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Lee YJ, Kim JH, Lee SY, Jo DH. A Comprehensive Genotype-Phenotype Study in 203 Individuals with Retinoblastoma. Exp Eye Res 2024; 248:110102. [PMID: 39303840 DOI: 10.1016/j.exer.2024.110102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 09/08/2024] [Accepted: 09/17/2024] [Indexed: 09/22/2024]
Abstract
Retinoblastoma is the most common intraocular tumor in children and is caused by biallelic inactivation of the RB1 gene. The identification of RB1 germline variants in patients with retinoblastoma and their families is critical for early diagnosis and prevention. In this study, genetic testing was conducted on the genomic DNA of 203 patients with retinoblastoma using a combined approach of direct sequencing and multiplex ligation-dependent probe amplification (MLPA) assays for genotype-phenotype correlation studies. Sixty-five germline variants were identified in 80 of the 203 patients, with 67 bilateral and 13 unilateral retinoblastoma cases. The variant detection rates in the bilateral and unilateral cases were 88% and 10%, respectively. Eighteen novel variants were identified. Variants were classified according to their presence, mutation pattern, location, molecular consequences, and pathogenicity. Subsequently, the genotypes and phenotypes of the 203 patients were evaluated. Variants were associated with age at diagnosis (p<0.001), laterality (p<0.001), and tumor size (p=0.010). The molecular consequences of the variants were related to laterality (p<0.001) and tumor size (p=0.001). The pathogenicity of the variants was associated with age at diagnosis (p=0.001), laterality (p=0.0212), treatment response (p=0.0470), and tumor size (p=0.002). These results suggest that patient phenotypes are associated with the inherent characteristics of germline RB1 variants. These findings indicate the potential application of genetic testing results in clinical practice.
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Affiliation(s)
- Yoo Jin Lee
- Department of Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Jeong Hun Kim
- Department of Biomedical Sciences and Ophthalmology, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Dong Hyun Jo
- Department of Anatomy and Cell Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.
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Zheng J, Li T, Ye H, Jiang Z, Jiang W, Yang H, Wu Z, Xie Z. Comprehensive identification of pathogenic variants in retinoblastoma by long- and short-read sequencing. Cancer Lett 2024; 598:217121. [PMID: 39009069 DOI: 10.1016/j.canlet.2024.217121] [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: 10/18/2023] [Revised: 06/16/2024] [Accepted: 07/11/2024] [Indexed: 07/17/2024]
Abstract
Retinoblastoma (RB) is the most common intraocular malignancy in childhood. The causal variants in RB are mostly characterized by previously used short-read sequencing (SRS) analysis, which has technical limitations in identifying structural variants (SVs) and phasing information. Long-read sequencing (LRS) technology has advantages over SRS in detecting SVs, phased genetic variants, and methylation. In this study, we comprehensively characterized the genetic landscape of RB using combinatorial LRS and SRS of 16 RB tumors and 16 matched blood samples. We detected a total of 232 somatic SVs, with an average of 14.5 SVs per sample across the whole genome in our cohort. We identified 20 distinct pathogenic variants disrupting RB1 gene, including three novel small variants and five somatic SVs. We found more somatic SVs were detected from LRS than SRS (140 vs. 122) in RB samples with WGS data, particularly the insertions (18 vs. 1). Furthermore, our analysis shows that, with the exception of one sample who lacked the methylation data, all samples presented biallelic inactivation of RB1 in various forms, including two cases with the biallelic hypermethylated promoter and four cases with compound heterozygous mutations which were missing in SRS analysis. By inferring relative timing of somatic events, we reveal the genetic progression that RB1 disruption early and followed by copy number changes, including amplifications of Chr2p and deletions of Chr16q, during RB tumorigenesis. Altogether, we characterize the comprehensive genetic landscape of RB, providing novel insights into the genetic alterations and mechanisms contributing to RB initiation and development. Our work also establishes a framework to analyze genomic landscape of cancers based on LRS data.
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Affiliation(s)
- Jingjing Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Tong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Huijing Ye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zehang Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wenbing Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Huasheng Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.
| | - Zhikun Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.
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Price EA, Sagoo MS, Reddy MA, Onadim Z. An overview of RB1 transcript alterations detected during retinoblastoma genetic screening. Ophthalmic Genet 2024; 45:235-245. [PMID: 37932244 DOI: 10.1080/13816810.2023.2270570] [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: 07/14/2023] [Revised: 08/24/2023] [Accepted: 10/09/2023] [Indexed: 11/08/2023]
Abstract
Identification of pathogenic RB1 variants aids in the clinical management of families with retinoblastoma. We routinely screen DNA for RB1 variants, but transcript analysis can also be used for variant screening, and to help decide variant pathogenicity. DNA was screened by conformation analysis followed by Sanger sequencing. Large deletion/insertions were detected by polymorphism analysis, MLPA and quantitative-PCR. Methylation-specific PCR was used to detect hypermethylation. RNA screening was performed when a DNA pathogenic variant was missing, or to determine effects on splicing.Two hundred and thirteen small coding variants were predicted to affect splicing in 207 patients. Splice donor (sd) variants were nearly twice as frequent as splice acceptor (sa) with the most affected positions being sd + 1 and sa-1. Some missense and nonsense codons altered splicing, while some splice consensus variants did not. Large deletion/insertions can disrupt splicing, but RNA analysis showed that some of these are more complex than indicated by DNA testing. RNA screening found pathogenic variants in 53.8% of samples where DNA analysis did not. RB1 splicing is altered by changes at consensus splice sites, some missense and nonsense codons, deep intronic changes and large deletion/insertions. Common alternatively spliced transcripts may complicate analysis. An effective molecular screening strategy would include RNA analysis to help determine pathogenicity.
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Affiliation(s)
- Elizabeth A Price
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, London, UK
| | - Mandeep S Sagoo
- Retinoblastoma Service, Royal London Hospital, Barts Health NHS Trust, London, UK
- NIHR Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital, Institute of Ophthalmology, University College London, London, UK
| | - M Ashwin Reddy
- Retinoblastoma Service, Royal London Hospital, Barts Health NHS Trust, London, UK
- Faculty of Medicine, Queen Mary University of London, London, UK
| | - Zerrin Onadim
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, London, UK
- Faculty of Medicine, Queen Mary University of London, London, UK
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Zhou L, Tong Y, Ho BM, Li J, Chan HYE, Zhang T, Du L, He JN, Chen LJ, Tham CC, Yam JC, Pang CP, Chu WK. Etiology including epigenetic defects of retinoblastoma. Asia Pac J Ophthalmol (Phila) 2024:100072. [PMID: 38789041 DOI: 10.1016/j.apjo.2024.100072] [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: 02/24/2024] [Revised: 04/09/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Retinoblastoma (RB), originating from the developing retina, is an aggressive intraocular malignant neoplasm in childhood. Biallelic loss of RB1 is conventionally considered a prerequisite for initiating RB development in most RB cases. Additional genetic mutations arising from genome instability following RB1 mutations are proposed to be required to promote RB development. Recent advancements in high throughput sequencing technologies allow a deeper and more comprehensive understanding of the etiology of RB that additional genetic alterations following RB1 biallelic loss are rare, yet epigenetic changes driven by RB1 loss emerge as a critical contributor promoting RB tumorigenesis. Multiple epigenetic regulators have been found to be dysregulated and to contribute to RB development, including noncoding RNAs, DNA methylations, RNA modifications, chromatin conformations, and histone modifications. A full understanding of the roles of genetic and epigenetic alterations in RB formation is crucial in facilitating the translation of these findings into effective treatment strategies for RB. In this review, we summarize current knowledge concerning genetic defects and epigenetic dysregulations in RB, aiming to help understand their links and roles in RB tumorigenesis.
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Affiliation(s)
- Linbin Zhou
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Yan Tong
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Bo Man Ho
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Jiahui Li
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Hoi Ying Emily Chan
- Medicine Programme Global Physician-Leadership Stream, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Tian Zhang
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Lin Du
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Jing Na He
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Li Jia Chen
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China; Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Clement C Tham
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China; Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Jason C Yam
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China; Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Chi Pui Pang
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China; Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China.
| | - Wai Kit Chu
- Department of Ophthalmology & Visual Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China; Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China.
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Gerrish A, Mashayamombe-Wolfgarten C, Stone E, Román-Montañana C, Abbott J, Jenkinson H, Millen G, Gurney S, McCalla M, Staveley SJ, Kainth A, Kirk M, Bowen C, Cavanagh S, Bunstone S, Carney M, Mohite A, Clokie S, Reddy MA, Foster A, Allen S, Parulekar M, Cole T. Genetic Diagnosis of Retinoblastoma Using Aqueous Humour-Findings from an Extended Cohort. Cancers (Basel) 2024; 16:1565. [PMID: 38672657 PMCID: PMC11049382 DOI: 10.3390/cancers16081565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/10/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
The identification of somatic RB1 variation is crucial to confirm the heritability of retinoblastoma. We and others have previously shown that, when tumour DNA is unavailable, cell-free DNA (cfDNA) derived from aqueous humour (AH) can be used to identify somatic RB1 pathogenic variation. Here we report RB1 pathogenic variant detection, as well as cfDNA concentration in an extended cohort of 75 AH samples from 68 patients. We show cfDNA concentration is highly variable and significantly correlated with the collection point of the AH. Cell-free DNA concentrations above 5 pg/µL enabled the detection of 93% of known or expected RB1 pathogenic variants. In AH samples collected during intravitreal chemotherapy treatment (Tx), the yield of cfDNA above 5 pg/µL and subsequent variant detection was low (≤46%). However, AH collected by an anterior chamber tap after one to three cycles of primary chemotherapy (Dx1+) enabled the detection of 75% of expected pathogenic variants. Further limiting our analysis to Dx1+ samples taken after ≤2 cycles (Dx ≤ 2) provided measurable levels of cfDNA in all cases, and a subsequent variant detection rate of 95%. Early AH sampling is therefore likely to be important in maximising cfDNA concentration and the subsequent detection of somatic RB1 pathogenic variants in retinoblastoma patients undergoing conservative treatment.
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Affiliation(s)
- Amy Gerrish
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
| | - Chipo Mashayamombe-Wolfgarten
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
| | - Edward Stone
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
- North West Genomic Laboratory Hub (Manchester), St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; (S.B.); (M.C.)
| | - Claudia Román-Montañana
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
| | - Joseph Abbott
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Helen Jenkinson
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Gerard Millen
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Sam Gurney
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Maureen McCalla
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Sarah-Jane Staveley
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Anu Kainth
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Maria Kirk
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Claire Bowen
- Birmingham Children’s Hospital Histopathology Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK (S.C.)
| | - Susan Cavanagh
- Birmingham Children’s Hospital Histopathology Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK (S.C.)
| | - Sancha Bunstone
- North West Genomic Laboratory Hub (Manchester), St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; (S.B.); (M.C.)
| | - Megan Carney
- North West Genomic Laboratory Hub (Manchester), St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK; (S.B.); (M.C.)
| | - Ajay Mohite
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Samuel Clokie
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
| | - M. Ashwin Reddy
- Retinoblastoma Unit, Royal London Hospital, Barts Health NHS Trust, London E1 1BB, UK
| | - Alison Foster
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
| | - Stephanie Allen
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
| | - Manoj Parulekar
- Birmingham Children’s Hospital Eye Department, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK (E.S.); (C.R.-M.); (S.C.); (S.A.)
