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Cao W, Kuang L, Gan R, Huang T, Yan X. A novel compound heterozygous variant of MYO7A in Usher syndrome type 1. Exp Eye Res 2024; 247:110047. [PMID: 39151776 DOI: 10.1016/j.exer.2024.110047] [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: 10/31/2023] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Usher syndrome (USH) is a recessive genetic disorder manifested by congenital sensorineural hearing loss and progressive retinitis pigmentosa, which leads to audiovisual impairment. We report a patient with Usher syndrome type 1 with new compound heterozygous MYO7A variants. A total of four members from the USH family were included. Medical history and retinal examinations were taken and genomic DNA from peripheral blood was extracted in the proband and other members. 381 retinal disease-associated genes were screened using targeted sequence capture array technology and Sanger sequencing was used to confirm the screening results. Scanning laser ophthalmoscope showed bone spicule pigmentary deposits in the mid-peripheral retina and whitish and thin retinal blood vessels especially in the arterioles. Optical coherence tomography showed that the centrality of the macular ellipsoid band disappeared in both eyes, and only remained near the fovea. Visual field examination showed a progressive loss of the visual field in a concentric pattern in both eyes. The electroretinography showed a significant decrease in the amplitudes of a- and b-waves in the scotopic and photopic condition. DNA sequencing identified the compound heterozygous variants including c.1003+1G > A: p. (?) and c.5957_5958del: p.G1987Lfs*50 of MYO7A, with the latter being novel. In this study, we found a novel compound heterozygous variant in MYO7A, which enriched the mutation spectrum and expanded our understanding of the heterogeneity of phenotype and genotype of Usher syndrome type 1.
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Affiliation(s)
- Wenchao Cao
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, China
| | - Longhao Kuang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, China
| | - Run Gan
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, China
| | - Tao Huang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, China
| | - Xiaohe Yan
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, China.
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Del Pozo-Valero M, Almoallem B, Dueñas Rey A, Mahieu Q, Van Heetvelde M, Jeddawi L, Bauwens M, De Baere E. Autozygome-guided exome-first study in a consanguineous cohort with early-onset retinal disease uncovers an isolated RIMS2 phenotype and a retina-enriched RIMS2 isoform. Clin Genet 2024; 106:127-139. [PMID: 38468396 DOI: 10.1111/cge.14517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/13/2024]
Abstract
Leber congenital amaurosis (LCA) and early-onset retinal degeneration (EORD) are inherited retinal diseases (IRD) characterized by early-onset vision impairment. Herein, we studied 15 Saudi families by whole exome sequencing (WES) and run-of-homozygosity (ROH) detection via AutoMap in 12/15 consanguineous families. This revealed (likely) pathogenic variants in 11/15 families (73%). A potential founder variant was found in RPGRIP1. Homozygous pathogenic variants were identified in known IRD genes (ATF6, CRB1, CABP4, RDH12, RIMS2, RPGRIP1, SPATA7). We established genotype-driven clinical reclassifications for ATF6, CABP4, and RIMS2. Specifically, we observed isolated IRD in the individual with the novel RIMS2 variant, and we found a retina-enriched RIMS2 isoform conserved but not annotated in mouse. The latter illustrates potential different phenotypic consequences of pathogenic variants depending on the particular tissue/cell-type specific isoforms they affect. Lastly, a compound heterozygous genotype in GUCY2D in one non-consanguineous family was demonstrated, and homozygous variants in novel candidate genes ATG2B and RUFY3 were found in the two remaining consanguineous families. Reporting these genes will allow to validate them in other IRD cohorts. Finally, the missing heritability of the two unsolved IRD cases may be attributed to variants in non-coding regions or structural variants that remained undetected, warranting future WGS studies.
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Affiliation(s)
- Marta Del Pozo-Valero
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Basamat Almoallem
- Department of Ophthalmology, College of Medicine, King Saud University (KSU), Riyadh, Saudi Arabia
- Department of Ophthalmology, King Saud University Medical City (KSUMC), Riyadh, Saudi Arabia
| | - Alfredo Dueñas Rey
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Quinten Mahieu
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Mattias Van Heetvelde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Laila Jeddawi
- Pediatric Ophthalmology Division, Dr. Sulaiman AL Habib Medical Group, AL Khobar, Saudi Arabia
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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Zhao D, Gu VY, Wang Y, Peng J, Lyu J, Fei P, Xu Y, Zhang X, Zhao P. Clinical and genetic features in autosomal recessive bestrophinopathy in Chinese cohort. BMC Ophthalmol 2024; 24:308. [PMID: 39048936 PMCID: PMC11267682 DOI: 10.1186/s12886-024-03574-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 07/15/2024] [Indexed: 07/27/2024] Open
Abstract
PURPOSE To provide a genotype and phenotype characterization of the BEST1 mutation in Chinese patients with autosomal recessive bestrophinopathy (ARB) through multimodal imaging and next-generation sequencing (NGS). METHODS Seventeen patients from 17 unrelated families of Chinese origin with ARB were included in a retrospective cohort study. Phenotypic characteristics, including anterior segment features, were assessed by multimodal imaging. Multigene panel testing, involving 586 ophthalmic disease-associated genes, and Sanger sequencing were performed to identify disease-causing variants. RESULTS Among 17 ARB patients, the mean follow-up was 15.65 months and average onset age was 30.53 years (range: 9-68). Best corrected visual acuity ranged from light perception to 0.8. EOG recordings showed a typically decreased Arden ratio in 12 patients, and a normal or slightly decreased Arden ratio in two patients. Anterior features included shallow anterior chambers (16/17), ciliary pronation (16/17), iris bombe (13/17), iridoschisis (2/17), iris plateau (1/17), narrow angles (16/17) and reduced axial lengths (16/17). Sixteen patients had multiple bilateral small, round, yellow vitelliform deposits distributed throughout the posterior pole, surrounding the optic disc. Initial diagnoses included angle-closure glaucoma (four patients), Best disease (three patients), and central serous chorioretinopathy secondary to choroidal neovascularization (CNV) (one patient), with the remainder diagnosed with ARB. Fourteen patients underwent preventive laser peripheral iridotomy, four of whom also received combined trabeculectomy and iridotomy in both eyes for uncontrolled intraocular pressure. One patient received intravitreal conbercept for CNV. Overall, 15 distinct disease-causing variants of BEST1 were identified, with 14 (82.35%) patients having missense mutations. Common mutations included p. Arg255-256 and p. Ala195Val (both 23.68%), with the most frequent sites in exons 7 and 5. CONCLUSIONS This study provides a comprehensive characterization of anterior segment and genetic features in ARB, with a wide array of morphological abnormalities. Findings are relevant for refining clinical practices and genetic counseling and advancing pathogenesis research.
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Affiliation(s)
- Dongsheng Zhao
- Department of Ophthalmology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Victoria Y Gu
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Yafu Wang
- Department of Ophthalmology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Peng
- Department of Ophthalmology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiao Lyu
- Department of Ophthalmology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Fei
- Department of Ophthalmology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Xu
- Department of Ophthalmology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiang Zhang
- Department of Ophthalmology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Peiquan Zhao
- Department of Ophthalmology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Puertas-Neyra K, Coco-Martin RM, Hernandez-Rodriguez LA, Gobelli D, Garcia-Ferrer Y, Palma-Vecino R, Tellería JJ, Simarro M, de la Fuente MA, Fernandez-Bueno I. Clinical exome analysis and targeted gene repair of the c.1354dupT variant in iPSC lines from patients with PROM1-related retinopathies exhibiting diverse phenotypes. Stem Cell Res Ther 2024; 15:192. [PMID: 38956727 PMCID: PMC11218195 DOI: 10.1186/s13287-024-03804-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/16/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Inherited retinal dystrophies (IRD) are one of the main causes of incurable blindness worldwide. IRD are caused by mutations in genes that encode essential proteins for the retina, leading to photoreceptor degeneration and loss of visual function. IRD generates an enormous global financial burden due to the lack of understanding of a significant part of its pathophysiology, molecular diagnosis, and the near absence of non-palliative treatment options. Patient-derived induced pluripotent stem cells (iPSC) for IRD seem to be an excellent option for addressing these questions, serving as exceptional tools for in-depth studies of IRD pathophysiology and testing new therapeutic approaches. METHODS From a cohort of 8 patients with PROM1-related IRD, we identified 3 patients carrying the same variant (c.1354dupT) but expressing three different IRD phenotypes: Cone and rod dystrophy (CORD), Retinitis pigmentosa (RP), and Stargardt disease type 4 (STGD4). These three target patients, along with one healthy relative from each, underwent comprehensive ophthalmic examinations and their genetic panel study was expanded through clinical exome sequencing (CES). Subsequently, non-integrative patient-derived iPSC were generated and fully characterized. Correction of the c.1354dupT mutation was performed using CRISPR/Cas9, and the genetic restoration of the PROM1 gene was confirmed through flow cytometry and western blotting in the patient-derived iPSC lines. RESULTS CES revealed that 2 target patients with the c.1354dupT mutation presented monoallelic variants in genes associated with the complement system or photoreceptor differentiation and peroxisome biogenesis disorders, respectively. The pluripotency and functionality of the patient-derived iPSC lines were confirmed, and the correction of the target mutation fully restored the capability of encoding Prominin-1 (CD133) in the genetically repaired patient-derived iPSC lines. CONCLUSIONS The c.1354dupT mutation in the PROM1 gene is associated to three distinct AR phenotypes of IRD. This pleotropic effect might be related to the influence of monoallelic variants in other genes associated with retinal dystrophies. However, further evidence needs to be provided. Future experiments should include gene-edited patient-derived iPSC due to its potential as disease modelling tools to elucidate this matter in question.
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Affiliation(s)
- Kevin Puertas-Neyra
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Universidad de Valladolid, Valladolid, Spain
| | - Rosa M Coco-Martin
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Universidad de Valladolid, Valladolid, Spain.
- Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORS-REI), Inflamación E Inmunopatologia de Organos y Sistemas, Instituto de Salud Carlos III, Valladolid, Spain.
- Centro en Red de Medicina Regenerativa, y Terapia Celular de Castilla y León, Valladolid, Spain.
| | | | - Dino Gobelli
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid y Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
- Departamento de Biología Celular, Genética, Histología y Farmacología, Facultad de Medicina, Universidad de Valladolid, Valladolid, Spain
| | - Yenisey Garcia-Ferrer
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Universidad de Valladolid, Valladolid, Spain
| | - Raicel Palma-Vecino
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Universidad de Valladolid, Valladolid, Spain
| | - Juan José Tellería
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid y Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Maria Simarro
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid y Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
- Departamento de Biología Celular, Genética, Histología y Farmacología, Facultad de Medicina, Universidad de Valladolid, Valladolid, Spain
| | - Miguel A de la Fuente
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid y Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
- Departamento de Biología Celular, Genética, Histología y Farmacología, Facultad de Medicina, Universidad de Valladolid, Valladolid, Spain
| | - Ivan Fernandez-Bueno
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Universidad de Valladolid, Valladolid, Spain
- Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORS-REI), Inflamación E Inmunopatologia de Organos y Sistemas, Instituto de Salud Carlos III, Valladolid, Spain
- Centro en Red de Medicina Regenerativa, y Terapia Celular de Castilla y León, Valladolid, Spain
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Moya R, Angée C, Hanein S, Jabot-Hanin F, Kaplan J, Perrault I, Rozet JM, Fares Taie L. Four Unique Genetic Variants in Three Genes Account for 62.7% of Early-Onset Severe Retinal Dystrophy in Chile: Diagnostic and Therapeutic Consequences. Int J Mol Sci 2024; 25:6151. [PMID: 38892339 PMCID: PMC11172861 DOI: 10.3390/ijms25116151] [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: 04/04/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Leber congenital amaurosis (LCA)/early-onset severe retinal dystrophy (EOSRD) stand as primary causes of incurable childhood blindness. This study investigates the clinical and molecular architecture of syndromic and non-syndromic LCA/EOSRD within a Chilean cohort (67 patients/60 families). Leveraging panel sequencing, 95.5% detection was achieved, revealing 17 genes and 126 variants (32 unique). CRB1, LCA5, and RDH12 dominated (71.9%), with CRB1 being the most prevalent (43.8%). Notably, four unique variants (LCA5 p.Glu415*, CRB1 p.Ser1049Aspfs*40 and p.Cys948Tyr, RDH12 p.Leu99Ile) constituted 62.7% of all disease alleles, indicating their importance for targeted analysis in Chilean patients. This study underscores a high degree of inbreeding in Chilean families affected by pediatric retinal blindness, resulting in a limited mutation repertoire. Furthermore, it complements and reinforces earlier reports, indicating the involvement of ADAM9 and RP1 as uncommon causes of LCA/EOSRD. These data hold significant value for patient and family counseling, pharmaceutical industry endeavors in personalized medicine, and future enrolment in gene therapy-based treatments, particularly with ongoing trials (LCA5) or advancing preclinical developments (CRB1 and RDH12).
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Affiliation(s)
- Rene Moya
- Department of Ophthalmology, Hospital del Salvador, Universidad de Chile, Santiago 7500922, Chile;
| | - Clémentine Angée
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France (I.P.)
| | - Sylvain Hanein
- Bioinformatic Platform, INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France
| | - Fabienne Jabot-Hanin
- Bioinformatic Platform, INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France (I.P.)
| | - Isabelle Perrault
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France (I.P.)
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France (I.P.)
| | - Lucas Fares Taie
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France (I.P.)
