, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Janet R Sparrow
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| |
Collapse
|
34
|
Zolnikova IV, Strelnikov VV, Skvortsova NA, Tanas AS, Barh D, Rogatina EV, Egorova IV, Levina DV, Demenkova ON, Prikaziuk EG, Ivanova ME. Stargardt disease-associated mutation spectrum of a Russian Federation cohort. Eur J Med Genet 2016; 60:140-147. [PMID: 27939946 DOI: 10.1016/j.ejmg.2016.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/26/2016] [Accepted: 12/01/2016] [Indexed: 12/24/2022]
Abstract
ABCA4-associated mutation screening is extensively performed in European, African, American and several other populations for various retinopathies. However, it has not been well studied in a Russian cohort. Using next-generation (325 genes inherited disease panel) and Sanger sequencing technologies for the first time we documented the spectrum of genetic variations in a Russian retinopathy cohort of 51 patients from 10 ethnic groups. We found ABCA4 variations in 70.5% cases and one case with BEST1 variation. Multiple ABCA4 variations, ABCA4 + RDH12, and ABCA4 + BEST1 variations are also observed and the disease severity is found proportionate to the variation burden. Ten novel ABCA4 variations are detected of which 8 belongs to non-Slavonian population. Most of the detected known variations are found in European and American Stargardt disease populations. No retinopathy causing variation is detected in 14 (27%) cases suggesting that in this Russian retinopathies cohort the causal variants could be in genes that are not covered by our 325 gene panel. Therefore, whole genome/exome analysis is required to identify novel retinopathy associated genes and provide better disease management for this heterogeneous cohort.
Collapse
Affiliation(s)
- Inna V Zolnikova
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | | | - Natalia A Skvortsova
- Posterior Eye Segment Diagnostics and Surgery Centre, 2nd Vladimirskaya Str. b.2, 4th Floor, Moscow 111123, Russia
| | - Alexander S Tanas
- Research Centre for Medical Genetics, Moskvorechie Str. 1, Moscow 15478, Russia
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB 721172, India; Xcode Life Sciences, 3D Eldorado, 112 Nungambakkam High Road, Nungambakkam, Chennai, Tamil Nadu 600034, India.
| | - Elena V Rogatina
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Irina V Egorova
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Darja V Levina
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Olga N Demenkova
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Egor G Prikaziuk
- Bioinformatics Institute, Kantemirovskaya Str. b.2a, Saint Petersburg 197342, Russia
| | | |
Collapse
|
35
|
Nõupuu K, Lee W, Zernant J, Greenstein VC, Tsang S, Allikmets R. Recessive Stargardt disease phenocopying hydroxychloroquine retinopathy. Graefes Arch Clin Exp Ophthalmol 2015; 254:865-72. [PMID: 26311262 DOI: 10.1007/s00417-015-3142-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/10/2015] [Accepted: 08/17/2015] [Indexed: 11/29/2022] Open
Abstract
PURPOSE To describe a series of patients with Stargardt disease (STGD1) exhibiting a phenotype usually associated with hydroxychloroquine (HCQ) retinopathy on spectral domain-optical coherence tomography (SD-OCT). METHODS Observational case series from Columbia University Medical Center involving eight patients with genetically-confirmed STGD1. Patients selected for the study presented no history of HCQ use. Horizontal macular SD-OCT scans and accompanying 488-nm autofluorescence (AF) images, color fundus photographs, and full-field electroretinograms were analyzed. RESULTS All study patients exhibited an abrupt thinning of the parafoveal region or disruption of the outer retinal layers on SD-OCT resembling the transient HCQ retinopathy phenotype. Funduscopy and AF imaging revealed variations of bull's eye maculopathy (BEM). Five patients exhibited local fleck-like deposits around the lesion. Genetic screening confirmed two disease-causing ABCA4 mutations in five patients and one mutation in three patients. CONCLUSIONS A transient SD-OCT phenotype ascribed to patients with HCQ retinopathy is associated with an early subtype of STGD1. This finding may also present with HCQ retinopathy-like BEM lesions on AF imaging and funduscopy. A possible phenotypic overlap is unsurprising, given certain shared mechanistic disease processes between the two conditions. A thorough work-up, including screening of genes that are causal in retinal dystrophies associated with foveal sparing, may prevent misdiagnosis of more ambiguous cases.