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6
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Liu H, Liu F, Wei Z, Liu P, Liu Q, Chen L, Hou X. Identification and functional characterization of compound heterozygous CYP11B1 gene mutations. Endocrine 2024; 84:253-264. [PMID: 38285409 DOI: 10.1007/s12020-023-03614-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 11/10/2023] [Indexed: 01/30/2024]
Abstract
PURPOSE 11β-Hydroxylase deficiency (11β-OHD) is the second leading cause of congenital adrenal hyperplasia (CAH), a rare autosomal recessive disease caused by mutations in the CYP11B1 gene. We previously reported the case of a male Chinese patient with typical 11β-OHD symptoms. Sanger sequencing revealed that the patient carried a splice-site mutation, c.595+1G>A in the CYP11B1 gene. His mother and sister harbored the heterozygous mutation, c.595+1G>A. Paradoxically, Sanger sequencing did not detect any abnormality in the CYP11B1 gene of his father and brother. Therefore, in this study, we aimed to further explore the exact genetic etiology of 11β-OHD in this pedigree and analyze the functional consequence of the c.595+1G>A mutation. METHODS Gemomic DNA was extracted from the peripheral blood leukocytes of the family members and normal control individuals, followed by quantitative real-time polymerase chain reaction (qPCR) to detect the copy number of the target CYP11B1 gene fragment. Mutation analysis was also performed via whole-exome sequencing (WES) followed by Sanger sequencing validation. In vitro minigene assay was also performed to investigate the impact of the c.595+1G>A mutation on pre-mRNA splicing. RESULTS qPCR results suggested a heterozygous deletion encompassing position c.595+1 along with flanking exonic and intronic sequences in the CYP11B1 gene of the patient and his father. WES followed by Sanger sequencing verified that the patient carried compound heterozygous mutations in the CYP11B1 gene, including a novel 2840-bp deletion (c.395+661_c.1121+180del) and c.595+1G>A, while his father carried the heterozygous c.395+661_c.1121+180del mutation. No other novel CYP11B1 mutations were found in the rest of the family members. Furthermore, minigene assay revealed that the c.595+1G>A mutation resulted in a 70-bp deletion of exon 3 in the mRNA, and this altered the reading frame at amino acid 176 and created a premature stop codon at amino acid 197. CONCLUSION We identified a novel 2840-bp-sized large deletion and confirmed that the c.595+1G>A mutation disrupts normal pre-mRNA splicing. Either mutation could significantly alter the reading frame and abolish CYP11B1 enzyme activity. Therefore, our findings widen the mutation spectrum of CYP11B1 and provide an accurate diagnosis of 11β-OHD at a molecular genetic level.
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Affiliation(s)
- He Liu
- School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, 6699 Qingdao Road, Jinan, Shandong, 250117, China
- Department of Endocrinology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China
| | - Fuqiang Liu
- Department of Endocrinology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China
- Institute of Endocrine and Metabolic Diseases of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China
- Key Laboratory of Endocrine and Metabolic Diseases, Shandong Province Medicine & Health, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China
- Jinan Clinical Research Center for Endocrine and Metabolic Diseases, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China
| | - Zichun Wei
- Department of Endocrinology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China
| | - Pan Liu
- Department of Endocrinology, Tai'an City Central Hospital, 29 Longtan Road, Tai'an, Shandong, 271000, China
| | - Qiao Liu
- MOE Key Laboratory of Experimental Teratology, Department of Genetics, Shandong University School of Basic Medical Sciences, 44 Wenhuaxi Road, Lixia District, Jinan, Shandong, 250012, China
| | - Li Chen
- Department of Endocrinology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China.
- Institute of Endocrine and Metabolic Diseases of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China.
- Key Laboratory of Endocrine and Metabolic Diseases, Shandong Province Medicine & Health, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China.
- Jinan Clinical Research Center for Endocrine and Metabolic Diseases, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China.
| | - Xinguo Hou
- Department of Endocrinology, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China.
- Institute of Endocrine and Metabolic Diseases of Shandong University, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China.
- Key Laboratory of Endocrine and Metabolic Diseases, Shandong Province Medicine & Health, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China.
- Jinan Clinical Research Center for Endocrine and Metabolic Diseases, 107 Wenhuaxi Road, Jinan, Shandong, 250012, China.
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Marković L, Bukovac A, Varošanec AM, Šlaus N, Pećina-Šlaus N. Genetics in ophthalmology: molecular blueprints of retinoblastoma. Hum Genomics 2023; 17:82. [PMID: 37658463 PMCID: PMC10474694 DOI: 10.1186/s40246-023-00529-w] [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: 04/18/2023] [Accepted: 08/25/2023] [Indexed: 09/03/2023] Open
Abstract
This review presents current knowledge on the molecular biology of retinoblastoma (RB). Retinoblastoma is an intraocular tumor with hereditary and sporadic forms. 8,000 new cases of this ocular malignancy of the developing retina are diagnosed each year worldwide. The major gene responsible for retinoblastoma is RB1, and it harbors a large spectrum of pathogenic variants. Tumorigenesis begins with mutations that cause RB1 biallelic inactivation preventing the production of functional pRB proteins. Depending on the type of mutation the penetrance of RB is different. However, in small percent of tumors additional genes may be required, such as MYCN, BCOR and CREBBP. Additionally, epigenetic changes contribute to the progression of retinoblastoma as well. Besides its role in the cell cycle, pRB plays many additional roles, it regulates the nucleosome structure, participates in apoptosis, DNA replication, cellular senescence, differentiation, DNA repair and angiogenesis. Notably, pRB has an important role as a modulator of chromatin remodeling. In recent years high-throughput techniques are becoming essential for credible biomarker identification and patient management improvement. In spite of remarkable advances in retinoblastoma therapy, primarily in high-income countries, our understanding of retinoblastoma and its specific genetics still needs further clarification in order to predict the course of this disease and improve therapy. One such approach is the tumor free DNA that can be obtained from the anterior segment of the eye and be useful in diagnostics and prognostics.
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Affiliation(s)
- Leon Marković
- Department of Ophthalmology, Reference Center of the Ministry of Health of the Republic of Croatia for Pediatric Ophthalmology and Strabismus, University Hospital "Sveti Duh", Zagreb, Croatia
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Anja Bukovac
- Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000, Zagreb, Croatia
- Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Salata 12, 10000, Zagreb, Croatia
| | - Ana Maria Varošanec
- Department of Ophthalmology, Reference Center of the Ministry of Health of the Republic of Croatia for Pediatric Ophthalmology and Strabismus, University Hospital "Sveti Duh", Zagreb, Croatia
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Nika Šlaus
- Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000, Zagreb, Croatia
| | - Nives Pećina-Šlaus
- Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000, Zagreb, Croatia.
- Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Salata 12, 10000, Zagreb, Croatia.
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8
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Retinoblastoma: From genes to patient care. Eur J Med Genet 2022; 66:104674. [PMID: 36470558 DOI: 10.1016/j.ejmg.2022.104674] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/04/2022] [Accepted: 11/27/2022] [Indexed: 12/12/2022]
Abstract
Retinoblastoma is the most common paediatric neoplasm of the retina, and one of the earliest model of cancer genetics since the identification of the master tumour suppressor gene RB1. Tumorigenesis has been shown to be driven by pathogenic variants of the RB1 locus, but also genomic and epigenomic alterations outside the locus. The increasing knowledge on this "mutational landscape" is used in current practice for precise genetic testing and counselling. Novel methods provide access to pre-therapeutic tumour DNA, by isolating cell-free DNA from aqueous humour or plasma. This is expected to facilitate assessment of the constitutional status of RB1, to provide an early risk stratification using molecular prognostic markers, to follow the response to the treatment in longitudinal studies, and to predict the response to targeted therapies. The aim of this review is to show how molecular genetics of retinoblastoma drives diagnosis, treatment, monitoring of the disease and surveillance of the patients and relatives. We first recap the current knowledge on retinoblastoma genetics and its use in every-day practice. We then focus on retinoblastoma subgrouping at the era of molecular biology, and the expected input of cell-free DNA in the field.
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9
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Bisht S, Chawla B, Kumar A, Vijayan V, Kumar M, Sharma P, Dada R. Identification of novel genes by targeted exome sequencing in Retinoblastoma. Ophthalmic Genet 2022; 43:771-788. [PMID: 35930312 DOI: 10.1080/13816810.2022.2106497] [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: 01/27/2023]
Abstract
BACKGROUND Retinoblastoma (RB) is initiated by mutation in both alleles of RB1 gene. However, few cases may occur even in the absence of RB1 mutation suggesting the role of genes other than RB1. METHODOLOGY The current study was planned to utilize targeted exome sequencing in Indian RB patients affected with unilateral non-familial RB. 75 unilateral RB patients below 5 years of age were enrolled. Genomic DNA was extracted from blood and tumor tissue. From peripheral blood DNA, all coding and exon/intron regions were amplified using PCR and direct sequencing. Cases which did not harbor pathogenic variants in peripheral blood DNA were further screened for mutations in their tumor tissue DNA using targeted exome sequencing. Three pathogenicity prediction tools (Mutation Taster, SIFT, and PolyPhen-2) were used to determine the pathogenicity of non-synonymous variations. An in-house bioinformatics pipeline was devised for the mutation screening by targeted exome sequencing. Protein modeling studies were also done to predict the effect of the mutations on the protein structure and function. RESULTS Using the mentioned approach, we found two novel variants (g.69673_69674insT and g.48373314C>A) in RB1 gene in peripheral blood DNA. We also found novel variants in eight genes (RB1, ACAD11, GPR151, KCNA1, OTOR, SOX30, ARL11, and MYCT1) that may be associated with RB pathogenesis. CONCLUSION The present study expands our current knowledge regarding the genomic landscape of RB and also highlights the importance of NGS technologies to detect genes and novel variants that may play an important role in cancer initiation, progression, and prognosis.
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Affiliation(s)
- Shilpa Bisht
- Laboratory for Molecular Reproduction and Genetics, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
| | - Bhavna Chawla
- Ocular Oncology Service, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Amit Kumar
- Computational Genomics Centre, Indian Council of Medical Research, New Delhi, India
| | - Viswanathan Vijayan
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Manoj Kumar
- Laboratory for Molecular Reproduction and Genetics, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Rima Dada
- Laboratory for Molecular Reproduction and Genetics, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
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10
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Five novel RB1 gene mutations and genotype-phenotype correlations in Chinese children with retinoblastoma. Int Ophthalmol 2022; 42:3421-3430. [PMID: 35960463 PMCID: PMC9587959 DOI: 10.1007/s10792-022-02341-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/18/2022] [Indexed: 11/22/2022]
Abstract
Purpose To identify the spectrum of RB1 gene mutations in 114 Chinese patients with retinoblastoma. Methods Genomic DNA was extracted from the peripheral blood of 114 Rb patients. Polymerase chain reactions (PCRs) followed by direct Sanger sequencing were used to screen for mutations in the RB1 gene, which contains 26 exons with flanking intronic sequences, except exon 15. Clinical data, including gender, age at diagnosis, laterality of ocular lesions, and associated symptoms, were recorded and compared. Results We identified five novel mutations in the RB1 gene. Twenty-five other mutations found in this study have been previously reported. A higher rate of RB1 mutations, with 47.3% of mutations among bilaterally affected patients vs. 6.8% within unilaterally affected patients, was also observed (p < 0.0001). Bilaterally affected patients were diagnosed earlier when compared to unilaterally affected patients (11 ± 7 months versus 20 ± 14 months, p = 0.0002). Furthermore, nonsense mutations were abundant (n = 14), followed by frameshift mutations (n = 8), splicing site mutations (n = 5), while missense mutations were few (n = 3). Conclusions We found five novel mutations in RB1 genes, which expands the mutational spectrum of the gene. Children with bilateral Rb exhibited higher mutation rates and were diagnosed earlier than those with unilateral Rb. These findings will inform clinical diagnosis and genetic therapeutic targeting in Rb patients. Supplementary Information The online version contains supplementary material available at 10.1007/s10792-022-02341-2.
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11
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Xie Y, Xu XL, Wei WB. The RB1 Mutation Spectrum and Genetic Management Consultation in Pediatric Patients with Retinoblastoma in Beijing, China. Risk Manag Healthc Policy 2021; 14:3453-3463. [PMID: 34456592 PMCID: PMC8387327 DOI: 10.2147/rmhp.s322373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022] Open
Abstract
Objective The present study screened the structural mutations of the retinoblastoma (RB1) gene using gene capture and a preliminary exploration of the correlation between the genotypes and phenotypes. Methods A total of 45 formalin-fixed paraffin-embedded (FFPE) tissue samples and 12 peripheral venous blood samples from patients with retinoblastoma (RB) confirmed by pathological examination at Beijing Tongren Hospital were collected between May 2019 and May 2021. DNA from the samples was extracted, sequenced, and analyzed to detect the mutations in the RB1 gene by designing the targeted capture probes for exons and the flanking sequences of the gene. Results Of the 45 FFPE tissue samples, 23 were from male patients and 22 were from female patients, all aged between 4 months and 10 years, with an average age of 2.5 ± 1.3 years. Two of these patients had bilateral RB and 43 had unilateral RB (23 in the right eye and 20 in the left eye). Of the 12 peripheral venous blood samples, 7 were from male patients and 5 were from female patients, all aged between 8 months and 4 years, with an average age of 1.3 ± 0.9 years. Two of these patients had bilateral RB and 10 had unilateral RB (8 in the right eye and 2 in the left eye). Three de novo pathogenic mutations were found in the FFPE tissues, along with one de novo potentially pathogenic mutation, while three de novo potentially pathogenic mutations were found in the blood samples. Conclusion Gene capture is a low-cost and efficient method for the gene sequencing of RB. A total of seven de novo mutations were identified through mutation testing of the pathogenic gene RB1 in 56 pediatric patients with RB. This complemented the mutation spectrum of the RB1 gene and helped to improve the molecular diagnosis of RB, thereby providing a basis for genetic counseling and prediction of the clinical phenotype, as well as for the genetic testing of the offspring of patients with RB. Clinical Registration Number ChiCTR-EPC-17013892.