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Hayman T, Millo T, Hendler K, Chowers I, Gross M, Banin E, Sharon D. Whole exome sequencing of 491 individuals with inherited retinal diseases reveals a large spectrum of variants and identification of novel candidate genes. J Med Genet 2024; 61:224-231. [PMID: 37798099 DOI: 10.1136/jmg-2023-109482] [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: 06/27/2023] [Accepted: 09/14/2023] [Indexed: 10/07/2023]
Abstract
BACKGROUND Inherited retinal diseases (IRDs) include a range of vision loss conditions caused by variants in different genes. The clinical and genetic heterogeneity make identification of the genetic cause challenging. Here, a cohort of 491 unsolved cases from our cohort of Israeli and Palestinian families with IRDs underwent whole exome sequencing (WES), including detection of CNVs as well as single nucleotide variants (SNVs). METHODS All participants underwent clinical examinations. Following WES on DNA samples by 3 billion, initial SNV analysis was performed by 3 billion and SNV and CNV analysis by Franklin Genoox. The CNVs indicated by the programme were confirmed by PCR followed by gel electrophoresis. RESULTS WES of 491 IRD cases revealed the genetic cause of disease in 51% of cases, of which 11% were due wholly or in part to CNVs. In two cases, we clarified previously incorrect or unclear clinical diagnoses. This analysis also identified ESRRB and DNM1 as potential novel genes. CONCLUSION This analysis is the most extensive one to include CNVs to examine IRD causing genes in the Israeli and Palestinian populations. It has allowed us to identify the causative variant of many patients with IRDs including ones with unclear diagnoses and potential novel genes.
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Affiliation(s)
- Tamar Hayman
- Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Talya Millo
- Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Karen Hendler
- Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Itay Chowers
- Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Menachem Gross
- Otolaryngology/Head and Neck Surgery, Hadassah Medical Center, Jerusalem, Jerusalem, Israel
| | - Eyal Banin
- Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dror Sharon
- Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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Guo L, Cheng H, Liu J, Shao W, Luo L, Zheng W, Sun S, Kong D, Chen C. Based on whole-exome sequencing to explore the rule of Herceptin and TKI resistance in breast cancer patients. BMC Med Genomics 2024; 17:25. [PMID: 38243282 PMCID: PMC10799408 DOI: 10.1186/s12920-023-01762-x] [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: 05/09/2023] [Accepted: 12/05/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Breast cancer is the second leading cause of cancer-related death in women, and drug resistance during treatment is a major challenge. However, the mechanisms underlying drug resistance are not fully understood. Here we applied whole-exome sequencing (WES) to clarify resistant rules to Herceptin and tyrosine kinase inhibitors (TKIs). METHODS There are 12 HER2+ breast cancer patients who were done WES. Samples from tumor and surrounding tissues underwent DNA sequencing and analysis. Various experimental and bioinformatics techniques were employed, including genomic capture, mutation analysis (Genome Analysis Toolkit (GATK), etc.), bioinformatics assessments, and drug-gene interaction investigations. Ultimately, the study explored the association of APOB gene expression with breast cancer recurrence rates, immune cell infiltration, and drug response. RESULTS The C > T mutation frequency was highest in the Herceptin-insensitive (HI) and verification groups, codenamed YI, contrasting with the Herceptin-sensitive (HE) group. No microsatellite instability (MSI)-H patients were in the HE group, but both HI and YI groups had 1 each. Significant differences in transition-transversion (TiTv) were observed in the HI and YI groups rather than the HE group. In the TKI- insensitive (TI) group, C > T mutations were highest, differing from the TKI-sensitive (TE) group. TE group included 2 MSI-H patients. Significant differences in TiTv were found in the TI group rather than the TE group. Mutated APOB may resist Herceptin and TKI, increasing immune infiltration. We identified potential drugs targeting it. CONCLUSIONS Our study suggested that a higher percentage of C > T mutations, significant differences in TiTv, and MSI-H status may indicate Herceptin resistance, while a higher percentage of C > T mutations, significant differences in TiTv, and the absence of MSI-H may indicate TKI resistance in breast cancer patients. For patients resistant to both Herceptin and TKI, mutated APOB may play a crucial role in resistance.
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Affiliation(s)
- Liantao Guo
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuhan, Hubei, 430060, People's Republic of China
| | - Hong Cheng
- Department of Breast Surgery, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, 430060, People's Republic of China
| | - Jianhua Liu
- Department of breast surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Provincial Clinical Research Center for Breast Cancer, Wuhan Clinical Research Center for Breast Cancer, No.116 Zhuo Daoquan South Road, Wuhan, Hubei, 430079, People's Republic of China
| | - Weikang Shao
- Genecast Biotechnology Co., Ltd., Wuxi, Jiangsu, 214000, People's Republic of China
| | - Lan Luo
- Department of Breast Surgery, The Affiliated Hospital of Guizhou Medical University, No. 28 Guiyi Road, Yunyan District, Guiyang, Guizhou, 550001, People's Republic of China
| | - Weijie Zheng
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuhan, Hubei, 430060, People's Republic of China
| | - Shengrong Sun
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuhan, Hubei, 430060, People's Republic of China
| | - Deguang Kong
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuhan, Hubei, 430060, People's Republic of China.
| | - Chuang Chen
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuhan, Hubei, 430060, People's Republic of China.
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Yu H, Yu H, Zhang R, Peng D, Yan D, Gu Y, Bao Y, Jia W, Zhang H, Hu C. Targeted gene panel provides advantages over whole-exome sequencing for diagnosing obesity and diabetes mellitus. J Mol Cell Biol 2023; 15:mjad040. [PMID: 37327085 PMCID: PMC10847719 DOI: 10.1093/jmcb/mjad040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/12/2023] [Accepted: 06/15/2023] [Indexed: 06/18/2023] Open
Abstract
A small fraction of patients diagnosed with obesity or diabetes mellitus has an underlying monogenic cause. Here, we constructed a targeted gene panel consisting of 83 genes reported to be causative for monogenic obesity or diabetes. We performed this panel in 481 patients to detect causative variants and compared these results with whole-exome sequencing (WES) data available for 146 of these patients. The coverage of targeted gene panel sequencing was significantly higher than that of WES. The diagnostic yield in patients sequenced by the panel was 32.9% with subsequent WES leading to three additional diagnoses with two novel genes. In total, 178 variants in 83 genes were detected in 146 patients by targeted sequencing. Three of the 178 variants were missed by WES, although the WES-only approach had a similar diagnostic yield. For the 335 samples only receiving targeted sequencing, the diagnostic yield was 32.2%. In conclusion, taking into account the lower costs, shorter turnaround time, and higher quality of data, targeted sequencing is a more effective screening method for monogenic obesity and diabetes compared to WES. Therefore, this approach could be routinely established and used as a first-tier test in clinical practice for specific patients.
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Affiliation(s)
- Hairong Yu
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Haoyong Yu
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Rong Zhang
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Danfeng Peng
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Dandan Yan
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Yunjuan Gu
- Department of Endocrinology, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Yuqian Bao
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Weiping Jia
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Hong Zhang
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Cheng Hu
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
- Institute for Metabolic Disease, Fengxian Central Hospital Affiliated to Southern Medical University, Shanghai 201499, China
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Yang S, Li Y, Yang L, Guo Q, You Y, Lei B. Pathogenicity and functional analysis of CFAP410 mutations causing cone-rod dystrophy with macular staphyloma. Front Med (Lausanne) 2023; 10:1216427. [PMID: 37901396 PMCID: PMC10601463 DOI: 10.3389/fmed.2023.1216427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Background Cone-rod dystrophy (CORD) caused by pathogenic variants in CFAP410 is a very rare disease. The mechanisms by which the variants caused the disease remained largely unknown. CFAP410 pathogenic variants were identified in a cone-rod dystrophy with macular staphyloma patient. We explored the pathogenicity and performed functional analysis of two compound heterozygous mutations. Methods A 6-year-old boy complained decreased vision for 1 year, underwent ocular examinations together with systemic X-ray check. Blood sample was taken for targeted next generation sequencing (Tg-NGS). Pathogenicity of identified variants was determined by ACMG guideline. Mutated plasmids were constructed and transferred to HEK293T cells. Cell cycle, protein stability, and protein ubiquitination level was measured. Results The best-corrected visual acuity of proband was 0.20 bilaterally. Fundus showed macular staphyloma and uneven granular pigment disorder in the periphery of the retina. SS-OCT showed thinning and atrophy of the outer retina, residual ellipsoid zone (EZ) in the fovea. Scotopic and photopic ERG responses severe reduced. Two heterozygous missense pathogenic variants, c.319 T > C (p.Tyr107His) and c.347 C > T (p.Pro116Leu) in exon 4 of the CFAP410, were found and were pathogenic by the ACMG guideline. In vitro, pathogenic variants affect cell cycle. Immunofluorescence and western blotting showed that the mutant proteins decreased expression levels protein stability. Meanwhile, co-IP data suggested that ubiquitination level was altered in cells transferred with the mutated plasmids. Conclusion Compound heterozygous pathogenic variants c.319 T > C and c.347 C > T in CFAP410 caused CORD with macular staphyloma. The pathogenic mechanisms may be associated with alternations of protein stability and degradation through the ubiquitin-proteasome pathway.
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Affiliation(s)
- Shaoqing Yang
- Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Ya Li
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Lin Yang
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Qingge Guo
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Ya You
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Bo Lei
- Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, China
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
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10
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Sakti DH, Cornish EE, Nash BM, Jamieson RV, Grigg JR. IMPDH1-associated autosomal dominant retinitis pigmentosa: natural history of novel variant Lys314Gln and a comprehensive literature search. Ophthalmic Genet 2023; 44:437-455. [PMID: 37259572 DOI: 10.1080/13816810.2023.2215310] [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: 01/27/2023] [Revised: 05/11/2023] [Accepted: 05/14/2023] [Indexed: 06/02/2023]
Abstract
BACKGROUND Inosine monophosphate dehydrogenase (IMPDH) is a key regulatory enzyme in the de novo synthesis of the purine base guanine. Mutations in the inosine monophosphate dehydrogenase 1 gene (IMPDH1) are causative for RP10 autosomal dominant retinitis pigmentosa (adRP). This study reports a novel variant in a family with IMPDH1-associated retinopathy. We also performed a comprehensive review of all reported IMPDH1 disease causing variants with their associated phenotype. MATERIALS AND METHODS Multimodal imaging and functional studies documented the phenotype including best-corrected visual acuity (BCVA), fundus photograph, fundus autofluorescence (FAF), full field electroretinogram (ffERG), optical coherence tomography (OCT) and visual field (VF) data were collected. A literature search was performed in the PubMed and LOVD repositories. RESULTS We report 3 cases from a 2-generation family with a novel heterozygous likely pathogenic variant p. (Lys314Gln) (exon 10). The ophthalmic phenotype showed diffuse outer retinal atrophy with mild pigmentary changes with sparse pigmentary changes. FAF showed early macular involvement with macular hyperautofluorescence (hyperAF) surrounded by hypoAF. Foveal ellipsoid zone island can be found in the youngest patient but not in the older ones. The literature review identified a further 56 heterozygous, 1 compound heterozygous, and 2 homozygous variant. The heterozygous group included 43 missense, 3 in-frame, 1 nonsense, 2 frameshift, 1 synonymous, and 6 intronic variants. Exon 10 was noted as a hotspot harboring 18 variants. CONCLUSIONS We report a novel IMPDH1 variant. IMPDH1-associated retinopathy presents most frequently in the first decade of life with early macular involvement.
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Affiliation(s)
- Dhimas H Sakti
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Department of Ophthalmology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Elisa E Cornish
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Benjamin M Nash
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
| | - Robyn V Jamieson
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - John R Grigg
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
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11
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Schlottmann PG, Luna JD, Labat N, Yadarola MB, Bainttein S, Esposito E, Ibañez A, Barbaro EI, Álvarez Mendiara A, Picotti CP, Chirino Misisian A, Andreussi L, Gras J, Capalbo L, Visotto M, Dipierri JE, Alcoba E, Fernández Gabrielli L, Ávila S, Aucar ME, Martin DM, Ormaechea GJ, Inga ME, Francone AA, Charles M, Zompa T, Pérez PJ, Lotersztein V, Nuova PJ, Canonero IB, Mahroo OA, Michaelides M, Arno G, Daich Varela M. Nationwide genetic analysis of more than 600 families with inherited eye diseases in Argentina. NPJ Genom Med 2023; 8:8. [PMID: 37217489 DOI: 10.1038/s41525-023-00352-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/05/2023] [Indexed: 05/24/2023] Open
Abstract
This study corresponds to the first large-scale genetic analysis of inherited eye diseases (IED) in Argentina and describes the comprehensive genetic profile of a large cohort of patients. Medical records of 22 ophthalmology and genetics services throughout 13 Argentinian provinces were analyzed retrospectively. Patients with a clinical diagnosis of an ophthalmic genetic disease and a history of genetic testing were included. Medical, ophthalmological and family history was collected. A total of 773 patients from 637 families were included, with 98% having inherited retinal disease. The most common phenotype was retinitis pigmentosa (RP, 62%). Causative variants were detected in 379 (59%) patients. USH2A, RPGR, and ABCA4 were the most common disease-associated genes. USH2A was the most frequent gene associated with RP, RDH12 early-onset severe retinal dystrophy, ABCA4 Stargardt disease, PROM1 cone-rod dystrophy, and BEST1 macular dystrophy. The most frequent variants were RPGR c.1345 C > T, p.(Arg449*) and USH2A c.15089 C > A, p.(Ser5030*). The study revealed 156/448 (35%) previously unreported pathogenic/likely pathogenic variants and 8 possible founder mutations. We present the genetic landscape of IED in Argentina and the largest cohort in South America. This data will serve as a reference for future genetic studies, aid diagnosis, inform counseling, and assist in addressing the largely unmet need for clinical trials to be conducted in the region.
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Affiliation(s)
| | - José D Luna
- Centro Privado de Ojos Romagosa SA, Córdoba, Argentina
| | - Natalia Labat
- Centro Privado de Ojos Romagosa SA, Córdoba, Argentina
| | | | | | - Evangelina Esposito
- University Clinic Reina Fabiola, Córdoba, Córdoba, Argentina
- Catholic University of Cordoba, Cordoba, Argentina
| | - Agustina Ibañez
- University Clinic Reina Fabiola, Córdoba, Córdoba, Argentina
- Catholic University of Cordoba, Cordoba, Argentina
| | | | | | | | | | | | | | | | - Mauro Visotto
- Instituto Oftalmológico Trelew, Trelew, Chubut, Argentina
| | | | - Emilio Alcoba
- Hospital Materno Infantil Dr Héctor Quintana, Jujuy, Argentina
| | | | - Silvia Ávila
- Facultad de Ciencias Médicas, Universidad Nacional del Comahue, Río Negro, Argentina
| | | | | | | | - M Eugenia Inga
- Organización Medica de Investigación, Buenos Aires, Argentina
| | | | | | - Tamara Zompa
- Charles Centro Oftalmológico, Buenos Aires, Argentina
| | | | | | - Pedro J Nuova
- Ocularyb Oftalmoclinica, Yerba Buena, Tucumán, Argentina
| | | | - Omar A Mahroo
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Michel Michaelides
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Gavin Arno
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Malena Daich Varela
- Moorfields Eye Hospital, London, UK.