Collapse
Affiliation(s)
- Kalev Nõupuu
- Department of Ophthalmology, Columbia University, Eye Research Annex Rm 202, 160 Ft Washington Ave, New York, NY, 10032, USA.,Department of Ophthalmology, University of Tartu, Tartu, Estonia
| | - Winston Lee
- Department of Ophthalmology, Columbia University, Eye Research Annex Rm 202, 160 Ft Washington Ave, New York, NY, 10032, USA
| | - Jana Zernant
- Department of Ophthalmology, Columbia University, Eye Research Annex Rm 202, 160 Ft Washington Ave, New York, NY, 10032, USA
| | - Vivienne C Greenstein
- Department of Ophthalmology, Columbia University, Eye Research Annex Rm 202, 160 Ft Washington Ave, New York, NY, 10032, USA
| | - Stephen Tsang
- Department of Ophthalmology, Columbia University, Eye Research Annex Rm 202, 160 Ft Washington Ave, New York, NY, 10032, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, Eye Research Annex Rm 202, 160 Ft Washington Ave, New York, NY, 10032, USA. .,Department of Pathology & Cell Biology, Columbia University, New York, NY, USA.
| |
Collapse
|
36
|
Identification of Novel Mutations in ABCA4 Gene: Clinical and Genetic Analysis of Indian Patients with Stargardt Disease. BIOMED RESEARCH INTERNATIONAL 2015; 2015:940864. [PMID: 25922843 PMCID: PMC4398921 DOI: 10.1155/2015/940864] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 02/13/2015] [Accepted: 03/09/2015] [Indexed: 11/17/2022]
Abstract
Stargardt disease (STGD) is the leading cause of juvenile macular degeneration associated with progressive central vision loss, photophobia, and colour vision abnormalities. In this study, we have described the clinical and genetic features of Stargardt patients from an Indian cohort. The next generation sequencing was carried out in five clinically confirmed unrelated patients and their family members using a gene panel comprising 184 retinal specific genes. Sequencing results were analyzed by read mapping and variant calling in genes of interest, followed by their verification and interpretation. Genetic analysis revealed ABCA4 mutations in all of the five unrelated patients. Among these, four patients were found with compound heterozygous mutations and another one had homozygous mutation. All the affected individuals showed signs and symptoms consistent with the disease phenotype. We report two novel ABCA4 mutations in Indian patients with STGD disease, which expands the existing spectrum of disease-causing variants and the understanding of phenotypic and genotypic correlations. Screening for causative mutations in patients with STGD using panel of targeted gene sequencing by NGS would be a cost effective tool, might be helpful in confirming the precise diagnosis, and contributes towards the genetic counselling of asymptomatic carriers and isolated patients.
Collapse
|
37
|
Yuan B, Pehlivan D, Karaca E, Patel N, Charng WL, Gambin T, Gonzaga-Jauregui C, Sutton VR, Yesil G, Bozdogan ST, Tos T, Koparir A, Koparir E, Beck CR, Gu S, Aslan H, Yuregir OO, Al Rubeaan K, Alnaqeb D, Alshammari MJ, Bayram Y, Atik MM, Aydin H, Geckinli BB, Seven M, Ulucan H, Fenercioglu E, Ozen M, Jhangiani S, Muzny DM, Boerwinkle E, Tuysuz B, Alkuraya FS, Gibbs RA, Lupski JR. Global transcriptional disturbances underlie Cornelia de Lange syndrome and related phenotypes. J Clin Invest 2015; 125:636-51. [PMID: 25574841 DOI: 10.1172/jci77435] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 12/09/2014] [Indexed: 01/05/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a genetically heterogeneous disorder that presents with extensive phenotypic variability, including facial dysmorphism, developmental delay/intellectual disability (DD/ID), abnormal extremities, and hirsutism. About 65% of patients harbor mutations in genes that encode subunits or regulators of the cohesin complex, including NIPBL, SMC1A, SMC3, RAD21, and HDAC8. Wiedemann-Steiner syndrome (WDSTS), which shares CdLS phenotypic features, is caused by mutations in lysine-specific methyltransferase 2A (KMT2A). Here, we performed whole-exome sequencing (WES) of 2 male siblings clinically diagnosed with WDSTS; this revealed a hemizygous, missense mutation in SMC1A that was predicted to be deleterious. Extensive clinical evaluation and WES of 32 Turkish patients clinically diagnosed with CdLS revealed the presence of a de novo heterozygous nonsense KMT2A mutation in 1 patient without characteristic WDSTS features. We also identified de novo heterozygous mutations in SMC3 or SMC1A that affected RNA splicing in 2 independent patients with combined CdLS and WDSTS features. Furthermore, in families from 2 separate world populations segregating an autosomal-recessive disorder with CdLS-like features, we identified homozygous mutations in TAF6, which encodes a core transcriptional regulatory pathway component. Together, our data, along with recent transcriptome studies, suggest that CdLS and related phenotypes may be "transcriptomopathies" rather than cohesinopathies.
Collapse
|