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Affiliation(s)
- Ying Xie
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology and Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, People's Republic of China.,Department of Opthalmology, Shanxi Provincial People's Hospital, Taiyuan, 030012, People's Republic of China
| | - Xiao-Lin Xu
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology and Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, People's Republic of China
| | - Wen-Bin Wei
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology and Visual Sciences Key Lab, Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, People's Republic of China
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12
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Gupta H, Malaichamy S, Mallipatna A, Murugan S, Jeyabalan N, Suresh Babu V, Ghosh A, Ghosh A, Santhosh S, Seshagiri S, Ramprasad VL, Kumaramanickavel G. Retinoblastoma genetics screening and clinical management. BMC Med Genomics 2021; 14:188. [PMID: 34294096 PMCID: PMC8296631 DOI: 10.1186/s12920-021-01034-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND India accounts for 20% of the global retinoblastoma (RB) burden. However, the existing data on RB1 gene germline mutations and its influence on clinical decisions is minimally explored. METHODS Fifty children with RB underwent complete clinical examination and appropriate multidisciplinary management. Screening of germline RB1 gene mutations was performed through next-generation sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA) analysis. The mutation and non-mutation groups were compared for clinical parameters especially severity, progression and recurrence. RESULTS Twenty-nine patients had bilateral RB (BLRB) and 21 had unilateral RB (ULRB). The genetic analysis revealed 20 RB1 variations in 29 probands, inclusive of 3 novel mutations, known 16 mutations and heterozygous whole gene deletions. The mutation detection rate (MDR) was 86.2% in BLRB and 19% in ULRB. Associations of disease recurrence (p = 0.021), progression (p = 0.000) and higher percentage of optic nerve invasion, subretinal seeds and high-risk pathological factors were observed in the mutation group. Clinical management was influenced by the presence of germline mutations, particularly while deciding on enucleation, frequency of periodic follow up and radiotherapy. CONCLUSIONS We identified novel RB1 mutations, and our mutation detection rate was on par with the previous global studies. In our study, genetic results influenced clinical management and we suggest that it should be an essential and integral component of RB-care in India and elsewhere.
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Affiliation(s)
| | | | | | | | | | | | - Anuprita Ghosh
- Grow Lab, Narayana Nethralaya Foundation, Bangalore, India
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Kim HA, Yoon YH, Kim JG, Lee JY. Clinical Features and Long-term Prognosis of Retinoblastoma according to Age at Diagnosis. KOREAN JOURNAL OF OPHTHALMOLOGY 2021; 34:242-250. [PMID: 32495533 PMCID: PMC7269736 DOI: 10.3341/kjo.2019.0097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 02/24/2020] [Accepted: 03/11/2020] [Indexed: 12/17/2022] Open
Abstract
PURPOSE We aimed to study the clinical characteristics and long-term prognoses of retinoblastoma according to the age at diagnosis. METHODS A retrospective chart review of non-screened patients newly diagnosed with retinoblastoma between January 2007 and February 2018. RESULTS Among the 20 patients analyzed, 11 were diagnosed at an age younger than 1 year (group 1) and nine at 1 year or older (group 2). The mean lag times until diagnosis were 1.0 ± 0.4 and 5.0 ± 2.1 months for groups 1 and 2, respectively (p = 0.056). The mean follow-up durations were 49.4 ± 12.7 and 58.3 ± 8.8 months, respectively (p = 0.412). Group 1 had a significantly higher proportion of bilateral retinoblastoma than did group 2 (72.7% vs. 11.1%, p = 0.010). Four of five patients (80.0%) with germline RB1 mutations were diagnosed with retinoblastoma at age 3 months or younger. The eyes of patients in group 2 had significantly higher International Intraocular Retinoblastoma Classification stages than did those of patients in group 1 (p for trend = 0.010). The proportion of eyes with optic nerve invasion and those that had undergone enucleation were significantly higher in group 2 (p = 0.033 and 0.046, respectively). Survival did not differ according to the age at diagnosis. CONCLUSIONS Early onset retinoblastoma does not seem to indicate poor ocular or survival prognosis in Korean children with retinoblastoma.
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Affiliation(s)
- Hyun Ah Kim
- Department of Ophthalmology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Young Hee Yoon
- Department of Ophthalmology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - June Gone Kim
- Department of Ophthalmology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Joo Yong Lee
- Department of Ophthalmology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
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14
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Price EA, Patel R, Scheimberg I, Kotiloglu Karaa E, Sagoo MS, Reddy MA, Onadim Z. MYCN amplification levels in primary retinoblastoma tumors analyzed by Multiple Ligation-dependent Probe Amplification. Ophthalmic Genet 2021; 42:604-611. [PMID: 34003079 DOI: 10.1080/13816810.2021.1923038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Background: Retinoblastoma (Rb) is a childhood tumor of the developing retina where predisposition is caused by RB1 pathogenic variants. MYCN amplification (MYCNA) has been implicated in around 2% of sporadic unilateral Rb tumors with no detectable RB1 variants. We audited data from tumors collected between 1993 and 2019 to determine if this is the case for patients treated at Barts Health NHS Trust, and how often it occurred alongside RB1 variants. Materials and methods: Screening for MYCNA was carried out by Multiple Ligation Probe Analysis of tumor and blood samples collected for RB1 genetic screening. The cohort consisted of 149 tumors, of which 114 had matched blood samples. Results: 10/149 (6.7%) tumors were positive for MYCNA in a population containing a disproportionate number of cases negative for RB1 pathogenic variants. Of 65 unbiased tumors collected from 2014 to 2019, 2 (3.1%) had MYCNA. All MYCNA samples were from sporadic, unilateral patients and 3/10 (30%) had RB1 pathogenic variants. MYCNA was not detected in any blood sample. No MYCNA tumor had 6p gain which is usually a common alteration in Rbs. Conclusions: MYCNA occurs in a small fraction of Rbs and can occur in the presence of pathogenic RB1 variants. However, where it occurs alongside RB1 alterations, the age of onset appears to be later. MYCNA has yet to be seen as a heritable change. In sporadic cases with early diagnosis, Rbs with no RB1 pathogenic variant identified should be tested for MYCNA. Conversely, tumors with MYCNA should still be screened for RB1 pathogenic variants.
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Affiliation(s)
- Elizabeth A Price
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, London, UK
| | - Roopal Patel
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, London, UK
| | | | | | - Mandeep S Sagoo
- Retinoblastoma Service, Royal London Hospital, Barts Health NHS Trust, London, UK.,NIHR Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, UK
| | - M Ashwin Reddy
- Retinoblastoma Service, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Zerrin Onadim
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, London, UK
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15
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Schieffer KM, Feldman AZ, Kautto EA, McGrath S, Miller AR, Hernandez-Gonzalez ME, LaHaye S, Miller KE, Koboldt DC, Brennan P, Kelly B, Wetzel A, Agarwal V, Shatara M, Conley S, Rodriguez DP, Abu-Arja R, Shaikhkhalil A, Snuderl M, Orr BA, Finlay JL, Osorio DS, Drapeau AI, Leonard JR, Pierson CR, White P, Magrini V, Mardis ER, Wilson RK, Cottrell CE, Boué DR. Molecular classification of a complex structural rearrangement of the RB1 locus in an infant with sporadic, isolated, intracranial, sellar region retinoblastoma. Acta Neuropathol Commun 2021; 9:61. [PMID: 33827698 PMCID: PMC8025529 DOI: 10.1186/s40478-021-01164-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/19/2021] [Indexed: 12/15/2022] Open
Abstract
Retinoblastoma is a childhood cancer of the retina involving germline or somatic alterations of the RB Transcriptional Corepressor 1 gene, RB1. Rare cases of sellar-suprasellar region retinoblastoma without evidence of ocular or pineal tumors have been described. A nine-month-old male presented with a sellar-suprasellar region mass. Histopathology showed an embryonal tumor with focal Flexner-Wintersteiner-like rosettes and loss of retinoblastoma protein (RB1) expression by immunohistochemistry. DNA array-based methylation profiling confidently classified the tumor as pineoblastoma group A/intracranial retinoblastoma. The patient was subsequently enrolled on an institutional translational cancer research protocol and underwent comprehensive molecular profiling, including paired tumor/normal exome and genome sequencing and RNA-sequencing of the tumor. Additionally, Pacific Biosciences (PacBio) Single Molecule Real Time (SMRT) sequencing was performed from comparator normal and disease-involved tissue to resolve complex structural variations. RNA-sequencing revealed multiple fusions clustered within 13q14.1-q21.3, including a novel in-frame fusion of RB1-SIAH3 predicted to prematurely truncate the RB1 protein. SMRT sequencing revealed a complex structural rearrangement spanning 13q14.11-q31.3, including two somatic structural variants within intron 17 of RB1. These events corresponded to the RB1-SIAH3 fusion and a novel RB1 rearrangement expected to correlate with the complete absence of RB1 protein expression. Comprehensive molecular analysis, including DNA array-based methylation profiling and sequencing-based methodologies, were critical for classification and understanding the complex mechanism of RB1 inactivation in this diagnostically challenging tumor.
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16
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Hülsenbeck I, Frank M, Biewald E, Kanber D, Lohmann DR, Ketteler P. Introduction of a Variant Classification System for Analysis of Genotype-Phenotype Relationships in Heritable Retinoblastoma. Cancers (Basel) 2021; 13:cancers13071605. [PMID: 33807189 PMCID: PMC8037437 DOI: 10.3390/cancers13071605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 11/22/2022] Open
Abstract
Simple Summary Heritable retinoblastoma is a genetic disease that predisposes to develop multiple retinoblastomas in childhood and other extraocular tumors later in life. It is caused by genetic variants in the RB1 gene. Here we present a new classification for genetic variants in the RB1 gene (REC) that focuses on the variant’s effect. The different classes, REC-I to -V, correlate with different risks of tumor predisposition. REC correlated with different clinical courses when applied in our study cohort. REC aims to facilitate risk estimation for physicians, patients and their families, and researchers and to improve the definition of the necessity of screening examination. Abstract Constitutional haploinsufficiency of the RB1 gene causes heritable retinoblastoma, a tumor predisposition syndrome. Patients with heritable retinoblastoma develop multiple retinoblastomas early in childhood and other extraocular tumors later in life. Constitutional pathogenic variants in RB1 are heterogeneous, and a few genotype-phenotype correlations have been described. To identify further genotype-phenotype relationships, we developed the retinoblastoma variant effect classification (REC), which considers each variant’s predicted effects on the common causal mediator, RB1 protein pRB. For validation, the RB1 variants of 287 patients were grouped according to REC. Multiple aspects of phenotypic expression were analyzed, known genotype-phenotype associations were revised, and new relationships were explored. Phenotypic expression of patients with REC-I, -II, and -III was distinct. Remarkably, the phenotype of patients with variants causing residual amounts of truncated pRB (REC-I) was more severe than patients with complete loss of RB1 (REC-II). The age of diagnosis of REC-I variants appeared to be distinct depending on truncation’s localization relative to pRB structure domains. REC classes identify genotype-phenotype relationships and, therefore, this classification framework may serve as a tool to develop tailored tumor screening programs depending on the type of RB1 variant.
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Affiliation(s)
- Isabel Hülsenbeck
- Department of Pediatric Hematology and Oncology, University Duisburg-Essen, University Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany;
- Eye Oncogenetics Research Group, University Hospital Essen, 45122 Essen, Germany; (D.K.); (D.R.L.)
| | - Mirjam Frank
- Institute for Medical Informatics, Biometry and Epidemiology, University Duisburg-Essen, University Hospital Essen, 45122 Essen, Germany;
| | - Eva Biewald
- Department of Ophthalmology, University Duisburg-Essen, University Hospital Essen, 45122 Essen, Germany;
| | - Deniz Kanber
- Eye Oncogenetics Research Group, University Hospital Essen, 45122 Essen, Germany; (D.K.); (D.R.L.)
- Institute of Human Genetics, University Duisburg-Essen, 45122 Essen, Germany
| | - Dietmar R. Lohmann
- Eye Oncogenetics Research Group, University Hospital Essen, 45122 Essen, Germany; (D.K.); (D.R.L.)