- UCL Institute of Ophthalmology, University College London, London, UK.
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12
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Jia R, Meng X, Chen S, Zhang F, Du J, Liu X, Yang L. AAV-mediated gene-replacement therapy restores viability of BCD patient iPSC derived RPE cells and vision of Cyp4v3 knockout mice. Hum Mol Genet 2023; 32:122-138. [PMID: 35925866 DOI: 10.1093/hmg/ddac181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/17/2022] [Accepted: 07/31/2022] [Indexed: 01/25/2023] Open
Abstract
Bietti crystalline corneoretinal dystrophy (BCD) is an autosomal recessive retinal degenerative disease characterized by yellow-white crystal deposits in the posterior pole, degeneration of the retinal pigment epithelium (RPE), and sclerosis of the choroid. Mutations in the cytochrome P450 4V2 gene (CYP4V2) cause BCD, which is associated with lipid metabolic disruption. The use of gene-replacement therapy in BCD has been hampered by the lack of disease models. To advance CYP4V2 gene-replacement therapy, we generated BCD patient-specific induced pluripotent stem cell (iPSC)-RPE cells and Cyp4v3 knockout (KO) mice as disease models and AAV2/8-CAG-CYP4V2 as treatment vectors. We demonstrated that after adeno-associated virus (AAV)-mediated CYP4V2 gene-replacement therapy BCD-iPSC-RPE cells presented restored cell survival and reduced lipid droplets accumulation; restoration of vision in Cyp4v3 KO mice was revealed by elevated electroretinogram amplitude and ameliorated RPE degeneration. These results suggest that AAV-mediated gene-replacement therapy in BCD patients is a promising strategy.
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Affiliation(s)
- Ruixuan Jia
- Key Laboratory of Vision Loss and Restoration, Department of Ophthalmology, Ministry of Education, Peking University Third Hospital, Beijing, People's Republic of China
| | - Xiang Meng
- Key Laboratory of Vision Loss and Restoration, Department of Ophthalmology, Ministry of Education, Peking University Third Hospital, Beijing, People's Republic of China
| | - Shaohong Chen
- Beijing Chinagene Corporation Ltd, Beijing, People's Republic of China
| | - Fan Zhang
- Beijing Chinagene Corporation Ltd, Beijing, People's Republic of China
| | - Juan Du
- Key Laboratory of Vision Loss and Restoration, Department of Ophthalmology, Ministry of Education, Peking University Third Hospital, Beijing, People's Republic of China.,Department of Anatomy, Histology, and Embryology, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, People's Republic of China
| | - Xiaozhen Liu
- Key Laboratory of Vision Loss and Restoration, Department of Ophthalmology, Ministry of Education, Peking University Third Hospital, Beijing, People's Republic of China
| | - Liping Yang
- Key Laboratory of Vision Loss and Restoration, Department of Ophthalmology, Ministry of Education, Peking University Third Hospital, Beijing, People's Republic of China
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13
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The Diagnostic Yield of Next Generation Sequencing in Inherited Retinal Diseases: A Systematic Review and Meta-analysis. Am J Ophthalmol 2022; 249:57-73. [PMID: 36592879 DOI: 10.1016/j.ajo.2022.12.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/16/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023]
Abstract
PURPOSE Accurate genotyping of individuals with inherited retinal diseases (IRD) is essential for patient management and identifying suitable candidates for gene therapies. This study evaluated the diagnostic yield of next generation sequencing (NGS) in IRDs. DESIGN Systematic review and meta-analysis. METHODS This systematic review was prospectively registered (CRD42021293619). Ovid MEDLINE and Ovid Embase were searched on 6 June 2022. Clinical studies evaluating the diagnostic yield of NGS in individuals with IRDs were eligible for inclusion. Risk of bias assessment was performed. Studies were pooled using a random...effects inverse variance model. Sources of heterogeneity were explored using stratified analysis, meta-regression, and sensitivity analysis. RESULTS This study included 105 publications from 28 countries. Most studies (90 studies) used targeted gene panels. The diagnostic yield of NGS was 61.3% (95% confidence interval: 57.8-64.7%; 51 studies) in mixed IRD phenotypes, 58.2% (51.6-64.6%; 41 studies) in rod-cone dystrophies, 57.7% (46.8-68.3%; eight studies) in macular and cone/cone-rod dystrophies, and 47.6% (95% CI: 41.0-54.3%; four studies) in familial exudative vitreoretinopathy. For mixed IRD phenotypes, a higher diagnostic yield was achieved pooling studies published between 2018-2022 (64.2% [59.5-68.7%]), studies using exome sequencing (73.5% [58.9-86.1%]), and studies using the American College of Medical Genetics variant interpretation standards (65.6% [60.8-70.4%]). CONCLUSION The current diagnostic yield of NGS in IRDs is between 52-74%. The certainty of the evidence was judged as low or very low. A key limitation of the current evidence is the significant heterogeneity between studies. Adoption of standardized reporting guidelines could improve confidence in future meta-analyses.
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14
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Karali M, Testa F, Di Iorio V, Torella A, Zeuli R, Scarpato M, Romano F, Onore ME, Pizzo M, Melillo P, Brunetti-Pierri R, Passerini I, Pelo E, Cremers FPM, Esposito G, Nigro V, Simonelli F, Banfi S. Genetic epidemiology of inherited retinal diseases in a large patient cohort followed at a single center in Italy. Sci Rep 2022; 12:20815. [PMID: 36460718 PMCID: PMC9718770 DOI: 10.1038/s41598-022-24636-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 11/17/2022] [Indexed: 12/04/2022] Open
Abstract
Inherited retinal diseases (IRDs) are the leading cause of vision loss in the working-age population. We performed a retrospective epidemiological study to determine the genetic basis of IRDs in a large Italian cohort (n = 2790) followed at a single referral center. We provided, mainly by next generation sequencing, potentially conclusive molecular diagnosis for 2036 patients (from 1683 unrelated families). We identified a total of 1319 causative sequence variations in 132 genes, including 353 novel variants, and 866 possibly actionable genotypes for therapeutic approaches. ABCA4 was the most frequently mutated gene (n = 535; 26.3% of solved cases), followed by USH2A (n = 228; 11.2%) and RPGR (n = 102; 5.01%). The other 129 genes had a lower contribution to IRD pathogenesis (e.g. CHM 3.5%, RHO 3.5%; MYO7A 3.4%; CRB1 2.7%; RPE65 2%, RP1 1.8%; GUCY2D 1.7%). Seventy-eight genes were mutated in five patients or less. Mitochondrial DNA variants were responsible for 2.1% of cases. Our analysis confirms the complex genetic etiology of IRDs and reveals the high prevalence of ABCA4 and USH2A mutations. This study also uncovers genetic associations with a spectrum of clinical subgroups and highlights a valuable number of cases potentially eligible for clinical trials and, ultimately, for molecular therapies.
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Affiliation(s)
- Marianthi Karali
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Francesco Testa
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Valentina Di Iorio
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Annalaura Torella
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Roberta Zeuli
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Margherita Scarpato
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Francesca Romano
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Maria Elena Onore
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Mariateresa Pizzo
- grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Paolo Melillo
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Raffaella Brunetti-Pierri
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Ilaria Passerini
- grid.24704.350000 0004 1759 9494Department of Genetic Diagnosis, Careggi Teaching Hospital, Florence, Italy
| | - Elisabetta Pelo
- grid.24704.350000 0004 1759 9494Department of Genetic Diagnosis, Careggi Teaching Hospital, Florence, Italy
| | - Frans P. M. Cremers
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gabriella Esposito
- grid.4691.a0000 0001 0790 385XDepartment of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy ,CEINGE-Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vincenzo Nigro
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Francesca Simonelli
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Sandro Banfi
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
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15
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Yi Z, Li S, Wang S, Xiao X, Sun W, Zhang Q. Clinical features and genetic spectrum of NMNAT1-associated retinal degeneration. Eye (Lond) 2022; 36:2279-2285. [PMID: 34837036 PMCID: PMC9674661 DOI: 10.1038/s41433-021-01853-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/14/2021] [Accepted: 11/10/2021] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES To systematically analyse the NMNAT1 variant spectrum and frequency, the associated phenotypic characteristics, and potential genotype-phenotype correlations based on our data and literature review. METHODS Biallelic potential pathogenic variants (PPV) in NMNAT1 were collected from our in-house exome sequencing data. Whole-genome sequencing was conducted subsequently for patients with only one heterozygous PPV detected in NMNAT1. The clinical data were reviewed and evaluated in detail. Furthermore, the literature was reviewed for reports of NMNAT1 variants and their associated phenotypes. RESULTS Eleven NMNAT1 variants, including two novel variants, were detected in 8 families from our cohort. All of the 9 available patients showed generalized tapetoretinal dystrophy at an early age (88.9% in the first decade), and disciform macular atrophy was identified in six patients from five unrelated families. Among a total of 125 patients from 8 families of our cohort and 91 families reported by the available literature, 92.9% patients showed onset of disease in the first year after birth, and 89.0% patients showed visual acuity of 0.05 or lower. All of the 39 patients with fundus photos available presented disciform macular atrophy with generalized tapetoretinal dystrophy. Most (54/80, 67.5%) of causative NMNAT1 variants were missense. The most frequent variants in Caucasian and Asian population are p.E257K and p.R237C, respectively. CONCLUSIONS Early-onset age, disciform macular atrophy with generalized tapetoretinal dystrophy, and poor visual acuity are the typical features of NMNAT1-associated retinal degeneration. Different variant hot spots of NMNAT1 were observed in different populations.
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Affiliation(s)
- Zhen Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Siyu Wang
- Department of Ophthalmology, Li Chuan People's Hospital, Enshi, HuBei, 445400, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China.
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16
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Jimenez HJ, Procopio RA, Thuma TBT, Marra MH, Izquierdo N, Klufas MA, Nagiel A, Pennesi ME, Pulido JS. Signal Peptide Variants in Inherited Retinal Diseases: A Multi-Institutional Case Series. Int J Mol Sci 2022; 23:13361. [PMID: 36362148 PMCID: PMC9658040 DOI: 10.3390/ijms232113361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/20/2022] [Accepted: 10/30/2022] [Indexed: 08/29/2024] Open
Abstract
Signal peptide (SP) mutations are an infrequent cause of inherited retinal diseases (IRDs). We report the genes currently associated with an IRD that possess an SP sequence and assess the prevalence of these variants in a multi-institutional retrospective review of clinical genetic testing records. The online databases, RetNet and UniProt, were used to determine which IRD genes possess a SP. A multicenter retrospective review was performed to retrieve cases of patients with a confirmed diagnosis of an IRD and a concurrent SP variant. In silico evaluations were performed with MutPred, MutationTaster, and the signal peptide prediction tool, SignalP 6.0. SignalP 6.0 was further used to determine the locations of the three SP regions in each gene: the N-terminal region, hydrophobic core, and C-terminal region. Fifty-six (56) genes currently associated with an IRD possess a SP sequence. Based on the records review, a total of 505 variants were present in the 56 SP-possessing genes. Six (1.18%) of these variants were within the SP sequence and likely associated with the patients' disease based on in silico predictions and clinical correlation. These six SP variants were in the CRB1 (early-onset retinal dystrophy), NDP (familial exudative vitreoretinopathy) (FEVR), FZD4 (FEVR), EYS (retinitis pigmentosa), and RS1 (X-linked juvenile retinoschisis) genes. It is important to be aware of SP mutations as an exceedingly rare cause of IRDs. Future studies will help refine our understanding of their role in each disease process and assess therapeutic approaches.
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Affiliation(s)
- Hiram J. Jimenez
- Vickie and Jack Farber Vision Research Center, Wills Eye Hospital, Philadelphia, PA 19107, USA
| | | | - Tobin B. T. Thuma
- Department of Pediatric Ophthalmology and Strabismus, Wills Eye Hospital, Philadelphia, PA 19107, USA
| | - Molly H. Marra
- Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Natalio Izquierdo
- Department of Surgery, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00921, USA
| | | | - Aaron Nagiel
- The Vision Center, Department of Surgery, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Mark E. Pennesi
- Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jose S. Pulido
- Retina Service, Wills Eye Hospital, Philadelphia, PA 19107, USA
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17
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Liu X, Jia R, Meng X, Wang L, Yang L. Analysis of RPGR gene mutations in 41 Chinese families affected by X-linked inherited retinal dystrophy. Front Genet 2022; 13:999695. [PMID: 36276946 PMCID: PMC9582779 DOI: 10.3389/fgene.2022.999695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Background: This study analyzed the phenotypes and genotypes of 41 Chinese families with inherited retinal dystrophy (IRD) and RPGR gene mutations.Methods: This retrospective analysis evaluated a cohort of 41 patients who were subjected to a specific Hereditary Eye Disease Enrichment Panel (HEDEP) analysis. All (likely) pathogenic variants were determined by Sanger sequencing, and co-segregation analyses were performed on the available family members. All cases were subjected to Sanger sequencing for RPGR open reading frame 15 (ORF15) mutations.Results: A total of 41 probands from different families with a clinical diagnosis of retinitis pigmentosa (RP; 34 cases) and cone-rod dystrophy (CORD; 7 cases) were included in this cohort. According to clinical information, 2, 18, and 21 cases were first assigned as autosomal dominant (AD), sporadic, and X-linked (XL) inheritance, respectively. Several cases of affected females who presented with a male phenotype have been described, posing challenges at diagnosis related to the apparent family history of AD. Mutations were located in RPGR exons or introns 1–14 and in ORF15 of 12 of 41 (29.3%) and 29 of 41 (70.7%) subjects, respectively. Thirty-four (likely) pathogenic mutations were identified. Frameshifts were the most frequently observed variants, followed by nonsense, splice, and missense mutations. Herein, a detailed description of four RP patients carrying RPGR intronic mutations is reported, and in vitro splice assays were performed to confirm the pathogenicity of these intronic mutations.Conclusion: Our findings provide useful insights for the genetic and clinical counseling of patients with XL IRD, which will be useful for ongoing and future gene therapy trials.