- Institute of Human Genetics, University Duisburg-Essen, 45122 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, 69120 Heidelberg, Germany
| | - Petra Ketteler
- Department of Pediatric Hematology and Oncology, University Duisburg-Essen, University Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany;
- Eye Oncogenetics Research Group, University Hospital Essen, 45122 Essen, Germany; (D.K.); (D.R.L.)
- Institute of Human Genetics, University Duisburg-Essen, 45122 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, 69120 Heidelberg, Germany
- Correspondence:
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Gerrish A, Jenkinson H, Cole T. The Impact of Cell-Free DNA Analysis on the Management of Retinoblastoma. Cancers (Basel) 2021; 13:cancers13071570. [PMID: 33805427 PMCID: PMC8037190 DOI: 10.3390/cancers13071570] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Retinoblastoma is a childhood eye cancer, mainly caused by mutations in the RB1 gene, which can be somatic or constitutional. Unlike many other cancers, tumour biopsies are not performed due to the risk of tumour dissemination. As a result, until recently, somatic genetic analysis was only possible if an affected eye was removed as part of a treatment. Several recent proof of principle studies have demonstrated that the analysis of tumour-derived cell-free DNA, either obtained from ocular fluid or blood plasma, has the potential to advance the diagnosis and influence the prognosis of retinoblastoma patients. It has been shown that a confirmed diagnosis is possible in retinoblastoma patients undergoing conservative treatment. In vivo genetic analysis of retinoblastoma tumours is also now possible, allowing the potential identification of secondary genetic events as prognostic biomarkers. In addition, noninvasive prenatal diagnosis in children at risk of inheriting retinoblastoma has been developed. Here, we review the current literature and discuss the potential impact of cell-free DNA analysis on both the diagnosis and treatment of retinoblastoma patients and their families.
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Affiliation(s)
- Amy Gerrish
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK;
- Correspondence:
| | - Helen Jenkinson
- Department of Paediatric Oncology, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK;
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK;
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Davies HR, Broad KD, Onadim Z, Price EA, Zou X, Sheriff I, Karaa EK, Scheimberg I, Reddy MA, Sagoo MS, Ohnuma SI, Nik-Zainal S. Whole-Genome Sequencing of Retinoblastoma Reveals the Diversity of Rearrangements Disrupting RB1 and Uncovers a Treatment-Related Mutational Signature. Cancers (Basel) 2021; 13:754. [PMID: 33670346 PMCID: PMC7918943 DOI: 10.3390/cancers13040754] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/02/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
The development of retinoblastoma is thought to require pathological genetic changes in both alleles of the RB1 gene. However, cases exist where RB1 mutations are undetectable, suggesting alternative pathways to malignancy. We used whole-genome sequencing (WGS) and transcriptomics to investigate the landscape of sporadic retinoblastomas derived from twenty patients, sought RB1 and other driver mutations and investigated mutational signatures. At least one RB1 mutation was identified in all retinoblastomas, including new mutations in addition to those previously identified by clinical screening. Ten tumours carried structural rearrangements involving RB1 ranging from relatively simple to extremely complex rearrangement patterns, including a chromothripsis-like pattern in one tumour. Bilateral tumours obtained from one patient harboured conserved germline but divergent somatic RB1 mutations, indicating independent evolution. Mutational signature analysis showed predominance of signatures associated with cell division, an absence of ultraviolet-related DNA damage and a profound platinum-related mutational signature in a chemotherapy-exposed tumour. Most RB1 mutations are identifiable by clinical screening. However, the increased resolution and ability to detect otherwise elusive rearrangements by WGS have important repercussions on clinical management and advice on recurrence risks.
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Affiliation(s)
- Helen R. Davies
- Academic Department of Medical Genetics, University of Cambridge, Addenbrooke’s Treatment Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (H.R.D.); (X.Z.)
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Kevin D. Broad
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
| | - Zerrin Onadim
- Retinoblastoma Genetic Screening Unit, The Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (Z.O.); (E.A.P.)
| | - Elizabeth A. Price
- Retinoblastoma Genetic Screening Unit, The Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (Z.O.); (E.A.P.)
| | - Xueqing Zou
- Academic Department of Medical Genetics, University of Cambridge, Addenbrooke’s Treatment Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (H.R.D.); (X.Z.)
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Ibrahim Sheriff
- Retinoblastoma Service, Royal London Hospital, Barts Health Trust, London E1 1FR, UK; (I.S.); (M.A.R.)
| | - Esin Kotiloğlu Karaa
- Pathology Department, Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (E.K.K.); (I.S.)
| | - Irene Scheimberg
- Pathology Department, Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (E.K.K.); (I.S.)
| | - M. Ashwin Reddy
- Retinoblastoma Service, Royal London Hospital, Barts Health Trust, London E1 1FR, UK; (I.S.); (M.A.R.)
- NIHR Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital, Institute of Ophthalmology, University College London, London EC1V 2PD, UK
| | - Mandeep S. Sagoo
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
- Retinoblastoma Service, Royal London Hospital, Barts Health Trust, London E1 1FR, UK; (I.S.); (M.A.R.)
- NIHR Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital, Institute of Ophthalmology, University College London, London EC1V 2PD, UK
| | - Shin-ichi Ohnuma
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, University of Cambridge, Addenbrooke’s Treatment Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (H.R.D.); (X.Z.)
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XZ, UK
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Chai P, Luo Y, Yu J, Li Y, Yang J, Zhuang A, Fan J, Han M, Jia R. Clinical characteristics and germline mutation spectrum of RB1 in Chinese patients with retinoblastoma: A dual-center study of 145 patients. Exp Eye Res 2021; 205:108456. [PMID: 33493472 DOI: 10.1016/j.exer.2021.108456] [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: 06/28/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 02/06/2023]
Abstract
Retinoblastoma (Rb) is the most common primary intraocular childhood malignancy and one of the main causes of blindness in children. In China, most tumors are diagnosed at an advanced stage and have relatively poor outcomes compared to developed countries. Here, we aimed to update the clinical manifestations and RB transcriptional corepressor 1 (RB1) mutation spectrum in Chinese Rb patients. Medical charts of 184 eyes in 145 Chinese Rb patients belonging to unrelated families were reviewed. Genomic DNA was isolated from peripheral blood of the patients and their parents. Mutation analysis of whole coding regions, promoter regions and flanking splice sites in the RB1 gene was performed. In addition, multiplex ligation-dependent probe amplification (MLPA) was done to detect gross aberrations. Germline RB1 mutations were observed in 37.2% (54/145) of Rb patients. RB1-mutated patients presented with earlier age of diagnosis (p = 0.019), with a significantly larger proportion of bilateral cases (p = <0.001) and secondary malignancies (p = 0.027) relative to those without RB1 mutations. For ocular clinical presentations, RB1-mutated retinoblastomas presented with a larger proportion of ectropion uveae (p = 0.017) and iris neovascularization (p = 0.001). These RB1 mutations comprised of 13 (24.1%) nonsense mutation, 13 (24.1%) splicing mutations, 11 (20.4%) frameshift deletions, 11 (20.4%) gross mutations, 3 (5.6%) missense mutations, 2 (3.7%) promoter mutations and 1 (1.9%) non-frameshift deletion. In addition, 8 novel RB1 mutations were identified. These germline RB1 mutations were not related to age at diagnosis or laterality. Here, we provide a comprehensive spectrum of RB1 germline mutations in Chinese Rb patients and describe correlations between RB1 mutations and clinical presentations. Our study also provides new evidence that will inform management and genetic counselling of Rb patients and families.
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Affiliation(s)
- Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Yingxiu Luo
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jie Yu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Yongyun Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jie Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Ai Zhuang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jiayan Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Minglei Han
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China; Department of Ophthalmology, Qilu Children's Hospital of Shandong University, Shandong, China.
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
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20
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Salviat F, Gauthier-Villars M, Carton M, Cassoux N, Lumbroso-Le Rouic L, Dehainault C, Levy C, Golmard L, Aerts I, Doz F, Bonnet-Serrano F, Hayek S, Savignoni A, Stoppa-Lyonnet D, Houdayer C. Association Between Genotype and Phenotype in Consecutive Unrelated Individuals With Retinoblastoma. JAMA Ophthalmol 2021; 138:843-850. [PMID: 32556071 DOI: 10.1001/jamaophthalmol.2020.2100] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Importance Retinoblastoma (RB) is the most common pediatric intraocular neoplasm. RB is a complex model in which atypical pathogenic variants, modifier genes, imprinting, and mosaicism are known to be associated with the phenotype. In-depth understanding of RB therefore requires large genotype-phenotype studies. Objective To assess the association between genotype and phenotype in patients with RB. Design, Setting, and Participants This single-center, retrospective cohort study, conducted from January 1, 2000, to September 30, 2017, enrolled 1404 consecutive ascertained patients with RB who consulted an oncogeneticist. All patients had their genotype and phenotype recorded. Statistical analysis was performed from July 1, 2018, to December 31, 2018. Main Outcomes and Measures RB1 germline and somatic pathogenic variant types, family history, and disease presentation characteristics (ie, age at diagnosis, sex, laterality, and International Intraocular Retinoblastoma Classification group). Results Among 1404 patients with RB (734 [52.3%] female; mean [SD] age, 20.2 [21.2] months), 866 cases (61.7%) were unilateral and 538 cases (38.3%) were bilateral. Loss of function variants were found throughout the coding sequence, with 259 of 272 (95.2%) somatic pathogenic variants and 537 of 606 (88.6%) germline pathogenic variants (difference, 6.6%; 95% CI, 4.0%-9.2%; P < .001) after excluding tumor-specific pathogenic variants (ie, promoter methylation and loss of heterozygosity); a novel low-penetrance region was identified in exon 24. Compared with germline pathogenic variants estimated to retain RB protein expression, germline pathogenic variants estimated to abrogate RB protein expression were associated with an earlier mean (SD) age at diagnosis (12.3 [11.3] months among 457 patients vs 16.3 [13.2] months among 55 patients; difference, 4 months; 95% CI, 1.9-6.1 months; P = .01), more frequent bilateral involvement (84.2% among 452 patients vs 65.2% among 45 patients; difference, 18.9%; 95% CI, 14.5%-23.3%; P < .001), and more advanced International Intraocular Retinoblastoma Classification group (85.3% among 339 patients vs 73.9% among 34 patients; difference: 11.4%; 95% CI, 6.5%-16.3%; P = .047). Among the 765 nongermline carriers of an RB1 pathogenic variant, most were female (419 females [54.8%] vs 346 males [45.2%]; P = .008), and males were more likely to have bilateral RB (23 males [71.4%] vs 12 females [34.3%]; P = .01). Conclusions and Relevance These results suggest that RB risk is associated with the germline pathogenic variant and with maintenance of RB protein and that there is a sex-linked mechanism for nongermline carriers.
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Affiliation(s)
- Flore Salviat
- Department of Biostatistics, Institut Curie, PSL Research University, Saint-Cloud, France
| | - Marion Gauthier-Villars
- Department of Genetics, Institut Curie, PSL Research University, Department of Genetics, Paris, France
| | - Matthieu Carton
- Department of Biostatistics, Institut Curie, PSL Research University, Saint-Cloud, France
| | - Nathalie Cassoux
- Faculty of Medicine Paris-Descartes, Paris University, Paris, France.,Service of Ophthalmology, Department of Surgical Oncology, Institut Curie, Paris, France
| | | | - Catherine Dehainault
- Department of Genetics, Institut Curie, PSL Research University, Department of Genetics, Paris, France
| | - Christine Levy
- Service of Ophthalmology, Department of Surgical Oncology, Institut Curie, Paris, France
| | - Lisa Golmard
- Department of Genetics, Institut Curie, PSL Research University, Department of Genetics, Paris, France
| | - Isabelle Aerts
- Oncology Center, Soins, Innovation, Recherche en Oncologie de l'Enfant, l'Adolescent et du Jeune Adulte, Institut Curie, Paris, France
| | - François Doz
- Faculty of Medicine Paris-Descartes, Paris University, Paris, France.,Oncology Center, Soins, Innovation, Recherche en Oncologie de l'Enfant, l'Adolescent et du Jeune Adulte, Institut Curie, Paris, France
| | - Fidéline Bonnet-Serrano
- Department of Genetics, Institut Curie, PSL Research University, Department of Genetics, Paris, France
| | - Stéphanie Hayek
- Department of Genetics, Institut Curie, PSL Research University, Department of Genetics, Paris, France
| | - Alexia Savignoni
- Department of Biostatistics, Institut Curie, PSL Research University, Saint-Cloud, France
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, PSL Research University, Department of Genetics, Paris, France.,Faculty of Medicine Paris-Descartes, Paris University, Paris, France.,Research Center Institut National de la Santé et de la Recherche Médicale, Unit U830, Institut Curie, Paris, France
| | - Claude Houdayer
- Department of Genetics, Institut Curie, PSL Research University, Department of Genetics, Paris, France.,Department of Genetics, Rouen University Hospital, Rouen, France.,University of Rouen Normandy, UNIROUEN, Mont-Saint-Aignan, France.,Institut National de la Santé et de la Recherche Médicale U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, France
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21
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Reddy MA, Butt M, Hinds AM, Duncan C, Price EA, Sagoo MS, Onadim Z. Prognostic Information for Known Genetic Carriers of RB1 Pathogenic Variants (Germline and Mosaic). Ophthalmol Retina 2020; 5:381-387. [PMID: 32835838 DOI: 10.1016/j.oret.2020.08.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 11/28/2022]
Abstract
PURPOSE To compare the number of tumors per eye for mosaic carriers of RB1 pathogenic variants with full germline variants and the conversion from unilateral to bilateral disease. DESIGN Retrospective cohort study comparing patients with retinoblastoma and different genetic subtypes: high penetrance (HP), low penetrance (LP), and mosaicism. PARTICIPANTS Data were analyzed between 1992 and 2018 at the Retinoblastoma Unit, Royal London Hospital, London, United Kingdom. All familial patients had a parent with a known pathogenic variant even if the parent did not manifest the disease. MAIN OUTCOME MEASURES Number of tumors per eye in children who developed retinoblastoma in that eye. Other outcomes included total number of tumors per patient, age at diagnosis, laterality at presentation and later, sex, and stage according to International Intraocular Retinoblastoma Classification. RESULTS A total of 111 patients were included: 64 full germline, familial patients (53 HP and 11 LP) and 47 mosaic patients. Twelve HP patients (23%) were unilateral, and 8 of 12 patients (67%) developed tumors in their previously unaffected eye. A total of 34 mosaic patients (72%) were unilateral, and only 2 (6%) developed tumors in their unaffected eye. Age at diagnosis was higher in mosaic patients (median, 22 months) than in HP patients (median 7) (P < 0.00002). The number of tumors per eye was fewer in patients with mosaic alleles (median, 1.0; range, 1-6) compared with patients with HP alleles (median, 3.0; range, 1-8) (P < 0.0003). All 3 children (4 eyes) with mosaicism and more than 2 tumors per eye had high levels of mosaicism. CONCLUSIONS Children with mosaic alleles have fewer tumors per eye compared with those with known high-penetrant pathogenic variants and are more likely to remain unilateral. The level of mosaicism has an impact on laterality and number of tumors.
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Affiliation(s)
- M Ashwin Reddy
- Retinoblastoma Service, Royal London Hospital, London, United Kingdom; NIHR Biomedical Research Centre for Ophthalmology at Moorfields Eye Hospital and University College London, Institute of Ophthalmology, London, United Kingdom.
| | - Mussa Butt
- Retinoblastoma Service, Royal London Hospital, London, United Kingdom
| | - Anne-Marie Hinds
- Retinoblastoma Service, Royal London Hospital, London, United Kingdom
| | - Catriona Duncan
- Retinoblastoma Service, Royal London Hospital, London, United Kingdom; Paediatric Oncology Department, Great Ormond Street Hospital, London, United Kingdom
| | - Elizabeth A Price
- Retinoblastoma Genetic Screening Unit, Royal London Hospital, London, United Kingdom
| | - Mandeep S Sagoo
- Retinoblastoma Service, Royal London Hospital, London, United Kingdom; NIHR Biomedical Research Centre for Ophthalmology at Moorfields Eye Hospital and University College London, Institute of Ophthalmology, London, United Kingdom
| | - Zerrin Onadim
- Retinoblastoma Genetic Screening Unit, Royal London Hospital, London, United Kingdom
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22
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Kothari P, Marass F, Yang JL, Stewart CM, Stephens D, Patel J, Hasan M, Jing X, Meng F, Enriquez J, Huberman K, Viale A, Francis JH, Berger MF, Shukla N, Abramson DH, Dunkel IJ, Tsui DW. Cell‐free DNA profiling in retinoblastoma patients with advanced intraocular disease: An MSKCC experience. Cancer Med 2020; 9:6093-6101. [PMID: 32633890 PMCID: PMC7476838 DOI: 10.1002/cam4.3144] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 04/20/2020] [Accepted: 05/04/2020] [Indexed: 12/26/2022] Open
Abstract
Purpose The enucleation rate for retinoblastoma has dropped from over 95% to under 10% in the past 10 years as a result of improvements in therapy. This reduces access to tumor tissue for molecular profiling, especially in unilateral retinoblastoma, and hinders the confirmation of somatic RB1 mutations necessary for genetic counseling. Plasma cell‐free DNA (cfDNA) has provided a platform for noninvasive molecular profiling in cancer, but its applicability in low tumor burden retinoblastoma has not been shown. We analyzed cfDNA collected from 10 patients with available tumor tissue to determine whether sufficient tumorderived cfDNA is shed in plasma from retinoblastoma tumors to enable noninvasive RB1 mutation detection. Methods Tumor tissue was collected from eye enucleations in 10 patients diagnosed with advanced intra‐ocular unilateral retinoblastoma, three of which went on to develop metastatic disease. Tumor RB1 mutation status was determined using an FDA‐cleared tumor sequencing assay, MSK‐IMPACT. Plasma samples were collected before eye enucleation and analyzed with a customized panel targeting all exons of RB1. Results Tumor‐guided genotyping detected 10 of the 13 expected somatic RB1 mutations in plasma cfDNA in 8 of 10 patients (average variant allele frequency 3.78%). Without referring to RB1 status in the tumor, de novo mutation calling identified 7 of the 13 expected RB1 mutations (in 6 of 10 patients) with high confidence. Conclusion Plasma cfDNA can detect somatic RB1 mutations in patients with unilateral retinoblastoma. Since intraocular biopsies are avoided in these patients because of concern about spreading tumor, cfDNA can potentially offer a noninvasive platform to guide clinical decisions about treatment, follow‐up schemes, and risk of metastasis.
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Affiliation(s)
| | - Francesco Marass
- ETH Zurich Basel Switzerland
- SIB Swiss Institute of Bioinformatics Basel Switzerland
| | - Julie L. Yang
- Memorial Sloan Kettering Cancer Center New York NY USA
| | | | | | - Juber Patel
- Memorial Sloan Kettering Cancer Center New York NY USA
| | - Maysun Hasan
- Memorial Sloan Kettering Cancer Center New York NY USA
| | - Xiaohong Jing
- Memorial Sloan Kettering Cancer Center New York NY USA
| | - Fanli Meng
- Memorial Sloan Kettering Cancer Center New York NY USA
| | | | - Kety Huberman
- Memorial Sloan Kettering Cancer Center New York NY USA
| | - Agnes Viale
- Memorial Sloan Kettering Cancer Center New York NY USA
| | - Jasmine H. Francis
- Memorial Sloan Kettering Cancer Center New York NY USA
- Weill Cornell Medical College NY USA
| | - Michael F. Berger
- Memorial Sloan Kettering Cancer Center New York NY USA
- Weill Cornell Medical College NY USA
| | - Neerav Shukla
- Memorial Sloan Kettering Cancer Center New York NY USA
| | - David H. Abramson
- Memorial Sloan Kettering Cancer Center New York NY USA
- Weill Cornell Medical College NY USA
| | - Ira J. Dunkel
- Memorial Sloan Kettering Cancer Center New York NY USA
- Weill Cornell Medical College NY USA
| | - Dana W.Y. Tsui
- Memorial Sloan Kettering Cancer Center New York NY USA
- Weill Cornell Medical College NY USA
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23
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Lan X, Xu W, Tang X, Ye H, Song X, Lin L, Ren X, Yu G, Zhang H, Wu S. Spectrum of RB1 Germline Mutations and Clinical Features in Unrelated Chinese Patients With Retinoblastoma. Front Genet 2020; 11:142. [PMID: 32218800 PMCID: PMC7080181 DOI: 10.3389/fgene.2020.00142] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/06/2020] [Indexed: 11/13/2022] Open
Abstract
Retinoblastoma (Rb) is a primary intraocular malignant tumor that occurs primarily in children, and results from loss-of-function mutations in the RB transcriptional corepressor 1 (RB1) gene. Genetic testing forms the basis of genetic counseling for affected families, as well as for clinical management of this disease. The aim of this study was to identify germline RB1 mutations and correlate the identified mutations with the clinical features of Rb patients. Genomic DNA was isolated from peripheral blood of 180 unrelated Rb patients and their parents (118 unilaterally and 62 bilaterally affected probands). Mutations in the RB1 gene, including the promoter region and exons 1-27 with flanking intronic sequences, were identified by Sanger sequencing. The samples with negative sequencing results were further subjected to methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) to detect gross deletions or duplications. Sixty-three distinct mutations were identified in 75 of the 180 (41.7%) probands. Of the 75 patients carrying RB1 mutations, 56 developed bilateral Rb, while 19 developed unilateral Rb. The total detection rates for bilateral and unilateral Rb were 90.3% (56/62) and 16.1% (19/118), respectively. Among the 75 patients, the spectrum of mutation types comprised 29.3% (22/75) nonsense mutations, 22.7% (17/75) splicing mutations, 17.3% (13/75) small insertions/deletions, 16.0% (12/75) large deletions/duplications, and 13.3% (10/75) missense mutations, while only 1% (1/75) of the mutations were in the promoter region of the RB1 gene. Age at diagnosis was significantly different (p < 0.01) between patients with positive and negative test results for germline RB1 mutations. A c.2359C > T mutation (p.R787X) was identified in identical twins, but one child was affected bilaterally and the other unilaterally. Of the five patients with deletion of the entire RB1 gene, the deletion of two patients was inherited from unaffected parents. In conclusion, in this study, we provide a comprehensive spectrum of RB1 germline mutations in Chinese Rb patients, and describe the correlations among RB1 mutations, age at diagnosis, and laterality; moreover, we report that the clinical features of individuals carrying an identical mutation in the RB1 gene were highly variable, indicating that the pathogenesis of Rb is more complicated than currently believed.
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Affiliation(s)
- Xiaoping Lan
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wuhen Xu
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaojun Tang
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Haiyun Ye
- Department of Ophthalmology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaozhen Song
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Longlong Lin
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Ren
- Department of Radiology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Guangjun Yu
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Shengnan Wu
- Molecular Diagnostic Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
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24
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Monteagudo-Sánchez A, Garin I, de Nanclares GP, Monk D. The Use of Methylation-Sensitive Multiplex Ligation-Dependent Probe Amplification for Quantification of Imprinted Methylation. Methods Mol Biol 2019; 1766:109-121. [PMID: 29605849 DOI: 10.1007/978-1-4939-7768-0_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Imprinting disorders are a group of congenital diseases that can result from multiple mechanisms affecting imprinted gene dosage including cytogenetic aberration and epigenetic anomalies. Quantification of CpG methylation and correct copy-number calling is required for molecular diagnosis. Methylation-sensitive multiplex ligation-dependent probe amplification (MS-MLPA) is a multiplex method that accurately measures both parameters in a single assay. This technique relies upon the ligation of MLPA probe oligonucleotides and digestion of the genomic DNA-probe hybrid complexes with the Hha1 methylation-sensitive restriction endonuclease prior to fluorescent PCR amplification with a single primer pair. Since each targeted probe contains stuffer sequence of varying length, each interrogated position is visualized as an amplicon of different size upon capillary electrophoresis.
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Affiliation(s)
- Ana Monteagudo-Sánchez
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), Hospital Duran and Reynals, Barcelona, Spain
| | - Intza Garin
- Molecular (Epi)Genetics Laboratory, BioAraba National Health Institute, OSI Araba-Txagorritxu, Vitoria-Gasteiz, Spain
| | - Guiomar Perez de Nanclares
- Molecular (Epi)Genetics Laboratory, BioAraba National Health Institute, OSI Araba-Txagorritxu, Vitoria-Gasteiz, Spain
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), Hospital Duran and Reynals, Barcelona, Spain.