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Affiliation(s)
- Xiaozhen Liu
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Ruixuan Jia
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Xiang Meng
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Likun Wang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center of Life Sciences, Peking University Health Science Center, Beijing, China
- *Correspondence: Likun Wang, ; Liping Yang,
| | - Liping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
- *Correspondence: Likun Wang, ; Liping Yang,
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18
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Griffith J, Sioufi K, Wilbanks L, Magrath GN, Say EAT, Lyons MJ, Wilkes M, Pai GS, Peterseim MMW. Inherited Retinal Dystrophy in Southeastern United States: Characterization of South Carolina Patients and Comparative Literature Review. Genes (Basel) 2022; 13:genes13081490. [PMID: 36011402 PMCID: PMC9407983 DOI: 10.3390/genes13081490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) are a group of rare diseases involving more than 340 genes and a variety of clinical phenotypes that lead to significant visual impairment. The aim of this study is to evaluate the rates and genetic characteristics of IRDs in the southeastern region of the United States (US). A retrospective chart review was performed on 325 patients with a clinical diagnosis of retinal dystrophy. Data including presenting symptoms, visual acuity, retinal exam findings, imaging findings, and genetic test results were compiled and compared to national and international IRD cohorts. The known ethnic groups included White (64%), African American or Black (30%), Hispanic (3%), and Asian (2%). The most prevalent dystrophies identified clinically were non-syndromic retinitis pigmentosa (29.8%), Stargardt disease (8.3%), Usher syndrome (8.3%), cone-rod dystrophy (8.0%), cone dystrophy (4.9%), and Leber congenital amaurosis (4.3%). Of the 101 patients (31.1%) with genetic testing, 54 (53.5%) had causative genetic variants identified. The most common pathogenic genetic variants were USH2A (n = 11), ABCA4 (n = 8), CLN3 (n = 7), and CEP290 (n = 3). Our study provides initial information characterizing IRDs within the diverse population of the southeastern US, which differs from national and international genetic and diagnostic trends with a relatively high proportion of retinitis pigmentosa in our African American or Black population and a relatively high frequency of USH2A pathogenic variants.
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Affiliation(s)
- Joseph Griffith
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Kareem Sioufi
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Laurie Wilbanks
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - George N. Magrath
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Emil A. T. Say
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC 29425, USA
| | | | - Meg Wilkes
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Gurpur Shashidhar Pai
- Department of Genetics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Mae Millicent Winfrey Peterseim
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC 29425, USA
- Correspondence: ; Tel.: +1-843-792-3758
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19
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Ganapathi M, Thomas-Wilson A, Buchovecky C, Dharmadhikari A, Barua S, Lee W, Ruan MZC, Soucy M, Ragi S, Tanaka J, Clark LN, Naini AB, Liao J, Mansukhani M, Tsang S, Jobanputra V. Clinical exome sequencing for inherited retinal degenerations at a tertiary care center. Sci Rep 2022; 12:9358. [PMID: 35672425 PMCID: PMC9174483 DOI: 10.1038/s41598-022-13026-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/19/2022] [Indexed: 11/18/2022] Open
Abstract
Inherited retinal degenerations are clinically and genetically heterogeneous diseases characterized by progressive deterioration of vision. This study aimed at assessing the diagnostic yield of exome sequencing (ES) for an unselected cohort of individuals with hereditary retinal disorders. It is a retrospective study of 357 unrelated affected individuals, diagnosed with retinal disorders who underwent clinical ES. Variants from ES were filtered, prioritized, and classified using the ACMG recommendations. Clinical diagnosis of the individuals included rod-cone dystrophy (60%), macular dystrophy (20%), cone-rod dystrophy (9%), cone dystrophy (4%) and other phenotypes (7%). Majority of the cases (74%) were singletons and 6% were trios. A confirmed molecular diagnosis was obtained in 24% of cases. In 6% of cases, two pathogenic variants were identified with phase unknown, bringing the potential molecular diagnostic rate to ~ 30%. Including the variants of uncertain significance (VUS), potentially significant findings were reported in 57% of cases. Among cases with a confirmed molecular diagnosis, variants in EYS, ABCA4, USH2A, KIZ, CERKL, DHDDS, PROM1, NR2E3, CNGB1, ABCC6, PRPH2, RHO, PRPF31, PRPF8, SNRNP200, RP1, CHM, RPGR were identified in more than one affected individual. Our results support the utility of clinical ES in the diagnosis of genetically heterogeneous retinal disorders.
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Affiliation(s)
- Mythily Ganapathi
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Amanda Thomas-Wilson
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Christie Buchovecky
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Avinash Dharmadhikari
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Subit Barua
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Winston Lee
- Department of Ophthalmology, Columbia University, Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Merry Z C Ruan
- College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Megan Soucy
- Department of Ophthalmology, Columbia University, Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Sara Ragi
- Department of Ophthalmology, Columbia University, Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Joy Tanaka
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Lorraine N Clark
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Ali B Naini
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Jun Liao
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Mahesh Mansukhani
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Stephen Tsang
- Department of Ophthalmology, Columbia University, Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
- Jonas Children's Vision Care, Bernard & Shirlee Brown Glaucoma Laboratory, Columbia Stem Cell Initiative-Departments of Ophthalmology, Biomedical Engineering, Pathology & Cell Biology, Institute of Human Nutrition, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Vaidehi Jobanputra
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA.
- Precision Genomics Laboratory, Columbia University Irving Medical Center, 701 West 168th St., HHSC 1412, New York, NY, 10032, USA.
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20
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Bellingrath JS, McClements ME, Shanks M, Clouston P, Fischer MD, MacLaren RE. Envisioning the development of a CRISPR-Cas mediated base editing strategy for a patient with a novel pathogenic CRB1 single nucleotide variant. Ophthalmic Genet 2022; 43:661-670. [PMID: 35538629 DOI: 10.1080/13816810.2022.2073599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Inherited retinal degeneration (IRD) associated with mutations in the Crumbs homolog 1 (CRB1) gene is associated with a severe, early-onset retinal degeneration for which no therapy currently exists. Base editing, with its capability to precisely catalyse permanent nucleobase conversion in a programmable manner, represents a novel therapeutic approach to targeting this autosomal recessive IRD, for which a gene supplementation is challenging due to the need to target three different retinal CRB1 isoforms. PURPOSE To report and classify a novel CRB1 variant and envision a possible therapeutic approach in form of base editing. METHODS Case report. RESULTS A 16-year-old male patient with a clinical diagnosis of early-onset retinitis pigmentosa (RP) and characteristic clinical findings of retinal thickening and coarse lamination was seen at the Oxford Eye Hospital. He was found to be compound heterozygous for two CRB1 variants: a novel pathogenic nonsense variant in exon 9, c.2885T>A (p.Leu962Ter), and a likely pathogenic missense change in exon 6, c.2056C>T (p.Arg686Cys). While a base editing strategy for c.2885T>A would encompass a CRISPR-pass mediated "read-through" of the premature stop codon, the resulting missense changes were predicted to be "possibly damaging" in in-silico analysis. On the other hand, the transversion missense change, c.2056C>T, is amenable to transition editing with an adenine base editor (ABE) fused to a SaCas9-KKH with a negligible chance of bystander edits due to an absence of additional Adenines (As) in the editing window. CONCLUSIONS This case report records a novel pathogenic nonsense variant in CRB1 and gives an example of thinking about a base editing strategy for a patient compound heterozygous for CRB1 variants.
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Affiliation(s)
- J-S Bellingrath
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - M E McClements
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - M Shanks
- Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - P Clouston
- Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - M D Fischer
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - R E MacLaren
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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21
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Fenner BJ, Tan TE, Barathi AV, Tun SBB, Yeo SW, Tsai ASH, Lee SY, Cheung CMG, Chan CM, Mehta JS, Teo KYC. Gene-Based Therapeutics for Inherited Retinal Diseases. Front Genet 2022; 12:794805. [PMID: 35069693 PMCID: PMC8782148 DOI: 10.3389/fgene.2021.794805] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022] Open
Abstract
Inherited retinal diseases (IRDs) are a heterogenous group of orphan eye diseases that typically result from monogenic mutations and are considered attractive targets for gene-based therapeutics. Following the approval of an IRD gene replacement therapy for Leber's congenital amaurosis due to RPE65 mutations, there has been an intensive international research effort to identify the optimal gene therapy approaches for a range of IRDs and many are now undergoing clinical trials. In this review we explore therapeutic challenges posed by IRDs and review current and future approaches that may be applicable to different subsets of IRD mutations. Emphasis is placed on five distinct approaches to gene-based therapy that have potential to treat the full spectrum of IRDs: 1) gene replacement using adeno-associated virus (AAV) and nonviral delivery vectors, 2) genome editing via the CRISPR/Cas9 system, 3) RNA editing by endogenous and exogenous ADAR, 4) mRNA targeting with antisense oligonucleotides for gene knockdown and splicing modification, and 5) optogenetic approaches that aim to replace the function of native retinal photoreceptors by engineering other retinal cell types to become capable of phototransduction.
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Affiliation(s)
- Beau J Fenner
- Singapore National Eye Centre, Singapore, Singapore.,Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Graduate Medical School, Ophthalmology and Visual Sciences Academic Clinical Programme, Singapore, Singapore
| | - Tien-En Tan
- Singapore National Eye Centre, Singapore, Singapore.,Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Graduate Medical School, Ophthalmology and Visual Sciences Academic Clinical Programme, Singapore, Singapore
| | | | - Sai Bo Bo Tun
- Singapore Eye Research Institute, Singapore, Singapore
| | - Sia Wey Yeo
- Singapore Eye Research Institute, Singapore, Singapore
| | - Andrew S H Tsai
- Singapore National Eye Centre, Singapore, Singapore.,Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Graduate Medical School, Ophthalmology and Visual Sciences Academic Clinical Programme, Singapore, Singapore
| | - Shu Yen Lee
- Singapore National Eye Centre, Singapore, Singapore.,Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Graduate Medical School, Ophthalmology and Visual Sciences Academic Clinical Programme, Singapore, Singapore
| | - Chui Ming Gemmy Cheung
- Singapore National Eye Centre, Singapore, Singapore.,Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Graduate Medical School, Ophthalmology and Visual Sciences Academic Clinical Programme, Singapore, Singapore
| | - Choi Mun Chan
- Singapore National Eye Centre, Singapore, Singapore.,Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Graduate Medical School, Ophthalmology and Visual Sciences Academic Clinical Programme, Singapore, Singapore
| | - Jodhbir S Mehta
- Singapore National Eye Centre, Singapore, Singapore.,Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Graduate Medical School, Ophthalmology and Visual Sciences Academic Clinical Programme, Singapore, Singapore.,School of Material Science and Engineering, Nanyang Technological University, Singapore, Singapore.,Yong Loo Lin School of Medicine, Department of Ophthalmology, National University of Singapore, Singapore, Singapore
| | - Kelvin Y C Teo
- Singapore National Eye Centre, Singapore, Singapore.,Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Graduate Medical School, Ophthalmology and Visual Sciences Academic Clinical Programme, Singapore, Singapore
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22
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Liu X, Jia R, Meng X, Li Y, Yang L. Retinal degeneration in humanized mice expressing mutant rhodopsin under the control of the endogenous murine promoter. Exp Eye Res 2021; 215:108893. [PMID: 34919893 DOI: 10.1016/j.exer.2021.108893] [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: 04/12/2021] [Revised: 10/31/2021] [Accepted: 12/08/2021] [Indexed: 11/04/2022]
Abstract
RHO is one of the most common genetic causes of autosomal dominant retinitis Pigmentosa (adRP) and there is no effective therapy for this disease. While rapidly developed CRISPR/Cas9 gene editing technology presents a promising therapeutic strategy to treat adRP. A large number of studies for treating adRP using CRISPR/Cas9 have been performed based on transgenic mouse models which are affected with adRP caused by mutant mouse rhodopsin allele, the counterpart of human rhodopsin. Recently, some RHO humanized mouse models like T17M, P23H are generated, which permit testing of the therapeutic effect of CRISPR/Cas9 in preclinical in vivo systems, without putting humans at risk. While available humanized mouse models are few compared to the number of known RHO mutations, but it is time-consuming and costly to build humanized mice for each mutation. We wonder whether a humanized mouse model having several mutations simultaneously can be developed, although which rarely occurs in patients, to investigate the therapeutic effect of CRISPR/Cas9 for RHO-mediated adRP in preclinical in vivo systems. Homology directed repair strategy combing with CRISPR/Cas9 was employed to introduce human RHO genomic fragment containing the replacement of mouse exon1(mE1) after the start codon to mE5 before the stop codon and all introns by the human counterparts. The human rhodopsin could express under the control of the endogenous murine promoter both transcriptionally and translationally in vivo. Human rhodopsin in humanized mouse lines (without mutation) could replace murine rhodopsin morphologically and functionally. While human rhodopsin containing T17M, G51D, G114R, R135W and P171R mutations simultaneously in mutant humanized (Mut-Rhowt/hum and Mut-Rhohum/hum) mouse lines caused retinal degeneration. Mut-Rhohum/hum mice suffered from severe retinal degeneration with defective formation of rod outer segment, leaving nonrecordable electroretinogram (ERG) at 3 months. Mut- Rhowt/hum mice had a slower rate of photoreceptors loss. In 7-month-old Mut- Rhowt/hum mice, statistically reduced scotopic ERG responses were visible compared with age-matched WT mice, but the shortened outer segment and thinner outer nuclear layer could be observed from 3 months. From 7 months to 9 months, significantly abnormal scotopic ERG responses were visible and photoreceptors loss were also obvious in 9-month-old Mut-Rhowt/hum mice. In 12-month-old Mut- Rhowt/hum mice, statistically reduced scotopic and photopic ERG responses and retinal degeneration throughout the retina were visible. Because scotopic responses were more affected than photopic responses in mutant humanized mice, demonstrating that rods dysfunction was more severe than cones dysfunction and deteriorated earlier, the pattern of retinal degeneration caused by mutant human rhodopsin was a typical rod-cone decay. Immunocytochemistry in cells indicated human rhodopsin proteins with 5 mutations aggregated in the cytoplasm and were also retained in the endoplasmic reticulum. The mutant human rhodopsin also accumulated in rod inner segments and cellular bodies in vivo. In conclusion, our humanized models provide excellent opportunities to study the human rhodopsin expression patterns. Our mutant humanized heterozygotes can provide opportunities to explore gene editing therapies via CRISPR/Cas9 for these five mutations in preclinical studies, it is time-saving and cost-effective.