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25
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Fabian ID, Shah V, Kapelushnik N, Naeem Z, Onadim Z, Price E, Chowdhury T, Duncan C, Stansfield D, Sagoo M, Reddy MA. Examinations under anaesthesia as a measure of disease burden in unilateral retinoblastoma: the London experience. Br J Ophthalmol 2019; 104:17-22. [PMID: 30862620 DOI: 10.1136/bjophthalmol-2018-313556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/19/2019] [Accepted: 02/23/2019] [Indexed: 11/03/2022]
Abstract
BACKGROUND Early diagnosis strategies and advances in retinoblastoma (Rb) management have resulted in nearly 100% survival. More attention should, therefore, be given to quality of life considerations. We aimed to quantify the number of examinations under anaesthesia (EUAs) in a cohort of patients with Rb, as a measure of disease burden. METHODS A retrospective analysis of patients with unilateral Rb that presented to the London Rb service from 2006 to 2013, were treated and had long-term follow-up. Correlations of clinical variables to number of EUAs were investigated. RESULTS A total of 107 patients with Rb were included that presented at a mean age of 26.51 ± 22.68 months. The International Intraocular Retinoblastoma Classification (IIRC) was group B in 5 (5%), C in 13 (12%), D in 48 (45%) and E in 41 (38%) of the cases. Primary treatment was intravenous chemotherapy in 36 (34%) and enucleation in 71 (66%) of the cases. Mean number of EUAs was 20.67 ± 6.62, 12.52 ± 6.23 and 11.15 ± 6.91 for combined groups B/C, group D and group E patients (p < 0.001), respectively. On analysis, early age atpresentation and conservative treatments were found to significantly correlate with increased number of EUAs (p < 0.001). Mean follow-up time was 74.42 ± 25.16 months and no metastasis or death were reported. CONCLUSION Families should be counselled regarding the number of EUAs associated with the patient's IIRC group, with B/C eyes undergoing twice the number as compared with D/E eyes. For group D cases, where both enucleation and conservative therapy are valid options, treatment choice has a significant impact on the number of EUAs.
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Affiliation(s)
- Ido Didi Fabian
- Moorfields Eye Hospital, London, UK .,Retinoblastoma Service, Royal London Hospital, London, UK.,Ocular Oncology Service, Goldschleger Eye Institute, Sheba Medical Center,Tel-Aviv University, Tel Aviv, Israel
| | | | - Noa Kapelushnik
- Ocular Oncology Service, Goldschleger Eye Institute, Sheba Medical Center,Tel-Aviv University, Tel Aviv, Israel
| | - Zishan Naeem
- Retinoblastoma Service, Royal London Hospital, London, UK
| | - Zerrin Onadim
- Retinoblastoma Service, Royal London Hospital, London, UK
| | | | - Tanzina Chowdhury
- Retinoblastoma Service, Royal London Hospital, London, UK.,Paediatric Oncology Department, Great Ormond Street Hospital, London, UK
| | - Catriona Duncan
- Retinoblastoma Service, Royal London Hospital, London, UK.,Paediatric Oncology Department, Great Ormond Street Hospital, London, UK
| | | | - Mandeep Sagoo
- Retinoblastoma Service, Royal London Hospital, London, UK.,NIHR Biomedical Research Centre for Ophthalmology at University CollegeLondon, Institute of Ophthalmology and Moorfields Eye Hospital, London, UK
| | - Maddy Ashwin Reddy
- Moorfields Eye Hospital, London, UK.,Retinoblastoma Service, Royal London Hospital, London, UK
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26
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Tsakogiannis D, Moschonas GD, Daskou M, Stylianidou Z, Kyriakopoulou Z, Kottaridi C, Dimitriou TG, Gartzonika C, Markoulatos P. Polymorphic variability in the exon 19 of the RB1 gene and its flanking intronic sequences in HPV16-associated precancerous lesions in the Greek population. J Med Microbiol 2018; 67:1638-1644. [PMID: 30303478 DOI: 10.1099/jmm.0.000843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
PURPOSE The tumour suppressor protein RB plays a decisive role in negative control of the cell cycle, inhibiting tumour development. The present analysis investigated the prevalence of the nucleotide polymorphism A153104G, which is located at intron 18 of the RB1 gene, and investigated the impact of the polymorphic variability in the exon 19 and its flanking intronic sequences on the severity of cervical disease in HPV16-positive Greek women. METHODOLOGY The nucleotide polymorphism A153104G was detected by PCR-RFLP assay, while the amplicons were further subjected to cloning and sequencing. Moreover, molecular evolutionary analysis was performed using the maximum-likelihood (ML) and empirical Bayesian (EB) methods in order to evaluate the selective pressure acting on exon 19 of the RB1 gene.Results/Key findings. The A153104G nucleotide polymorphism was only detected in one control case. Moreover, sequence analysis of the amplicons revealed that the polymorphic variability in the RB1 gene increased with the severity of the cervical dysplasia. The link between the observed polymorphic variability and the progress of cervical disease was reflected in the molecular evolutionary analysis that was performed on the exon 19 of the RB1 gene, since negative selective pressure was acting upon exon 19 in the control and low-grade squamous intraepithelial lesion (LSIL) cervical samples, while positive selective pressure was acting upon exon 19 in the high-grade squamous intraepithelial lesion (HSIL) specimens. CONCLUSIONS The A153104G nucleotide polymorphism did not emerge as a potential biomarker for the development of precancerous lesions in the Greek patients, while the accumulation of sequence variations in RB1 gene might influence patients' susceptibility towards the progression of cervical neoplasia.
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Affiliation(s)
- D Tsakogiannis
- 1Microbiology-Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - G D Moschonas
- 1Microbiology-Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - M Daskou
- 1Microbiology-Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Z Stylianidou
- 1Microbiology-Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Z Kyriakopoulou
- 1Microbiology-Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - C Kottaridi
- 2Department of Cytopathology, National and Kapodistrian University of Athens, Medical School, 'ATTIKON' University Hospital, 1 Rimini, Haidari, 12462, Athens, Greece
| | - T G Dimitriou
- 1Microbiology-Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - C Gartzonika
- 3Department of Microbiology, University of Ioannina, Medical School, Ioannina, Greece
| | - P Markoulatos
- 1Microbiology-Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500 Larissa, Greece
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27
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Abstract
Osteosarcoma (OS) is the most common primary bone tumor affecting predominantly adolescents and young adults. It accounts for about 5% of all childhood cancers. Although the majority of OSs are sporadic, a small percentage occur as a component of hereditary cancer syndromes. Early onset, bilateral, multifocal, and metachronous tumors suggest genetic predisposition. The inheritance patterns can be autosomal dominant or recessive. These syndromes predispose to a wide variety of mesenchymal and epithelial cancers with propensity for certain mutations being prevalent in specific cancer subtypes. Li-Fraumeni syndrome, retinoblastoma, Rothmund-Thompson syndrome (type 2), Werner syndrome, and Bloom syndrome, constitute the majority of the tumor syndromes predisposing to OS and will be the focus for this review.
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Price EA, Kolkiewicz K, Patel R, Hashim S, Karaa E, Scheimberg I, Sagoo MS, Reddy MA, Onadim Z. Detection and reporting of RB1 promoter hypermethylation in diagnostic screening. Ophthalmic Genet 2018; 39:526-531. [PMID: 29851531 DOI: 10.1080/13816810.2018.1479432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
BACKGROUND RB1 gene screening aids clinical management and genetic counselling in retinoblastoma families. Here we present epigenetic changes identified during routine molecular RB1 screening of tumor and blood samples. Complications in interpreting RB1 methylation are discussed. MATERIALS AND METHODS Screening for RB1 promoter hypermethylation was carried out by Methylation Specific PCR (MS-PCR) after bisulphite modification of DNA. The cohort consisted of 315 tumors, and 204 blood samples, from 497 retinoblastoma patients (22 patients had both blood and tumor screened). RESULTS 11.4% of retinoblastoma tumors had promoter hypermethylation. It was not routinely detected in blood samples, or in tumors with two other oncogenic RB1 changes. One blood sample had promoter hypermethylation due to an X;13 translocation. One tumor had low level methylation as well as two other oncogenic changes. Histopathological analysis of a small subset of age-matched tumors was similar regardless of promoter hypermethylation status. CONCLUSIONS Promoter hypermethylation was detected in 11.4% of the retinoblastoma tumors and should be tested for in routine RB1 screening programmes. Constitutional samples are not expected to display RB1 hypermethylation. In a small proportion of cases it may not be possible to use this somatic change in patient management.
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Affiliation(s)
- Elizabeth A Price
- a Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust , London , UK
| | - Kelly Kolkiewicz
- a Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust , London , UK
| | - Roopal Patel
- a Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust , London , UK
| | - Sugera Hashim
- a Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust , London , UK.,b Kennedy Galton Centre , London North West Healthcare NHS Trust , UK
| | - Esin Karaa
- c Department of Pathology , Barts Health NHS Trust , London , UK
| | - Irene Scheimberg
- c Department of Pathology , Barts Health NHS Trust , London , UK
| | - Mandeep S Sagoo
- d Retinoblastoma Service, Royal London Hospital, Barts Health NHS Trust , London , UK.,e NIHR Biomedical Research Centre for Ophthalmology , Moorfields Eye Hospital and University College London Institute of Ophthalmology , London , UK
| | - M Ashwin Reddy
- d Retinoblastoma Service, Royal London Hospital, Barts Health NHS Trust , London , UK
| | - Zerrin Onadim
- a Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust , London , UK
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29
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Imperatore V, Pinto AM, Gelli E, Trevisson E, Morbidoni V, Frullanti E, Hadjistilianou T, De Francesco S, Toti P, Gusson E, Roversi G, Accogli A, Capra V, Mencarelli MA, Renieri A, Ariani F. Parent-of-origin effect of hypomorphic pathogenic variants and somatic mosaicism impact on phenotypic expression of retinoblastoma. Eur J Hum Genet 2018; 26:1026-1037. [PMID: 29662154 DOI: 10.1038/s41431-017-0054-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/27/2017] [Accepted: 11/23/2017] [Indexed: 11/09/2022] Open
Abstract
Retinoblastoma is the most common eye cancer in children. Numerous families have been described displaying reduced penetrance and expressivity. An extensive molecular characterization of seven families led us to characterize the two main mechanisms impacting on phenotypic expression, as follows: (i) mosaicism of amorphic pathogenic variants; and (ii) parent-of-origin-effect of hypomorphic pathogenic variants. Somatic mosaicism for RB1 splicing variants (c.1960+5G>C and c.2106+2T>C), leading to a complete loss of function was demonstrated by high-depth NGS in two families. In both cases, the healthy carrier parent (one with retinoma) showed a variant frequency lower than that expected for a heterozygous individual, indicating a 56-60% mosaicism level. Previous evidences of a ~3-fold excess of RB1 maternal canonical transcript led us to hypothesize that this differential allelic expression could influence phenotypic outcome in families at risk for RB onset. Accordingly, in five families, we identified a higher tumor risk associated with paternally inherited hypomorphic pathogenic variants, namely a deletion resulting in the loss of 37 amino acids at the N-terminus (c.608-16_608del), an exonic substitution with a "leaky" splicing effect (c.1331A>G), a partially deleterious substitution (c.1981C>T) and a truncating C-terminal variant (c.2663+2T>C). The identification of these mechanisms changes the genetic/prenatal counseling and the clinical management of families, indicating a higher recurrence risk when the hypomorphic pathogenic variant is inherited from the father, and suggesting the need for second tumor surveillance in unaffected carriers at risk of developing adult-onset cancer such as osteosarcoma or leiomyosarcoma.
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Affiliation(s)
| | - Anna Maria Pinto
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Elisa Gelli
- Medical Genetics, University of Siena, Siena, Italy
| | - Eva Trevisson
- Department of Woman and Child Health, University of Padova Istituto di Ricerca Pediatrica, IRP, Città della Speranza, Padova, Italy.,Istituto di Ricerca Pediatrica, IRP, Città della Speranza, Padova, Italy
| | - Valeria Morbidoni
- Department of Woman and Child Health, University of Padova Istituto di Ricerca Pediatrica, IRP, Città della Speranza, Padova, Italy.,Istituto di Ricerca Pediatrica, IRP, Città della Speranza, Padova, Italy
| | | | - Theodora Hadjistilianou
- Unit of Ophthalmology and Retinoblastoma Referral Center, Department of Surgery, University of Siena, Policlinico 'Santa Maria alle Scotte', Siena, Italy
| | - Sonia De Francesco
- Unit of Ophthalmology and Retinoblastoma Referral Center, Department of Surgery, University of Siena, Policlinico 'Santa Maria alle Scotte', Siena, Italy
| | - Paolo Toti
- Department of Medical Biotechnology, Section of Pathology, University of Siena, Policlinico 'Santa Maria alle Scotte', Siena, Italy
| | - Elena Gusson
- Unit of Ophthalmology, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Gaia Roversi
- Department of Medicine and Surgery, University Milan-Bicocca; Ospedale San Gerardo, ASST Monza, Monza, Italy
| | | | | | - Maria Antonietta Mencarelli
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy. .,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy.
| | - Francesca Ariani
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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30
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31
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The management of retinoblastoma. Oncogene 2018; 37:1551-1560. [DOI: 10.1038/s41388-017-0050-x] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/20/2017] [Accepted: 09/24/2017] [Indexed: 01/10/2023]
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32
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Kannabiran C. A Fluorescent Quantitative Multiplex PCR Method to Detect Copy Number Changes in the RB1 Gene. Methods Mol Biol 2018; 1726:19-28. [PMID: 29468540 DOI: 10.1007/978-1-4939-7565-5_3] [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] [Indexed: 06/08/2023]
Abstract
Copy number changes comprising deletions or insertions involving single or multiple exons of a gene are known to occur in a significant proportion of cases in retinoblastoma. The protocol described here involves a two-step quantitative multiplex PCR process which is suitable for the detection of such mutations in the RB1 as well as in other genes. This is achieved through the use of suitable gene-specific primers designed to amplify individual exons, with universal tags attached to the 5' end of each primer. These tagged primers are used in the first step of PCR of the RB1 gene in patients. The second step is carried out through the use of "universal" primers complementary to the tag sequences alone. This technique facilitates the detection of fluorescent PCR products from multiple exons through the use of a single fluorescent tagged primer.
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Affiliation(s)
- Chitra Kannabiran
- Kallam Anji Reddy Molecular Genetics Laboratory, Prof. Brien Holden Eye Research Centre, L.V. Prasad Eye Institute, Hyderabad, India.
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33
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Foster A, Boyes L, Burgess L, Carless S, Bowyer V, Jenkinson H, Parulekar M, Ainsworth J, Hungerford J, Onadim Z, Sagoo M, Rosser E, Reddy MA, Cole T. Patient understanding of genetic information influences reproductive decision making in retinoblastoma. Clin Genet 2017; 92:587-593. [PMID: 28397259 DOI: 10.1111/cge.13035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 04/04/2017] [Accepted: 04/06/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND Retinoblastoma is the most common malignant tumour of the eye in childhood, with nearly all bilateral tumours and around 17% to 18% of unilateral tumours due to an oncogenic mutation in the RB1 gene in the germline. Genetic testing enables accurate risk assessment and optimal clinical management for the affected individual, siblings, and future offspring. MATERIAL AND METHODS We carried out the first UK-wide audit of understanding of genetic testing in individuals with retinoblastoma. A total of 292 individuals aged 16 to 45 years were included. RESULTS Patients with bilateral disease were significantly more likely to understand the implications of retinoblastoma for siblings and children. There was a significant association between not knowing the results of genetic testing or not understanding the implications and not having children, particularly in women. Surprisingly, this was also true for individuals treated for unilateral disease with a low risk of retinoblastoma for their offspring. CONCLUSION We are concerned that individuals may be making life choices based on insufficient information regarding risks of retinoblastoma and reproductive options. We suggest that improvement in transition care is needed to enable individuals to make informed reproductive decisions and to ensure optimal care for children born at risk of retinoblastoma.
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Affiliation(s)
- A Foster
- Department of Clinical Genetics, Birmingham Women's Hospital NHS Foundation Trust, Birmingham, UK
| | - L Boyes
- Department of Clinical Genetics, Birmingham Women's Hospital NHS Foundation Trust, Birmingham, UK
| | - L Burgess
- Department of Clinical Genetics, Birmingham Women's Hospital NHS Foundation Trust, Birmingham, UK
| | - S Carless
- Department of Clinical Genetics, Birmingham Women's Hospital NHS Foundation Trust, Birmingham, UK
| | - V Bowyer
- Department of Clinical Genetics, Birmingham Women's Hospital NHS Foundation Trust, Birmingham, UK
| | - H Jenkinson
- Birmingham Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - M Parulekar
- Birmingham Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - J Ainsworth
- Birmingham Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - J Hungerford
- Retinoblastoma Service, Royal London Hospital, Barts Health NHS Trust, London, UK.,Moorfields Eye Hospital NHS Trust, London, UK
| | - Z Onadim
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, London, UK
| | - M Sagoo
- Retinoblastoma Service, Royal London Hospital, Barts Health NHS Trust, London, UK.,Moorfields Eye Hospital NHS Trust, London, UK.,UCL Institute of Ophthalmology, London, UK
| | - E Rosser
- Retinoblastoma Service, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - M A Reddy
- Retinoblastoma Service, Royal London Hospital, Barts Health NHS Trust, London, UK.,Moorfields Eye Hospital NHS Trust, London, UK
| | - T Cole
- Department of Clinical Genetics, Birmingham Women's Hospital NHS Foundation Trust, Birmingham, UK
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34
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Yousef YA, Tbakhi A, Al-Hussaini M, AlNawaiseh I, Saab A, Afifi A, Naji M, Mohammad M, Deebajah R, Jaradat I, Sultan I, Mehyar M. Mutational analysis of the RB1 gene and the inheritance patterns of retinoblastoma in Jordan. Fam Cancer 2017; 17:261-268. [DOI: 10.1007/s10689-017-0027-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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35
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Tomar S, Sethi R, Sundar G, Quah TC, Quah BL, Lai PS. Mutation spectrum of RB1 mutations in retinoblastoma cases from Singapore with implications for genetic management and counselling. PLoS One 2017; 12:e0178776. [PMID: 28575107 PMCID: PMC5456385 DOI: 10.1371/journal.pone.0178776] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 05/18/2017] [Indexed: 12/21/2022] Open
Abstract
Retinoblastoma (RB) is a rare childhood malignant disorder caused by the biallelic inactivation of RB1 gene. Early diagnosis and identification of carriers of heritable RB1 mutations can improve disease outcome and management. In this study, mutational analysis was conducted on fifty-nine matched tumor and peripheral blood samples from 18 bilateral and 41 unilateral unrelated RB cases by a combinatorial approach of Multiplex Ligation-dependent Probe Amplification (MLPA) assay, deletion screening, direct sequencing, copy number gene dosage analysis and methylation assays. Screening of both blood and tumor samples yielded a mutation detection rate of 94.9% (56/59) while only 42.4% (25/59) of mutations were detected if blood samples alone were analyzed. Biallelic mutations were observed in 43/59 (72.9%) of tumors screened. There were 3 cases (5.1%) in which no mutations could be detected and germline mutations were detected in 19.5% (8/41) of unilateral cases. A total of 61 point mutations were identified, of which 10 were novel. There was a high incidence of previously reported recurrent mutations, occurring at 38.98% (23/59) of all cases. Of interest were three cases of mosaic RB1 mutations detected in the blood from patients with unilateral retinoblastoma. Additionally, two germline mutations previously reported to be associated with low-penetrance phenotypes: missense-c.1981C>T and splice variant-c.607+1G>T, were observed in a bilateral and a unilateral proband, respectively. These findings have implications for genetic counselling and risk prediction for the affected families. This is the first published report on the spectrum of mutations in RB patients from Singapore and shows that further improved mutation screening strategies are required in order to provide a definitive molecular diagnosis for every case of RB. Our findings also underscore the importance of genetic testing in supporting individualized disease management plans for patients and asymptomatic family members carrying low-penetrance, germline mosaicism or heritable unilateral mutational phenotypes.
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Affiliation(s)
- Swati Tomar
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Raman Sethi
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Gangadhara Sundar
- Department of Ophthalmology, National University Hospital, Singapore, Singapore
| | - Thuan Chong Quah
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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36
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Mosaicism and prenatal diagnosis options: insights from retinoblastoma. Eur J Hum Genet 2016; 25:381-383. [PMID: 28000698 DOI: 10.1038/ejhg.2016.174] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/23/2016] [Accepted: 11/01/2016] [Indexed: 01/17/2023] Open
Abstract
In sporadic cases, a post-zygotic mutational event signifies a somatic mosaicism in the affected child only, which implies that these mutations affect only a portion of the body. Therefore siblings do not need follow-up. On the other hand, a pre-zygotic mutation transmitted by an unaffected mosaic parent implies recurrent risks in offspring. To better estimate the contribution of pre- and post-zygotic events, we analysed 124 consecutive bilateral retinoblastoma probands, carrying a heterozygous RB1 pathogenic variant and their unaffected, non-carrier parents. In order to evaluate somatic mosaicism in blood, the deleterious RB1 pathogenic variant identified in the proband, was searched for in the unaffected parents, using targeted deep sequencing. Observed recurrences, which represent an estimation of germline and somatic mosaicisms, were recorded and computed in the sibships. Deep sequencing revealed one mosaic-unaffected parent out of 124 tested couples, which provides an estimation of the maximal risk of recurrence, due to parental mosaicism, at 0.4%. Follow-up in the sibships showed one recurrence, providing a maximal recurrence risk, due to parental mosaicism, at 0.8%. Two different statistical strategies led to close estimates (0.4 and 0.8% risks) which appeared 266-533-fold higher, as compared with the general population. These recurrence estimates could be considered when counselling couples with retinoblastoma or diseases with a high de novo mutation rate.
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37
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Sagi M, Frenkel A, Eilat A, Weinberg N, Frenkel S, Pe'er J, Abeliovich D, Lerer I. Genetic screening in patients with Retinoblastoma in Israel. Fam Cancer 2016; 14:471-80. [PMID: 25754945 DOI: 10.1007/s10689-015-9794-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Retinoblastoma (Rb) is a childhood tumor (~1 in 20,000 live births) developing in the retina due to mutations in the RB1 gene. Identification of the oncogenic mutations in the RB1 gene is important for the clinical management and for genetic counseling to families with a child or a parent affected with the tumor. Here we present our experience in detecting the pathogenic mutations in blood samples, from 150 unrelated Rb patients and highlight the relevant counseling issues. Mutation screening in the RB1 gene was based on Sanger sequencing, mosaicism of recurrent CpG transition mutations was detected by allele specific PCR and multiplex ligation dependent probe amplification for detecting of large deletions/duplications. The overall detection rate of mutations in our cohort was 55% (82/150). In the familial cases it was 100% (17/17), in bilateral and unilateral-multifocal sporadic cases 91% (50/55), and in the unilateral sporadic cases 19% (15/78). Nonsense mutations and small deletions or insertions that results in transcripts with premature termination codons that are subject to nonsense mediated decay were the most frequent, detected in 50/82 (61%) of the patients. The rest were large deletions detected in 14/82 (17%), splice site mutations detected in 11/82 (13%), missense mutations in four patients and mutations in the promoter sequence in three patients. Mutation mosaicism ranging from 10 to 30% was detected by allele specific PCR in ten patients, 9% (5/55) of patients with bilateral tumor and 33% (5/15) of the patients with unilateral tumor. In three patients rare variants were detected as the only finding which was also detected in other healthy family members. Allele specific amplification of recurrent mutations raises in our cohort the identification rate from 82 to 91% in the sporadic bilateral cases and from 13 to 19% in the unilateral sporadic cases. Most mosaic cases could not be identified by Sanger sequencing and therefore screening for recurrent CpG transition mutations by allele specific amplification is of utmost importance. Molecular screening is important for the genetic counseling regarding the risk for tumor development and the relevance for prenatal diagnosis but in several families is accompanied by detecting rare variants that might be rare polymorphisms or low penetrant mutations.
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Affiliation(s)
- Michal Sagi
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Kiryat Hadassah, POB 12000, 91120, Jerusalem, Israel
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38
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Li F, Wen X, Zhang H, Fan X. Novel Insights into the Role of Long Noncoding RNA in Ocular Diseases. Int J Mol Sci 2016; 17:478. [PMID: 27043545 PMCID: PMC4848934 DOI: 10.3390/ijms17040478] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/18/2016] [Accepted: 03/18/2016] [Indexed: 12/19/2022] Open
Abstract
Recent advances have suggested that long noncoding RNAs (lncRNAs) are differentially expressed in ocular tissues and play a critical role in the pathogenesis of different types of eye diseases. Here, we summarize the functions and mechanisms of known aberrantly-expressed lncRNAs and present a brief overview of relevant reports about lncRNAs in such ocular diseases as glaucoma, proliferative vitreoretinopathy (PVR), diabeticretinopathy (DR), and ocular tumors. We intend to highlight comprehensive studies that provide detailed data about the mechanisms of lncRNAs, their applications as diagnostic or prognostic biomarkers, and their potential therapeutic targets. Although our understanding of lncRNAs is still in its infancy, these examples may provide helpful insights into the methods by which lncRNAs interfere with ocular diseases.