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Affiliation(s)
- Xiaozhen Liu
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Ruixuan Jia
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Xiang Meng
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Ying Li
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Liping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China.
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23
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Schneider N, Sundaresan Y, Gopalakrishnan P, Beryozkin A, Hanany M, Levanon EY, Banin E, Ben-Aroya S, Sharon D. Inherited retinal diseases: Linking genes, disease-causing variants, and relevant therapeutic modalities. Prog Retin Eye Res 2021; 89:101029. [PMID: 34839010 DOI: 10.1016/j.preteyeres.2021.101029] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022]
Abstract
Inherited retinal diseases (IRDs) are a clinically complex and heterogenous group of visual impairment phenotypes caused by pathogenic variants in at least 277 nuclear and mitochondrial genes, affecting different retinal regions, and depleting the vision of affected individuals. Genes that cause IRDs when mutated are unique by possessing differing genotype-phenotype correlations, varying inheritance patterns, hypomorphic alleles, and modifier genes thus complicating genetic interpretation. Next-generation sequencing has greatly advanced the identification of novel IRD-related genes and pathogenic variants in the last decade. For this review, we performed an in-depth literature search which allowed for compilation of the Global Retinal Inherited Disease (GRID) dataset containing 4,798 discrete variants and 17,299 alleles published in 31 papers, showing a wide range of frequencies and complexities among the 194 genes reported in GRID, with 65% of pathogenic variants being unique to a single individual. A better understanding of IRD-related gene distribution, gene complexity, and variant types allow for improved genetic testing and therapies. Current genetic therapeutic methods are also quite diverse and rely on variant identification, and range from whole gene replacement to single nucleotide editing at the DNA or RNA levels. IRDs and their suitable therapies thus require a range of effective disease modelling in human cells, granting insight into disease mechanisms and testing of possible treatments. This review summarizes genetic and therapeutic modalities of IRDs, provides new analyses of IRD-related genes (GRID and complexity scores), and provides information to match genetic-based therapies such as gene-specific and variant-specific therapies to the appropriate individuals.
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Affiliation(s)
- Nina Schneider
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Yogapriya Sundaresan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Prakadeeswari Gopalakrishnan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Avigail Beryozkin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Mor Hanany
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Shay Ben-Aroya
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel.
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24
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Rafati M, Mohamadhashem F, Jalilian K, Hoseininasab F, Fakhri L, Hoseini A, Amiri H, Barati Z, Darzi Ramandi S, Mostofinezhad N, Mahmoudi AH, Ghaffari SR. Identification of a novel de novo variant in OTX2 in a patient with congenital microphthalmia using targeted next-generation sequencing followed by prenatal diagnosis. Ophthalmic Genet 2021; 43:262-267. [PMID: 34791963 DOI: 10.1080/13816810.2021.2002915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND Next-generation sequencing has been proven to be a reliable method for the detection of genetic causes in heterogeneous ocular disorders. In this report an NGS-based diagnostic approach was taken to uncover the genetic etiology in a patient with coloboma and microphthalmia, a highly heterogeneous disease with intrafamilial phenotypic variability. MATERIALS AND METHODS Next generation sequencing using a targeted panel of 316 genes, was carried out in the proband. Prioritized variants were then identified and confirmed using Sanger sequencing. Prenatal diagnosis of the detected variant was then performed in the family. RESULTS A novel de novo frameshift variant c.157_164delTTCACTCG (p.Phe53fs) in OTX2, leading to a truncated protein, was identified. Prenatal diagnosis identified the same variant in the fetus. CONCLUSIONS This report demonstrates the importance of genetic counseling and underscores the efficiency and effectiveness of targeted NGS as a means of detecting variants in inherited eye disorders.
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Affiliation(s)
- Maryam Rafati
- Comprehensive Genetic Center, Hope Generation Foundation, Tehran, Iran.,Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.,Department of Genomics Gene Clinic, Tehran, Iran
| | - Faezeh Mohamadhashem
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Koosha Jalilian
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Fatemeh Hoseininasab
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Laya Fakhri
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Azadeh Hoseini
- Comprehensive Genetic Center, Hope Generation Foundation, Tehran, Iran
| | - Hosna Amiri
- Comprehensive Genetic Center, Hope Generation Foundation, Tehran, Iran
| | - Zeinab Barati
- Comprehensive Genetic Center, Hope Generation Foundation, Tehran, Iran
| | | | | | | | - Saeed Reza Ghaffari
- Comprehensive Genetic Center, Hope Generation Foundation, Tehran, Iran.,Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.,Department of Genomics Gene Clinic, Tehran, Iran
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25
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Dai H, Zhang Y, Li R, Li Y, Li G. Genotype and Ocular Phenotype in Sixteen Chinese Patients with Bietti Corneoretinal Crystalline Dystrophy. Curr Eye Res 2021; 47:436-442. [PMID: 34724870 DOI: 10.1080/02713683.2021.1995004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE To investigate CYP4V2 gene variants and ocular clinical characteristics of Bietti corneoretinal crystalline dystrophy in China so as to provide more references for genotype and phenotype of BCD. METHODS Sixteen Chinese probands were recruited in Beijing Tongren Hospital in a retrospective study. All patients underwent CYP4V2 gene detection and ophthalmic clinical examinations. RESULTS CYP4V2 gene variants were detected in all patients. Eight variants were identified, and the most common one was c.802-8_810del17bpinsGC. Onset age of BCD was from 12 to 44 years, and the first symptoms mostly were decreased visual acuity or night blindness. Corneal crystalline depositions were observed in all patients and were found not only in epithelium and superficial stroma near the limbus but also in corneal endothelium. OCT showed atrophy of RPE in all patients, outer retinal tubulation in ten patients, macular edema in four patients, macular hole in three patients with one accompanied with retinal detachment, and choroidal neovascularization in one patient. CONCLUSION CYP4V2 gene variants were detected in all patients consistent with the genetic locus homogeneity of BCD, and c.802-8_810del17bpinsGC was the most common mutation. Corneal crystalline depositions were observed in all patients, which may be features of BCD and helpful for the diagnosis of BCD patients, especially those in the advanced stage without typical fundus crystalline depositions or without gene detection. However, considerable phenotypic variability was detected. Corneal crystalline deposits were observed not only in epithelium and superficial stroma but also in endothelium, which has not been reported before. This may provide further evidence for the variable phenotypic expression between affected individuals.
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Affiliation(s)
- Hehua Dai
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yang Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Ruyi Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yuyu Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Genlin Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
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Retinitis Punctata Albescens and RLBP1-Allied Phenotypes. OPHTHALMOLOGY SCIENCE 2021; 1:100052. [PMID: 36247817 PMCID: PMC9559097 DOI: 10.1016/j.xops.2021.100052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 11/21/2022]
Abstract
Purpose To identify relevant criteria for gene therapy based on clinical and genetic characteristics of rod–cone dystrophy associated with RLBP1 pathogenic variants in a large cohort comprising children and adults. Design Retrospective cohort study. Participants Patients with pathogenic variants in RLBP1 registered in a single French reference center specialized in inherited retinal dystrophies. Methods Clinical, multimodal imaging, and genetic findings were reviewed. Main Outcome Measures Age of onset; visual acuity; ellipsoid line length; nasal, temporal, and foveal retinal thickness; and pathogenic variants and related phenotypes, including Newfoundland rod–cone and Bothnia dystrophies (NFRCDs), were reappraised. Results Twenty-one patients (15 families) were included. The most frequent form was NFRCD with 12 patients (8 families) homozygous for the recurrent deletion of exons 7 through 9 in RLBP1 and 5 patients (4 families) with biallelic protein-truncating variants (2 novel: p.Gln16∗ and p.Tyr251∗). A novel combination of the p.Arg234Trp Bothnia variant with a nonsense variant in trans led to Bothnia dystrophy in 2 sisters. One proband carrying the p.Met266Lys Bothnia variant and in trans p.Arg121Trp and a second, with the p.Arg9Cys and p.Tyr111∗ combination, both demonstrated mild retinitis punctata albescens. Independently of genotype, all patients showed a visual acuity of worse than 20/200, an ellipsoid line width of less than 1000 μm, and a mean foveal thickness of less than 130 to 150 μm, with loss of both the interdigitation and ellipsoid lines. Conclusions The eligibility for RLBP1 gene therapy first should be determined according to the biallelic variant combination using a robust classification as proposed herein. An ellipsoid line width of more than 1200 μm and a central thickness of more than 130 to 150 μm with detectable ellipsoid and interdigitation lines should be 2 prerequisite imaging indicators for gene therapy.
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Sarkadi B, Liko I, Nyiro G, Igaz P, Butz H, Patocs A. Analytical Performance of NGS-Based Molecular Genetic Tests Used in the Diagnostic Workflow of Pheochromocytoma/Paraganglioma. Cancers (Basel) 2021; 13:4219. [PMID: 34439371 PMCID: PMC8392134 DOI: 10.3390/cancers13164219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/30/2022] Open
Abstract
Next Generation Sequencing (NGS)-based methods are high-throughput and cost-effective molecular genetic diagnostic tools. Targeted gene panel and whole exome sequencing (WES) are applied in clinical practice for assessing mutations of pheochromocytoma/paraganglioma (PPGL) associated genes, but the best strategy is debated. Germline mutations of at the least 18 PPGL genes are present in approximately 20-40% of patients, thus molecular genetic testing is recommended in all cases. We aimed to evaluate the analytical and clinical performances of NGS methods for mutation detection of PPGL-associated genes. WES (three different library preparation and bioinformatics workflows) and an in-house, hybridization based gene panel (endocrine-onco-gene-panel- ENDOGENE) was evaluated on 37 (20 WES and 17 ENDOGENE) samples with known variants. After optimization of the bioinformatic workflow, 61 additional samples were tested prospectively. All clinically relevant variants were validated with Sanger sequencing. Target capture of PPGL genes differed markedly between WES platforms and genes tested. All known variants were correctly identified by all methods, but methods of library preparations, sequencing platforms and bioinformatical settings significantly affected the diagnostic accuracy. The ENDOGENE panel identified several pathogenic mutations and unusual genotype-phenotype associations suggesting that the whole panel should be used for identification of genetic susceptibility of PPGL.
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Affiliation(s)
- Balazs Sarkadi
- MTA-SE Hereditary Tumors Research Group, Eotvos Lorand Research Network, H-1089 Budapest, Hungary; (B.S.); (I.L.); (H.B.)
| | - Istvan Liko
- MTA-SE Hereditary Tumors Research Group, Eotvos Lorand Research Network, H-1089 Budapest, Hungary; (B.S.); (I.L.); (H.B.)
- Bionics Innovation Center, H-1089 Budapest, Hungary;
| | - Gabor Nyiro
- Bionics Innovation Center, H-1089 Budapest, Hungary;
- MTA-SE Molecular Medicine Research Group, Eotvos Lorand Research Network, H-1083 Budapest, Hungary;
| | - Peter Igaz
- MTA-SE Molecular Medicine Research Group, Eotvos Lorand Research Network, H-1083 Budapest, Hungary;
- Department of Endocrinology, Department of Internal Medicine and Oncology, Semmelweis University, H-1083 Budapest, Hungary
| | - Henriett Butz
- MTA-SE Hereditary Tumors Research Group, Eotvos Lorand Research Network, H-1089 Budapest, Hungary; (B.S.); (I.L.); (H.B.)
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary
| | - Attila Patocs
- MTA-SE Hereditary Tumors Research Group, Eotvos Lorand Research Network, H-1089 Budapest, Hungary; (B.S.); (I.L.); (H.B.)
- Bionics Innovation Center, H-1089 Budapest, Hungary;
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary
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Song F, Owczarek-Lipska M, Ahmels T, Book M, Aisenbrey S, Menghini M, Barthelmes D, Schrader S, Spital G, Neidhardt J. High-Throughput Sequencing to Identify Mutations Associated with Retinal Dystrophies. Genes (Basel) 2021; 12:genes12081269. [PMID: 34440443 PMCID: PMC8391535 DOI: 10.3390/genes12081269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/16/2022] Open
Abstract
Retinal dystrophies (RD) are clinically and genetically heterogenous disorders showing mutations in over 270 disease-associated genes. Several millions of people worldwide are affected with different types of RD. Studying the relevance of disease-associated sequence alterations will assist in understanding disorders and may lead to the development of therapeutic approaches. Here, we established a whole exome sequencing (WES) pipeline to rapidly identify disease-associated mutations in patients. Sanger sequencing was applied to identify deep-intronic variants and to verify the co-segregation of WES results within families. We analyzed 26 unrelated patients with different syndromic and non-syndromic clinical manifestations of RD. All patients underwent ophthalmic examinations. We identified nine novel disease-associated sequence variants among 37 variants identified in total. The sequence variants located to 17 different genes. Interestingly, two cases presenting with Stargardt disease carried deep-intronic variants in ABCA4. We have classified 21 variants as pathogenic variants, 4 as benign/likely benign variants, and 12 as variants of uncertain significance. This study highlights the importance of WES-based mutation analyses in RD patients supporting clinical decisions, broadly based genetic diagnosis and support genetic counselling. It is essential for any genetic therapy to expand the mutation spectrum, understand the genes' function, and correlate phenotypes with genotypes.