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Affiliation(s)
- Fang Li
- Department of Ophthalmology, Ninth People's Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai 200025, China.
| | - Xuyang Wen
- Department of Ophthalmology, Ninth People's Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai 200025, China.
| | - He Zhang
- Department of Ophthalmology, Ninth People's Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai 200025, China.
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai 200025, China.
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39
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Smith T, Ho G, Christodoulou J, Price EA, Onadim Z, Gauthier-Villars M, Dehainault C, Houdayer C, Parfait B, van Minkelen R, Lohman D, Eyre-Walker A. Extensive Variation in the Mutation Rate Between and Within Human Genes Associated with Mendelian Disease. Hum Mutat 2016; 37:488-94. [PMID: 26857394 DOI: 10.1002/humu.22967] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/25/2016] [Indexed: 01/05/2023]
Abstract
We have investigated whether the mutation rate varies between genes and sites using de novo mutations (DNMs) from three genes associated with Mendelian diseases (RB1, NF1, and MECP2). We show that the relative frequency of mutations at CpG dinucleotides relative to non-CpG sites varies between genes and relative to the genomic average. In particular we show that the rate of transition mutation at CpG sites relative to the rate of non-CpG transversion is substantially higher in our disease genes than amongst DNMs in general; the rate of CpG transition can be several hundred-fold greater than the rate of non-CpG transversion. We also show that the mutation rate varies significantly between sites of a particular mutational type, such as non-CpG transversion, within a gene. We estimate that for all categories of sites, except CpG transitions, there is at least a 30-fold difference in the mutation rate between the 10% of sites with the highest and lowest mutation rates. However, our best estimate is that the mutation rate varies by several hundred-fold variation. We suggest that the presence of hypermutable sites may be one reason certain genes are associated with disease.
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Affiliation(s)
- Thomas Smith
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Gladys Ho
- NSW Centre for Rett Syndrome Research, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia
| | - John Christodoulou
- NSW Centre for Rett Syndrome Research, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, Australia.,Disciplines of Paediatrics and Child Health and Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Elizabeth Ann Price
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, The Royal London Hospital, 80 Newark Street, London, United Kingdom
| | - Zerrin Onadim
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, The Royal London Hospital, 80 Newark Street, London, United Kingdom
| | | | | | - Claude Houdayer
- Service de Génétique, Institut Curie, Paris, France.,INSERM U830, centre de recherche de l'Institut Curie, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Beatrice Parfait
- EA7331, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Service de Biochimie et de Génétique Moléculaire, Hôpital Cochin, AP-HP, Paris, France
| | - Rick van Minkelen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, Netherlands
| | - Dietmar Lohman
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
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40
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Abstract
Epigenetics is currently one of the most promising areas of study in the field of biomedical research. Scientists have dedicated their efforts to studying epigenetic mechanisms in cancer for centuries. Additionally, the field has expanded from simply studying DNA methylation to other areas, such as histone modification, non-coding RNA, histone variation, nucleosome location, and chromosome remodeling. In ocular tumors, a large amount of epigenetic exploration has expanded from single genes to the genome-wide level. Most importantly, because epigenetic changes are reversible, several epigenetic drugs have been developed for the treatment of cancer. Herein, we review the current understanding of epigenetic mechanisms in ocular tumors, including but not limited to retinoblastoma and uveal melanoma. Furthermore, the development of new pharmacological strategies is summarized.
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Affiliation(s)
- Xuyang Wen
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Linna Lu
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Zhang He
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
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41
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Rodríguez-Martín C, Cidre F, Fernández-Teijeiro A, Gómez-Mariano G, de la Vega L, Ramos P, Zaballos Á, Monzón S, Alonso J. Familial retinoblastoma due to intronic LINE-1 insertion causes aberrant and noncanonical mRNA splicing of the RB1 gene. J Hum Genet 2016; 61:463-6. [PMID: 26763876 DOI: 10.1038/jhg.2015.173] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 12/21/2015] [Accepted: 12/25/2015] [Indexed: 01/31/2023]
Abstract
Retinoblastoma (RB, MIM 180200) is the paradigm of hereditary cancer. Individuals harboring a constitutional mutation in one allele of the RB1 gene have a high predisposition to develop RB. Here, we present the first case of familial RB caused by a de novo insertion of a full-length long interspersed element-1 (LINE-1) into intron 14 of the RB1 gene that caused a highly heterogeneous splicing pattern of RB1 mRNA. LINE-1 insertion was inferred by mRNA studies and full-length sequenced by massive parallel sequencing. Some of the aberrant mRNAs were produced by noncanonical acceptor splice sites, a new finding that up to date has not been described to occur upon LINE-1 retrotransposition. Our results clearly show that RNA-based strategies have the potential to detect disease-causing transposon insertions. It also confirms that the incorporation of new genetic approaches, such as massive parallel sequencing, contributes to characterize at the sequence level these unique and exceptional genetic alterations.
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Affiliation(s)
- Carlos Rodríguez-Martín
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Florencia Cidre
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Ana Fernández-Teijeiro
- Unidad de Gestión Clínica Intercentros de Oncología Pediátricas, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, National Reference Unit for Retinoblastoma, Sevilla, Spain
| | - Gema Gómez-Mariano
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Leticia de la Vega
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Patricia Ramos
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Ángel Zaballos
- Unidad de Genómica, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sara Monzón
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER U758), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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Long Y, Han S, Zhang X, Zhang X, Chen T, Gao Y, Tian H. The combination of a novel 2 bp deletion mutation and p.D63H in CYP11B1 cause congenital adrenal hyperplasia due to steroid 11β-hydroxylase deficiency. Endocr J 2016; 63:301-10. [PMID: 26806323 DOI: 10.1507/endocrj.ej15-0433] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Deficiency of steroid 11β-hydroxylase activity occurs in 5-8% of patients with congenital adrenal hyperplasia (CAH). The aim of the current study was to identify mutations in the CYP11B1 gene of a patient with CAH due to deficiency of steroid 11β-hydroxylase activity, and to study the functional and structural consequences of these mutations. A molecular genetic analysis of the CYP11B1 gene in this patient and her parents identified a known missense mutation g.5194G>C (p.D63H) and a novel 2 bp deletion mutation (g.9525_9526delCT, corresponding to p.L380V…R420X) in the patient. In vitro expression studies in COS7 cells revealed a decreased 11β-hydroxylase activity in the p.D63H mutant to 2.0±0.8% and in the p.L380V…R420X mutant to 0.2±2.2% for the conversion of 11-deoxycortisol to cortisol. Three dimensional homology models for the normal and mutant proteins were built by using the recently published x-ray structure of the human CYP11B2 as a template. Presumably, the g.9525_9526delCT mutation in CYP11B1 resulted in a truncated protein with a misfolded C-terminal domain that could not efficiently bind heme iron, substrate, and adrenodoxin and had lost its biochemical function. In summary, CAH due to steroid 11β-hydroxylase deficiency can be attributed to both the novel deletion mutation (g.9525_9526delCT, corresponding to p.L380V…R420X) and known missense mutation (g.5194G>C corresponding to p.D63H) in CYP11B1.
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Affiliation(s)
- Yang Long
- Laboratory of Endocrinology and Metabolism, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P R China
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Thirumalairaj K, Abraham A, Devarajan B, Gaikwad N, Kim U, Muthukkaruppan V, Vanniarajan A. A stepwise strategy for rapid and cost-effective RB1 screening in Indian retinoblastoma patients. J Hum Genet 2015; 60:547-52. [PMID: 26084579 DOI: 10.1038/jhg.2015.62] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/28/2015] [Accepted: 04/30/2015] [Indexed: 01/02/2023]
Abstract
India has the highest number of retinoblastoma (RB) patients among the developing countries owing to its increasing population. Of the patients with RB, about 40% have the heritable form of the disease, making genetic analysis of the RB1 gene an integral part of disease management. However, given the large size of the RB1 gene with its widely dispersed exons and no reported hotspots, genetic testing can be cumbersome. To overcome this problem, we have developed a rapid screening strategy by prioritizing the order of exons to be analyzed, based on the frequency of nonsense mutations, deletions and duplications reported in the RB1-Leiden Open Variation Database and published literature on Indian patients. Using this strategy for genetic analysis, mutations were identified in 76% of patients in half the actual time and one third of the cost. This reduction in time and cost will allow for better risk prediction for siblings and offspring, thereby facilitating genetic counseling for families, especially in developing countries.
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Affiliation(s)
- Kannan Thirumalairaj
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India
| | - Aloysius Abraham
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India
| | | | - Namrata Gaikwad
- Department of Orbit, Oculoplasty and Oncology, Aravind Eye Hospital, Madurai, India
| | - Usha Kim
- Department of Orbit, Oculoplasty and Oncology, Aravind Eye Hospital, Madurai, India
| | | | - Ayyasamy Vanniarajan
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India
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Francis JH, Abramson DH. Update on Ophthalmic Oncology 2013: Retinoblastoma and Uveal Melanoma. Asia Pac J Ophthalmol (Phila) 2014; 3:241-56. [PMID: 26107765 DOI: 10.1097/apo.0000000000000079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
PURPOSE The aim of this study was to discuss the clinical and translational content of the literature as well as advancement in our knowledge pertaining to retinoblastoma and uveal melanoma that were published from January to December 2013. DESIGN This study is a literature review. METHODS The search terms retinoblastoma and uveal melanoma were used in a MEDLINE literature search. Abstracts were studied, and the most relevant articles were selected for inclusion and further in-depth review. RESULTS In retinoblastoma, fewer eyes are lost because of the expanded use of ophthalmic artery chemosurgery and intravitreal melphalan, and the past year marks a deepening in our understanding of these modalities. Knowledge on the genetic underpinnings of uveal melanoma has broadened to include genes associated with a favorable prognosis. This is accompanied by promising results in the treatment of metastatic uveal melanoma. CONCLUSIONS This past year, there were important advancements in our knowledge of retinoblastoma and uveal melanoma.
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Affiliation(s)
- Jasmine H Francis
- From the Ophthalmic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
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Dommering CJ, Mol BM, Moll AC, Burton M, Cloos J, Dorsman JC, Meijers-Heijboer H, van der Hout AH. RB1 mutation spectrum in a comprehensive nationwide cohort of retinoblastoma patients. J Med Genet 2014; 51:366-74. [PMID: 24688104 DOI: 10.1136/jmedgenet-2014-102264] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Retinoblastoma (Rb) is a childhood cancer of the retina, commonly initiated by biallelic inactivation of the RB1 gene. Knowledge of the presence of a heritable RB1 mutation can help in risk management and reproductive decision making. We report here on RB1 mutation scanning in a unique nationwide cohort of Rb patients from the Netherlands. METHODS From the 1173 Rb patients registered in the Dutch National Retinoblastoma Register until January 2013, 529 patients from 433 unrelated families could be included. RB1 mutation scanning was performed with different detection methods, depending on the time period. RESULTS Our mutation detection methods revealed RB1 mutations in 92% of bilateral and/or familial Rb patients and in 10% of non-familial unilateral cases. Overall an RB1 germline mutation was detected in 187 (43%) of 433 Rb families, including 33 novel mutations. The distribution of the type of mutation was 37% nonsense, 20% frameshift, 21% splice, 9% large indel, 5% missense, 7% chromosomal deletions and 1% promoter. Ten per cent of patients were mosaic for the RB1 mutation. Six three-generation families with incomplete penetrance RB1 mutations were found. We found evidence that two variants, previously described as pathogenic RB1 mutations, are likely to be neutral variants. CONCLUSIONS The frequency of the type of mutations in the RB1 gene in our unbiased national cohort is the same as the mutation spectrum described worldwide. Furthermore, our RB1 mutation detection regimen achieves a high scanning sensitivity.
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Affiliation(s)
- Charlotte J Dommering
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Berber M Mol
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Annette C Moll
- Department of Ophthalmology, VU University Medical Center, Amsterdam, The Netherlands
| | - Margaret Burton
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jacqueline Cloos
- Department of Hematology, VU University Medical Center, Amsterdam, The Netherlands Department of Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Josephine C Dorsman
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Annemarie H van der Hout
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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