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Affiliation(s)
- Fei Song
- Human Genetics Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, 26129 Oldenburg, Germany; (F.S.); (M.O.-L.)
| | - Marta Owczarek-Lipska
- Human Genetics Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, 26129 Oldenburg, Germany; (F.S.); (M.O.-L.)
- Research Center Neurosensory Science, University of Oldenburg, 26129 Oldenburg, Germany
| | - Tim Ahmels
- Department of Ophthalmology, Pius-Hospital, University of Oldenburg, 26121 Oldenburg, Germany; (T.A.); (S.S.)
| | - Marius Book
- Eye Centre at the St. Franziskus Hospital, 48145 Münster, Germany; (M.B.); (G.S.)
| | - Sabine Aisenbrey
- Department of Ophthalmology, Vivantes Health Network Ltd., Neukölln Hospital, 12351 Berlin, Germany;
| | - Moreno Menghini
- Department of Ophthalmology, Ospedale Regionale di Lugano, 6900 Lugano, Switzerland;
- Department of Ophthalmology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland;
| | - Daniel Barthelmes
- Department of Ophthalmology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland;
| | - Stefan Schrader
- Department of Ophthalmology, Pius-Hospital, University of Oldenburg, 26121 Oldenburg, Germany; (T.A.); (S.S.)
| | - Georg Spital
- Eye Centre at the St. Franziskus Hospital, 48145 Münster, Germany; (M.B.); (G.S.)
| | - John Neidhardt
- Human Genetics Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, 26129 Oldenburg, Germany; (F.S.); (M.O.-L.)
- Research Center Neurosensory Science, University of Oldenburg, 26129 Oldenburg, Germany
- Correspondence: ; Tel.: +49-(0)441-7983810
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Zhou C, Xiao Y, Xie H, Liu S, Wang J. A novel USH2A variant in a patient with hearing loss and prenatal diagnosis of a familial fetus: a case report. BMC Med Genomics 2021; 14:200. [PMID: 34376197 PMCID: PMC8353764 DOI: 10.1186/s12920-021-01052-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 08/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Usher syndrome (USH) is the most common cause of inherited deaf-blindness. The current study aimed to identify pathogenic variants in a Chinese patient with hearing loss and to report the identification of a novel p.(Phe1583Leufs*10) variant in USH2A, which met the needs of prenatal diagnosis of the patient's mother. CASE PRESENTATION Genomic DNA obtained from a five-year-old girl with hearing loss was analyzed via the hearing loss-targeted gene panels. We identified the compound heterozygous variants c.8559-2A>G and c.4749delT in Usher syndrome type 2A (USH2A) gene as the underlying cause of the patient; the former variation has been reported in the literature, but not the latter. The parents of the girl were heterozygous carriers. The two variants were classified as pathogenic. Based on these findings, amniotic fluid samples were used for prenatal diagnosis of the couple's fetus, which was found to carry c.4749delT but not c.8559-2A>G variation. During the follow-up period of more than 9 months after the birth of the fetus, it was confirmed that the infant was healthy. CONCLUSIONS The results of the present study identified two compound heterozygous USH2A variants in a patient with hearing loss and reported a novel USH2A variant which expands the spectrum of USH2A variants in USH.
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Affiliation(s)
- Cong Zhou
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Prenatal Diagnosis Center of Sichuan Province, 20 Section 3 Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People's Republic of China
| | - Yuanyuan Xiao
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Prenatal Diagnosis Center of Sichuan Province, 20 Section 3 Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People's Republic of China
| | - Hanbing Xie
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Prenatal Diagnosis Center of Sichuan Province, 20 Section 3 Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People's Republic of China
| | - Shanling Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Prenatal Diagnosis Center of Sichuan Province, 20 Section 3 Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People's Republic of China.
| | - Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Prenatal Diagnosis Center of Sichuan Province, 20 Section 3 Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People's Republic of China.
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Burdon KP. The utility of genomic testing in the ophthalmology clinic: A review. Clin Exp Ophthalmol 2021; 49:615-625. [PMID: 34231298 DOI: 10.1111/ceo.13970] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/25/2022]
Abstract
Genomic testing assesses many genes in one test. It is often used in the diagnosis of heterogeneous single gene disorders where pathogenic variation in one of many genes are known to cause similar phenotypes, or where a clinical diagnosis is difficult to reach. In the ophthalmic setting, genomic testing can be used to diagnose several groups of diseases, including inherited retinal dystrophies, paediatric cataract, glaucoma and anterior segment dysgenesis and other syndromic developmental disorders with eye involvement. The testing can encompass several modalities ranging from whole genome sequencing to exome sequencing or targeted gene panels. The advantages to the patient of receiving a molecular diagnosis include an end to the diagnostic odyssey, determination of prognosis and clarification of treatment, access to accurate genetic counselling, and confirming eligibility for clinical trials or genetic specific therapies. Genomic testing is a powerful addition to the diagnosis and management of inherited eye disease.
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Affiliation(s)
- Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
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31
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García Bohórquez B, Aller E, Rodríguez Muñoz A, Jaijo T, García García G, Millán JM. Updating the Genetic Landscape of Inherited Retinal Dystrophies. Front Cell Dev Biol 2021; 9:645600. [PMID: 34327195 PMCID: PMC8315279 DOI: 10.3389/fcell.2021.645600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/30/2021] [Indexed: 12/24/2022] Open
Abstract
Inherited retinal dystrophies (IRD) are a group of diseases characterized by the loss or dysfunction of photoreceptors and a high genetic and clinical heterogeneity. Currently, over 270 genes have been associated with IRD which makes genetic diagnosis very difficult. The recent advent of next generation sequencing has greatly facilitated the diagnostic process, enabling to provide the patients with accurate genetic counseling in some cases. We studied 92 patients who were clinically diagnosed with IRD with two different custom panels. In total, we resolved 53 patients (57.6%); in 12 patients (13%), we found only one mutation in a gene with a known autosomal recessive pattern of inheritance; and 27 patients (29.3%) remained unsolved. We identified 120 pathogenic or likely pathogenic variants; 30 of them were novel. Among the cone-rod dystrophy patients, ABCA4 was the most common mutated gene, meanwhile, USH2A was the most prevalent among the retinitis pigmentosa patients. Interestingly, 10 families carried pathogenic variants in more than one IRD gene, and we identified two deep-intronic variants previously described as pathogenic in ABCA4 and CEP290. In conclusion, the IRD study through custom panel sequencing demonstrates its efficacy for genetic diagnosis, as well as the importance of including deep-intronic regions in their design. This genetic diagnosis will allow patients to make accurate reproductive decisions, enroll in gene-based clinical trials, and benefit from future gene-based treatments.
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Affiliation(s)
- Belén García Bohórquez
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
| | - Elena Aller
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
- Unit of Genetics, University Hospital La Fe, Valencia, Spain
| | - Ana Rodríguez Muñoz
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
| | - Teresa Jaijo
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
- Unit of Genetics, University Hospital La Fe, Valencia, Spain
| | - Gema García García
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
| | - José M. Millán
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
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Next-Generation Sequencing Applications for Inherited Retinal Diseases. Int J Mol Sci 2021; 22:ijms22115684. [PMID: 34073611 PMCID: PMC8198572 DOI: 10.3390/ijms22115684] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal diseases (IRDs) represent a collection of phenotypically and genetically diverse conditions. IRDs phenotype(s) can be isolated to the eye or can involve multiple tissues. These conditions are associated with diverse forms of inheritance, and variants within the same gene often can be associated with multiple distinct phenotypes. Such aspects of the IRDs highlight the difficulty met when establishing a genetic diagnosis in patients. Here we provide an overview of cutting-edge next-generation sequencing techniques and strategies currently in use to maximise the effectivity of IRD gene screening. These techniques have helped researchers globally to find elusive causes of IRDs, including copy number variants, structural variants, new IRD genes and deep intronic variants, among others. Resolving a genetic diagnosis with thorough testing enables a more accurate diagnosis and more informed prognosis and should also provide information on inheritance patterns which may be of particular interest to patients of a child-bearing age. Given that IRDs are heritable conditions, genetic counselling may be offered to help inform family planning, carrier testing and prenatal screening. Additionally, a verified genetic diagnosis may enable access to appropriate clinical trials or approved medications that may be available for the condition.
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Lee IH, Lin Y, Alvarez WJ, Hernandez-Ferrer C, Mandl KD, Kong SW. WEScover: selection between clinical whole exome sequencing and gene panel testing. BMC Bioinformatics 2021; 22:259. [PMID: 34016036 PMCID: PMC8139020 DOI: 10.1186/s12859-021-04178-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/09/2021] [Indexed: 11/18/2022] Open
Abstract
Background Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for several exons in clinically implicated genes. In some cases, a targeted gene panel testing may be a dependable option to ascertain true negatives for genomic variants in known disease-associated genes. We developed a web-based tool to quickly gauge whether all genes of interest would be reliably covered by WES or whether targeted gene panel testing should be considered instead to minimize false negatives in candidate genes. Results WEScover is a novel web application that provides an intuitive user interface for discovering breadth and depth of coverage across population-scale WES datasets, searching either by phenotype, by targeted gene panel(s) or by gene(s). Moreover, the application shows metrics from the Genome Aggregation Database to provide gene-centric view on breadth of coverage. Conclusions WEScover allows users to efficiently query genes and phenotypes for the coverage of associated exons by WES and recommends use of panel tests for the genes with potential incomplete coverage by WES. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04178-5.
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Affiliation(s)
- In-Hee Lee
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA
| | - Yufei Lin
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA
| | - William Jefferson Alvarez
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA.,Agios Pharmaceuticals, Boston, MA, USA
| | - Carles Hernandez-Ferrer
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA.,Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Barcelona, Spain
| | - Kenneth D Mandl
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children's Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
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Unique Variant Spectrum in a Jordanian Cohort with Inherited Retinal Dystrophies. Genes (Basel) 2021; 12:genes12040593. [PMID: 33921607 PMCID: PMC8074154 DOI: 10.3390/genes12040593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022] Open
Abstract
Whole Exome Sequencing (WES) is a powerful approach for detecting sequence variations in the human genome. The aim of this study was to investigate the genetic defects in Jordanian patients with inherited retinal dystrophies (IRDs) using WES. WES was performed on proband patients' DNA samples from 55 Jordanian families. Sanger sequencing was used for validation and segregation analysis of the detected, potential disease-causing variants (DCVs). Thirty-five putatively causative variants (6 novel and 29 known) in 21 IRD-associated genes were identified in 71% of probands (39 of the 55 families). Three families showed phenotypes different from the typically reported clinical findings associated with the causative genes. To our knowledge, this is the largest genetic analysis of IRDs in the Jordanian population to date. Our study also confirms that WES is a powerful tool for the molecular diagnosis of IRDs in large patient cohorts.
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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.
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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.
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36
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Luo H, Xiao X, Li S, Sun W, Yi Z, Wang P, Zhang Q. Spectrum-frequency and genotype-phenotype analysis of rhodopsin variants. Exp Eye Res 2020; 203:108405. [PMID: 33347869 DOI: 10.1016/j.exer.2020.108405] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/23/2020] [Accepted: 12/14/2020] [Indexed: 12/18/2022]
Abstract
Mutations in RHO are the most common cause of autosomal dominant retinitis pigmentosa. However, the pathogenicity of many RHO variants is questionable. This study was designed to investigate the genotype-phenotype correlation for RHO variants. These RHO variants were collected from the in-house exome sequencing data of 7092 probands suffering from different types of eye conditions. The variants were classified using bioinformatics tools, family segregation, and clinical phenotypes. The RHO variants were assessed using multiple online tools and a genotype-phenotype analysis based on the data collected from of ours, gnomAD, and published literature. Totally, 52 heterozygous variants of RHO were detected in the 7092 probands. Of these 52, 17 were potentially pathogenic, were present in 35 families, and comprised 15 missense variants, one inframe deletion and one nonsense variant. All the 15 missense variants were predicted to be damaging by five different online tools. The analysis of the clinical data of the patients from the 35 families revealed certain common features, of an early damage to both the rods and the cones, relatively preserved visual acuity in adulthood, and mid-peripheral tapetoretinal degeneration with pigmentation or RPE atrophy. Our data, the data from gnomAD, and the systematic review of the 246 previously reported variants suggest that approximately two-thirds of the rare missense variants and most of the truncated variants involving upstream of K296 are likely benign. This study provides a brief summary of the characteristics of the pathogenic RHO variants. It emphasizes that the systematic evaluation of these variants at the individual-gene level is crucial in the current era of clinical genetic testing even for a well-known gene such as RHO.
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Affiliation(s)
- Hualei Luo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Zhen Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
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Genetic and Clinical Findings in an Ethnically Diverse Cohort with Retinitis Pigmentosa Associated with Pathogenic Variants in CERKL. Genes (Basel) 2020; 11:genes11121497. [PMID: 33322828 PMCID: PMC7763961 DOI: 10.3390/genes11121497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 01/06/2023] Open
Abstract
Autosomal recessive retinitis pigmentosa is caused by mutations in over 40 genes, one of which is the ceramide kinase-like gene (CERKL). We present a case series of six patients from six unrelated families diagnosed with inherited retinal dystrophies (IRD) and with two variants in CERKL recruited from a multi-ethnic British population. A retrospective review of clinical data in these patients was performed and included colour fundus photography, fundus autofluorescence (AF) imaging, spectral domain–optical coherence tomography (SD–OCT), visual fields and electroretinogram (ERG) assessment where available. Three female and three male patients were included. Age at onset ranged from 7 years old to 45 years, with three presenting in their 20s and two presenting in their 40s. All but one had central visual loss as one of their main presenting symptoms. Four patients had features of retinitis pigmentosa with significant variation in severity and extent of disease, and two patients had no pigment deposition with only macular involvement clinically. Seven variants in CERKL were identified, of which three are novel. The inherited retinopathies associated with the CERKL gene vary in age at presentation and in degree of severity, but generally are characterised by a central visual impairment early on.
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Martín-Sánchez M, Bravo-Gil N, González-del Pozo M, Méndez-Vidal C, Fernández-Suárez E, Rodríguez-de la Rúa E, Borrego S, Antiñolo G. A Multi-Strategy Sequencing Workflow in Inherited Retinal Dystrophies: Routine Diagnosis, Addressing Unsolved Cases and Candidate Genes Identification. Int J Mol Sci 2020; 21:E9355. [PMID: 33302505 PMCID: PMC7763277 DOI: 10.3390/ijms21249355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 01/17/2023] Open
Abstract
The management of unsolved inherited retinal dystrophies (IRD) cases is challenging since no standard pipelines have been established. This study aimed to define a diagnostic algorithm useful for the diagnostic routine and to address unsolved cases. Here, we applied a Next-Generation Sequencing-based workflow, including a first step of panel sequencing (PS) followed by clinical-exome sequencing (CES) and whole-exome sequencing (WES), in 46 IRD patients belonging to 42 families. Twenty-six likely causal variants in retinal genes were found by PS and CES. CES and WES allowed proposing two novel candidate loci (WDFY3 and a X-linked region including CITED1), both abundantly expressed in human retina according to RT-PCR and immunohistochemistry. After comparison studies, PS showed the best quality and cost values, CES and WES involved similar analytical efforts and WES presented the highest diagnostic yield. These results reinforce the relevance of panels as a first step in the diagnostic routine and suggest WES as the next strategy for unsolved cases, reserving CES for the simultaneous study of multiple conditions. Standardizing this algorithm would enhance the efficiency and equity of clinical genetics practice. Furthermore, the identified candidate genes could contribute to increase the diagnostic yield and expand the mutational spectrum in these disorders.
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Affiliation(s)
- Marta Martín-Sánchez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (M.M.-S.); (N.B.-G.); (M.G.-d.P.); (C.M.-V.); (E.F.-S.); (S.B.)
| | - Nereida Bravo-Gil
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (M.M.-S.); (N.B.-G.); (M.G.-d.P.); (C.M.-V.); (E.F.-S.); (S.B.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Seville, Spain
| | - María González-del Pozo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (M.M.-S.); (N.B.-G.); (M.G.-d.P.); (C.M.-V.); (E.F.-S.); (S.B.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Seville, Spain
| | - Cristina Méndez-Vidal
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (M.M.-S.); (N.B.-G.); (M.G.-d.P.); (C.M.-V.); (E.F.-S.); (S.B.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Seville, Spain
| | - Elena Fernández-Suárez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (M.M.-S.); (N.B.-G.); (M.G.-d.P.); (C.M.-V.); (E.F.-S.); (S.B.)
| | - Enrique Rodríguez-de la Rúa
- Department of Ophthalmology, University Hospital Virgen Macarena, 41013 Seville, Spain;
- Retics Patologia Ocular, OFTARED, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (M.M.-S.); (N.B.-G.); (M.G.-d.P.); (C.M.-V.); (E.F.-S.); (S.B.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Seville, Spain
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (M.M.-S.); (N.B.-G.); (M.G.-d.P.); (C.M.-V.); (E.F.-S.); (S.B.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Seville, Spain
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Liu X, Tao T, Zhao L, Li G, Yang L. Molecular diagnosis based on comprehensive genetic testing in 800 Chinese families with non-syndromic inherited retinal dystrophies. Clin Exp Ophthalmol 2020; 49:46-59. [PMID: 33090715 DOI: 10.1111/ceo.13875] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 09/23/2020] [Accepted: 10/05/2020] [Indexed: 12/16/2022]
Abstract
IMPORTANCE Inherited retinal dystrophies (IRDs) are a group of monogenic diseases, one of the leading causes of blindness. BACKGROUND Introducing a comprehensive genetic testing strategy by combining single gene Sanger sequencing, next-generation sequencing (NGS) including whole exome sequencing (WES), and a specific hereditary eye disease enrichment panel (HEDEP) sequencing, to identify the disease-causing variants of 800 Chinese probands affected with non-syndromic IRDs. DESIGN Retrospective analysis. PARTICIPANTS Eight hundred Chinese non-syndromic IRDs probands and their families. METHODS A total of 149 patients were subjected to Sanger sequencing. Of the 651 patients subjected to NGS, 86 patients underwent WES and 565 underwent HEDEP. Patients that likely carried copy number variations (CNVs) detected by HEDEP were further validated by multiplex ligation-dependent probe amplification (MLPA) or quantitative fluorescence PCR (QF-PCR). MAIN OUTCOME MEASURES The diagnostic rate. RESULTS (Likely) pathogenic variants were determined in 481 cases (60.13% detection rate). The detection rates of single gene Sanger sequencing, WES and HEDEP were 86.58%, 31.40% and 56.99%, respectively. Approximately 11.64% of 481 cases carried autosomal dominant variants, 72.97% carried AR variants and 15.39% were found to be X-linked. CNVs were confirmed by MLPA or QF-PCR in 17 families. Fourteen genes that each caused disease in 1% or more of the cohort were detected, and these genes were collectively responsible for disease in almost one half (46.38%) of the families. CONCLUSIONS AND RELEVANCE Sanger sequencing is ideal to detect pathogenic variants of clinical homogeneous diseases, whereas NGS is more appropriate for patients without an explicit clinical diagnosis.
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Affiliation(s)
- Xiaozhen Liu
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Tianchang Tao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Lin Zhao
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Genlin Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Liping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
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40
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Pontikos N, Arno G, Jurkute N, Schiff E, Ba-Abbad R, Malka S, Gimenez A, Georgiou M, Wright G, Armengol M, Knight H, Katz M, Moosajee M, Yu-Wai-Man P, Moore AT, Michaelides M, Webster AR, Mahroo OA. Genetic Basis of Inherited Retinal Disease in a Molecularly Characterized Cohort of More Than 3000 Families from the United Kingdom. Ophthalmology 2020; 127:1384-1394. [PMID: 32423767 PMCID: PMC7520514 DOI: 10.1016/j.ophtha.2020.04.008] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/27/2020] [Accepted: 04/06/2020] [Indexed: 01/22/2023] Open
Abstract
PURPOSE In a large cohort of molecularly characterized inherited retinal disease (IRD) families, we investigated proportions with disease attributable to causative variants in each gene. DESIGN Retrospective study of electronic patient records. PARTICIPANTS Patients and relatives managed in the Genetics Service of Moorfields Eye Hospital in whom a molecular diagnosis had been identified. METHODS Genetic screening used a combination of single-gene testing, gene panel testing, whole exome sequencing, and more recently, whole genome sequencing. For this study, genes listed in the Retinal Information Network online resource (https://sph.uth.edu/retnet/) were included. Transcript length was extracted for each gene (Ensembl, release 94). MAIN OUTCOME MEASURES We calculated proportions of families with IRD attributable to variants in each gene in the entire cohort, a cohort younger than 18 years, and a current cohort (at least 1 patient encounter between January 1, 2017, and August 2, 2019). Additionally, we explored correlation between numbers of families and gene transcript length. RESULTS We identified 3195 families with a molecular diagnosis (variants in 135 genes), including 4236 affected individuals. The pediatric cohort comprised 452 individuals from 411 families (66 genes). The current cohort comprised 2614 families (131 genes; 3130 affected individuals). The 20 most frequently implicated genes overall (with prevalence rates per families) were as follows: ABCA4 (20.8%), USH2A (9.1%), RPGR (5.1%), PRPH2 (4.6%), BEST1 (3.9%), RS1 (3.5%), RP1 (3.3%), RHO (3.3%), CHM (2.7%), CRB1 (2.1%), PRPF31 (1.8%), MY07A (1.7%), OPA1 (1.6%), CNGB3 (1.4%), RPE65 (1.2%), EYS (1.2%), GUCY2D (1.2%), PROM1 (1.2%), CNGA3 (1.1%), and RDH12 (1.1%). These accounted for 71.8% of all molecularly diagnosed families. Spearman coefficients for correlation between numbers of families and transcript length were 0.20 (P = 0.025) overall and 0.27 (P = 0.017), -0.17 (P = 0.46), and 0.71 (P = 0.047) for genes in which variants exclusively cause recessive, dominant, or X-linked disease, respectively. CONCLUSIONS Our findings help to quantify the burden of IRD attributable to each gene. More than 70% of families showed pathogenic variants in 1 of 20 genes. Transcript length (relevant to gene delivery strategies) correlated significantly with numbers of affected families (but not for dominant disease).
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Affiliation(s)
- Nikolas Pontikos
- UCL Institute of Ophthalmology, University College London, London, United Kingdom; Genetics Service, Moorfields Eye Hospital, London, United Kingdom
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, United Kingdom; Genetics Service, Moorfields Eye Hospital, London, United Kingdom; North East Thames Regional Genetics Service, Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Neringa Jurkute
- UCL Institute of Ophthalmology, University College London, London, United Kingdom; Genetics Service, Moorfields Eye Hospital, London, United Kingdom
| | - Elena Schiff
- UCL Institute of Ophthalmology, University College London, London, United Kingdom; Genetics Service, Moorfields Eye Hospital, London, United Kingdom
| | - Rola Ba-Abbad
- UCL Institute of Ophthalmology, University College London, London, United Kingdom; Genetics Service, Moorfields Eye Hospital, London, United Kingdom
| | - Samantha Malka
- UCL Institute of Ophthalmology, University College London, London, United Kingdom; Genetics Service, Moorfields Eye Hospital, London, United Kingdom
| | - Ainoa Gimenez
- UCL Institute of Ophthalmology, University College London, London, United Kingdom; Genetics Service, Moorfields Eye Hospital, London, United Kingdom
| | - Michalis Georgiou
- UCL Institute of Ophthalmology, University College London, London, United Kingdom; Genetics Service, Moorfields Eye Hospital, London, United Kingdom
| | - Genevieve Wright
- Genetics Service, Moorfields Eye Hospital, London, United Kingdom
| | - Monica Armengol
- Genetics Service, Moorfields Eye Hospital, London, United Kingdom
| | - Hannah Knight
- Genetics Service, Moorfields Eye Hospital, London, United Kingdom
| | - Menachem Katz
- Genetics Service, Moorfields Eye Hospital, London, United Kingdom
| | - Mariya Moosajee
- UCL Institute of Ophthalmology, University College London, London, United Kingdom; Genetics Service, Moorfields Eye Hospital, London, United Kingdom; North East Thames Regional Genetics Service, Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Patrick Yu-Wai-Man
- UCL Institute of Ophthalmology, University College London, London, United Kingdom; Genetics Service, Moorfields Eye Hospital, London, United Kingdom; Cambridge Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom; Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, United Kingdom
| | - Anthony T Moore
- UCL Institute of Ophthalmology, University College London, London, United Kingdom; Genetics Service, Moorfields Eye Hospital, London, United Kingdom; Department of Ophthalmology, University of California, San Francisco, San Francisco, California
| | - Michel Michaelides
- UCL Institute of Ophthalmology, University College London, London, United Kingdom; Genetics Service, Moorfields Eye Hospital, London, United Kingdom
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, United Kingdom; Genetics Service, Moorfields Eye Hospital, London, United Kingdom
| | - Omar A Mahroo
- UCL Institute of Ophthalmology, University College London, London, United Kingdom; Genetics Service, Moorfields Eye Hospital, London, United Kingdom; Section of Ophthalmology, King's College London, St. Thomas' Hospital Campus, London, United Kingdom; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.
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Genetic heterogeneity and prognostic impact of recurrent ANK2 and TP53 mutations in mantle cell lymphoma: a multi-centre cohort study. Sci Rep 2020; 10:13359. [PMID: 32770099 PMCID: PMC7414214 DOI: 10.1038/s41598-020-70310-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/21/2020] [Indexed: 12/13/2022] Open
Abstract
The molecular features of mantle cell lymphoma (MCL), including its increased incidence, and complex therapies have not been investigated in detail, particularly in East Asian populations. In this study, we performed targeted panel sequencing (TPS) and whole-exome sequencing (WES) to investigate the genetic alterations in Korean MCL patients. We obtained a total of 53 samples from MCL patients from five Korean university hospitals between 2009 and 2016. We identified the recurrently mutated genes such as SYNE1, ATM, KMT2D, CARD11, ANK2, KMT2C, and TP53, which included some known drivers of MCL. The mutational profiles of our cohort indicated genetic heterogeneity. The significantly enriched pathways were mainly involved in gene expression, cell cycle, and programmed cell death. Multivariate analysis revealed that ANK2 mutations impacted the unfavourable overall survival (hazard ratio [HR] 3.126; P = 0.032). Furthermore, TP53 mutations were related to worse progression-free survival (HR 7.813; P = 0.043). Among the recurrently mutated genes with more than 15.0% frequency, discrepancies were found in only 5 genes from 4 patients, suggesting comparability of the TPS to WES in practical laboratory settings. We provide the unbiased genetic landscape that might contribute to MCL pathogenesis and recurrent genes conferring unfavourable outcomes.
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Whole exome sequencing of a family revealed a novel variant in the CHM gene, c.22delG p.(Glu8Serfs*4), which co-segregated with choroideremia. Biosci Rep 2020; 40:223574. [PMID: 32364220 PMCID: PMC7218218 DOI: 10.1042/bsr20200067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/29/2020] [Accepted: 05/01/2020] [Indexed: 01/17/2023] Open
Abstract
Choroideremia is a complex form of blindness-causing retinal degeneration. The aim of the present study was to investigate the pathogenic variant and molecular etiology associated with choroideremia in a Chinese family. All available family members underwent detailed ophthalmological examinations. Whole exome sequencing, bioinformatics analysis, Sanger sequencing, and co-segregation analysis of family members were used to validate sequencing data and confirm the presence of the disease-causing gene variant. The proband was diagnosed with choroideremia on the basis of clinical manifestations. Whole exome sequencing showed that the proband had a hemizygous variant in the CHM gene, c.22delG p. (Glu8Serfs*4), which was confirmed by Sanger sequencing and found to co-segregate with choroideremia. The variant was classified as likely pathogenic and has not previously been described. These results expand the spectrum of variants in the CHM gene, thus potentially enriching the understanding of the molecular basis of choroideremia. Moreover, they may provide insight for future choroideremia diagnosis and gene therapy.
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43
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Butz H, Nyírő G, Kurucz PA, Likó I, Patócs A. Molecular genetic diagnostics of hypogonadotropic hypogonadism: from panel design towards result interpretation in clinical practice. Hum Genet 2020; 140:113-134. [PMID: 32222824 PMCID: PMC7864839 DOI: 10.1007/s00439-020-02148-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/05/2020] [Indexed: 12/13/2022]
Abstract
Congenital hypogonadotropic hypogonadism (CHH) is a clinically and genetically heterogeneous congenital disease. Symptoms cover a wide spectrum from mild forms to complex phenotypes due to gonadotropin-releasing hormone (GnRH) deficiency. To date, more than 40 genes have been identified as pathogenic cause of CHH. These genes could be grouped into two major categories: genes controlling development and GnRH neuron migration and genes being responsible for neuroendocrine regulation and GnRH neuron function. High-throughput, next-generation sequencing (NGS) allows to analyze numerous gene sequences at the same time. Nowadays, whole exome or whole genome datasets could be investigated in clinical genetic diagnostics due to their favorable cost-benefit. The increasing genetic data generated by NGS reveal novel candidate genes and gene variants with unknown significance (VUSs). To provide clinically valuable genetic results, complex clinical and bioinformatics work are needed. The multifaceted genetics of CHH, the variable mode of inheritance, the incomplete penetrance, variable expressivity and oligogenic characteristics further complicate the interpretation of the genetic variants detected. The objective of this work, apart from reviewing the currently known genes associated with CHH, was to summarize the advantages and disadvantages of the NGS-based platforms and through the authors' own practice to guide through the whole workflow starting from gene panel design, performance analysis and result interpretation. Based on our results, a genetic diagnosis was clearly identified in 21% of cases tested (8/38).
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Affiliation(s)
- Henriett Butz
- Department of Laboratory Medicine, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary.,Hereditary Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary.,Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Gábor Nyírő
- Department of Laboratory Medicine, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary.,Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Petra Anna Kurucz
- Department of Laboratory Medicine, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary
| | - István Likó
- Hereditary Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Attila Patócs
- Department of Laboratory Medicine, Semmelweis University, Nagyvárad tér 4, Budapest, 1089, Hungary. .,Hereditary Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary. .,Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.
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44
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Zanolli M, Oporto JI, Verdaguer JI, López JP, Zacharías S, Romero P, Ossandón D, Denk O, Acuña O, López JM, Stevenson R, Álamos B, Iturriaga H. Genetic testing for inherited ocular conditions in a developing country. Ophthalmic Genet 2020; 41:36-40. [DOI: 10.1080/13816810.2020.1734944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Mario Zanolli
- Clínica Alemana de Santiago- Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
- Departamento de oftalmología, Hospital de niños Roberto del Río, Santiago, Chile
| | - Joaquín I. Oporto
- Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan I. Verdaguer
- Fundación Oftalmológica Los Andes, Universidad de los Andes, Santiago, Chile
| | - Juan Pablo López
- Clínica Alemana de Santiago- Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
| | - Sergio Zacharías
- Fundación Oftalmológica Los Andes, Universidad de los Andes, Santiago, Chile
| | - Pablo Romero
- Clínica Alemana de Santiago- Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
| | - Diego Ossandón
- Clínica Alemana de Santiago- Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
- Departamento de oftalmología, Hospital de niños Roberto del Río, Santiago, Chile
| | - Oliver Denk
- Clínica Alemana de Santiago- Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
| | - Olga Acuña
- Fundación Oftalmológica Los Andes, Universidad de los Andes, Santiago, Chile
| | - José Manuel López
- Fundación Oftalmológica Los Andes, Universidad de los Andes, Santiago, Chile
| | | | | | - Hernán Iturriaga
- Fundación Oftalmológica Los Andes, Universidad de los Andes, Santiago, Chile
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45
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Rodríguez-Muñoz A, Aller E, Jaijo T, González-García E, Cabrera-Peset A, Gallego-Pinazo R, Udaondo P, Salom D, García-García G, Millán JM. Expanding the Clinical and Molecular Heterogeneity of Nonsyndromic Inherited Retinal Dystrophies. J Mol Diagn 2020; 22:532-543. [PMID: 32036094 DOI: 10.1016/j.jmoldx.2020.01.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/01/2019] [Accepted: 01/12/2020] [Indexed: 12/21/2022] Open
Abstract
A cohort of 172 patients diagnosed clinically with nonsyndromic retinal dystrophies, from 110 families underwent full ophthalmologic examination, including retinal imaging, electrophysiology, and optical coherence tomography, when feasible. Molecular analysis was performed using targeted next-generation sequencing (NGS). Variants were filtered and prioritized according to the minimum allele frequency, and finally classified according to the American College of Medical Genetics and Genomics guidelines. Multiplex ligation-dependent probe amplification and array comparative genomic hybridization were performed to validate copy number variations identified by NGS. The diagnostic yield of this study was 62% of studied families. Thirty novel mutations were identified. The study found phenotypic intra- and interfamilial variability in families with mutations in C1QTNF5, CERKL, and PROM1; biallelic mutations in PDE6B in a unilateral retinitis pigmentosa patient; interocular asymmetry RP in 50% of the symptomatic RPGR-mutated females; the first case with possible digenism between CNGA1 and CNGB1; and a ROM1 duplication in two unrelated retinitis pigmentosa families. Ten unrelated cases were reclassified. This study highlights the clinical utility of targeted NGS for nonsyndromic inherited retinal dystrophy cases and the importance of full ophthalmologic examination, which allows new genotype-phenotype associations and expands the knowledge of this group of disorders. Identifying the cause of disease is essential to improve patient management, provide accurate genetic counseling, and take advantage of gene therapy-based treatments.
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Affiliation(s)
- Ana Rodríguez-Muñoz
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Elena Aller
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Genetics Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Teresa Jaijo
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Genetics Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Emilio González-García
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Departments of Neurophysiology, Hospital de Manises, Valencia, Spain
| | | | - Roberto Gallego-Pinazo
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Macula Unit, Oftalvist Clinic, Valencia, Spain
| | - Patricia Udaondo
- Ophthalmology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - David Salom
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Departments of Ophthalmology, Hospital de Manises, Valencia, Spain
| | - Gema García-García
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
| | - José M Millán
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
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Abu-Ameerh M, Mohammad H, Dardas Z, Barham R, Ali D, Bijawi M, Tawalbeh M, Amr S, Hatmal MM, Al-Bdour M, Awidi A, Azab B. Extending the spectrum of CLRN1- and ABCA4-associated inherited retinal dystrophies caused by novel and recurrent variants using exome sequencing. Mol Genet Genomic Med 2020; 8:e1123. [PMID: 31968401 PMCID: PMC7057102 DOI: 10.1002/mgg3.1123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 12/14/2019] [Accepted: 12/27/2019] [Indexed: 01/13/2023] Open
Abstract
Background Inherited retinal dystrophies (IRDs) are characterized by extreme genetic and clinical heterogeneity. There are many genes that are known to cause IRD which makes the identification of the underlying genetic causes quite challenging. And in view of the emergence of therapeutic options, it is essential to combine molecular and clinical data to correctly diagnose IRD patients. In this study, we aimed to identify the disease‐causing variants (DCVs) in four consanguineous Jordanian families with IRDs and describe genotype–phenotype correlations. Methods Exome sequencing (ES) was employed on the proband patients of each family, followed by segregation analysis of candidate variants in affected and unaffected family members by Sanger sequencing. Simulation analysis was done on one novel CLRN1 variant to characterize its effect on mRNA processing. Clinical evaluation included history, slit‐lamp biomicroscopy, and indirect ophthalmoscopy. Results We identified two novel variants in CLRN1 [(c.433+1G>A) and (c.323T>C, p.Leu108Pro)], and two recurrent variants in ABCA4 [(c.1648G>A, p.Gly550Arg) and (c.5460+1G>A)]. Two families with the same DCV were found to have different phenotypes and another family was shown to have sector RP. Moreover, simulation analysis for the CLRN1 splice donor variant (c.433+1G>A) showed that the variant might affect mRNA processing resulting in the formation of an abnormal receptor. Also, a family that was previously diagnosed with nonsyndromic RP was found to have Usher syndrome based on their genetic assessment and audiometry. Conclusion Our findings extend the spectrum of CLRN1‐ and ABCA4‐associated IRDs and describe new phenotypes for these genes. We also highlighted the importance of combining molecular and clinical data to correctly diagnose IRDs and the utility of simulation analysis to predict the effect of splice donor variants on protein formation and function.
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Affiliation(s)
- Mohammed Abu-Ameerh
- Department of Ophthalmology, Jordan University Hospital, The University of Jordan, Amman, Jordan
| | | | - Zain Dardas
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
| | - Raghda Barham
- Cell Therapy Center, The University of Jordan, Amman, Jordan
| | - Dema Ali
- Cell Therapy Center, The University of Jordan, Amman, Jordan
| | - Maysa Bijawi
- Cell Therapy Center, The University of Jordan, Amman, Jordan
| | - Mohamed Tawalbeh
- Department of Otolaryngology, Jordan University Hospital, The University of Jordan, Amman, Jordan
| | - Sami Amr
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ma'mon M Hatmal
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, The Hashemite University, Zarqa, Jordan
| | - Muawyah Al-Bdour
- Department of Ophthalmology, Jordan University Hospital, The University of Jordan, Amman, Jordan
| | - Abdalla Awidi
- Cell Therapy Center, The University of Jordan, Amman, Jordan.,Department of Medicine and Hematology, Jordan University Hospital, The University of Jordan, Amman, Jordan
| | - Belal Azab
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan.,Human and Molecular Genetics, Medical College of Virginia, Virginia Commonwealth University, Richmond, VA, USA
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Gerth-Kahlert C, Koller S, Hanson JVM, Baehr L, Tiwari A, Kivrak-Pfiffner F, Bahr A, Berger W. Genotype-Phenotype Analysis of a Novel Recessive and a Recurrent Dominant SNRNP200 Variant Causing Retinitis Pigmentosa. Invest Ophthalmol Vis Sci 2019; 60:2822-2835. [PMID: 31260034 DOI: 10.1167/iovs.18-25643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To compare phenotype variability in retinitis pigmentosa patients with recessive and dominant mutations in the SNRNP200 gene. Methods In a retrospective study, patients of two unrelated families were identified: family A, five patients aged 36 to 77 years; family B, one patient aged 9 years and his asymptomatic parents and sister. All patients received a comprehensive eye examination with a detailed retinal functional and morphologic assessment. Genetic testing was performed by whole exome sequencing (WES) in the index patient from each family. Genes described to be involved in eye diseases (n > 450) were screened for rare variants and segregation analysis was performed. Results A known heterozygous missense variant (c.3260C>T, p.(Ser1087Leu)) in the SNRNP200 gene was identified in the index patient of family A while a novel homozygous missense mutation (c.1634G>A, p.(Arg545His)) was found in the index patient of family B. Nyctalopia and photophobia were reported by 6/6 and 2/6 patients, respectively. The phenotype associated with the dominant mutation was characterized by variable disease onset (early childhood to the sixth decade of life), disease severity (visual acuity of 20/20-20/200 in the seventh to eighth decade), and advanced rod-cone dysfunction. Characteristics of recessive disease included distinct fundus changes of dot-like hypopigmentation together with retinal atrophy and severe rod-cone dysfunction. Conclusions The phenotype characteristics in autosomal dominant and recessive SNRNP200 mutations show distinct features, with earlier severe disease in the recessive case and a variable disease expression in the dominant inheritance pattern.
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Affiliation(s)
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - James V M Hanson
- Department of Ophthalmology, University Hospital Zurich, Zurich, Switzerland
| | - Luzy Baehr
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - Amit Tiwari
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - Fatma Kivrak-Pfiffner
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - Angela Bahr
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University and ETH Zurich, Zurich, Switzerland
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Xiao X, Sun W, Li S, Jia X, Zhang Q. Spectrum, frequency, and genotype-phenotype of mutations in SPATA7. Mol Vis 2019; 25:821-833. [PMID: 31908400 PMCID: PMC6925664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/30/2019] [Indexed: 11/25/2022] Open
Abstract
PURPOSE To describe the mutation spectrum of SPATA7 and associated ocular phenotypes. METHODS As part of a continuing examination of the genetic basis of inherited ophthalmic diseases, sequencing variations in SPATA7 were identified in sequencing data from 5,090 probands. Mutations in SPATA7 were identified in 12 Chinese patients from ten families. Family history and clinical data were examined in detail in these patients. To evaluate possible gene-specific fundus changes, the results were combined with data from 66 patients from 50 families previously reported in the literature. RESULTS Seven homozygous or compound heterozygous mutations, including two novel mutations (c.367C>T, p.Q123* and c.1083-2A>G) and five known mutations in SPATA7, were identified in ten families, including six families with Leber congenital amaurosis (LCA), three families with juvenile retinitis pigmentosa, and one family with early-onset high myopia. These families accounted for approximately 2.2% (6/269) of LCA and 0.4% (10/2,252) of inherited retinal dystrophies in this case series. A combined analysis of data from the present study and data from 60 families reported in the literature showed that 93.3% (112/120) of mutant alleles were truncation mutations, whereas only about 5.0% were missense mutations, and 1.7% were non-frameshift indels. Common SPATA7-associated fundus changes, including narrow arterioles, a relatively well-preserved macular region, and widespread RPE atrophy resulting in diffuse mottled hypopigmentation in the midperipheral retina, were identified in this cohort and in patients in the literature. Missense mutations were not associated with specific phenotypic features or severity. CONCLUSIONS Narrow arterioles, a relatively well-preserved macular region, and widespread RPE atrophy resulting in diffuse mottling hypopigmentation in the midperipheral retina may be considered early and common fundus changes specific to SPATA7-associated retinopathy. The fact that similar mutations result in varied phenotypes points to the existence of other potential modifiers of the disease. Uncovering the identity of these modifiers might aid the development of novel treatments.
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