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Sirivolu S, Schmidt MJ, Prabakar RK, Kuhn P, Hicks J, Berry JL, Xu L. Single-cell somatic copy number alteration profiling of vitreous humor seeds in retinoblastoma. Ophthalmic Genet 2024:1-4. [PMID: 39016001 DOI: 10.1080/13816810.2024.2374886] [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: 02/12/2024] [Accepted: 06/26/2024] [Indexed: 07/18/2024]
Abstract
BACKGROUND Heterogeneity can impact biomarker identification. Thus, we investigated the somatic copy number alterations (SCNAs) of individual tumor cells in the vitreous humor of a retinoblastoma patient using single-cell whole-genome profiling and explored the genomic concordance among vitreous and aqueous humor, vitreous seeds, and tumor. METHODS Aqueous humor (AH), vitreous humor (VH), and tumor biopsy were obtained from an enucleated globe with retinoblastoma and vitreous seeding. Micromanipulation was used to manually isolate 39 live single tumor cells from vitreous seeds harvested from the VH. The SCNA profiles of these individual cells were generated via whole-genome sequencing and analyzed alongside profiles from the tumor mass and cell-free DNA (cfDNA) from AH and VH. RESULTS Heatmap of VH single-cell SCNA profiles demonstrates heterogeneity among individual vitreous seeds with one clearly dominant subclone (23 of 37 cells). The SCNA profiles from the cells in this subclone demonstrate an average concordance of 98% with cfDNA profiles from acellular AH and VH and with the tumor profile. CONCLUSIONS Our findings reveal some heterogeneity among single-cell SCNA profiles in individual VH seeds. Despite this heterogeneity, the dominant vitreous subclone exhibits extremely (>98%) high concordance with the SCNA profile from tumor and AH, suggesting AH cfDNA is representative of the dominant genomic subclone. This may facilitate tumoral biomarker identification via the AH. This preliminary work supports the potential of applying single-cell technology to VH seeds in retinoblastoma as a platform to study tumor subclones, which may provide insight into the genomic complexity of disease.
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Affiliation(s)
- Shreya Sirivolu
- The Vision Center, Children's Hospital Los Angeles, Los Angeles, California, USA
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Michael J Schmidt
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, USA
| | - Rishvanth K Prabakar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, USA
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jesse L Berry
- The Vision Center, Children's Hospital Los Angeles, Los Angeles, California, USA
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Liya Xu
- The Vision Center, Children's Hospital Los Angeles, Los Angeles, California, USA
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, USA
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Vanniarajan A, Maitra P, Saraswathi KK, Shah PK. Impact of RB1 gene screening from blood collected on a single day from 411 family members of 113 Retinoblastoma survivors in India. Eye (Lond) 2024; 38:1575-1580. [PMID: 38341497 PMCID: PMC11126713 DOI: 10.1038/s41433-024-02955-z] [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: 08/16/2023] [Revised: 12/20/2023] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
OBJECTIVES To analyse the profile and implication of genetic testing in a cohort of retinoblastoma (RB) patients and their families conducted on a single day during World Retinoblastoma Awareness Week 2017. METHODS Retrospective analysis of blood samples were collected from 411 subjects, including 113 probands at a camp organised for RB awareness and were analysed for RB1 mutations by Sanger sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA). If germline mutations were detected, the parents and siblings of the proband were tested for the same mutation. RESULTS Germline RB1 mutations were identified in 61/113(54%) probands with a mutation detection rate of 96% (47/49) and 22% (14/64) for bilateral and unilateral RB, respectively. Ten novel pathogenic mutations were identified. Splice mutation was most common (31%) followed by nonsense mutation (26%). The mean age at RB diagnosis was significantly lower in patients having germline RB1 mutation (mean 10.7 months ±2.5) compared to those without (mean 27.2 months ±6.5) (p = <0.0001). Parental transmission of the mutant allele was detected in 15/61(25%) cases of which 11(18%) parents were unaffected indicating incomplete penetrance. The origin of the variant allele was both paternal (n = 7) and maternal (n = 4) wherein 5 were bilateral and 6 unilateral. CONCLUSIONS The detection of a germline mutation impacts the proband and family members due to its implications on change in prognosis, frequency of subsequent evaluations, screening for ocular and non-ocular cancers, and surveillance of family and future progeny.
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Affiliation(s)
- Ayyasamy Vanniarajan
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India
- Department of Molecular Biology, Aravind Medical Research Foundation, Affiliated to Alagappa University, Karaikudi, India
| | - Puja Maitra
- Department of Vitreoretina Services, Aravind Eye Hospital, Chennai, India
| | - Karuvel Kannan Saraswathi
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India
- Department of Molecular Biology, Aravind Medical Research Foundation, Affiliated to Alagappa University, Karaikudi, India
| | - Parag K Shah
- Department of Pediatric Retina and Ocular Oncology, Aravind Eye Hospital, Coimbatore, India.
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Hanson B, Shaw J, Povarnitsyn N, Bowns B, Young E, Gerrish A, Allen S, Scotchman E, Chitty LS, Chandler NJ. Expanding Access to Noninvasive Prenatal Diagnosis for Monogenic Conditions to Consanguineous Families. Clin Chem 2024; 70:727-736. [PMID: 38592422 DOI: 10.1093/clinchem/hvae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/16/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Cell-free fetal DNA exists within the maternal bloodstream during pregnancy and provides a means for noninvasive prenatal diagnosis (NIPD). Our accredited clinical service offers definitive NIPD for several autosomal recessive (AR) and X-linked conditions using relative haplotype dosage analysis (RHDO). RHDO involves next-generation sequencing (NGS) of thousands of common single nucleotide polymorphism (SNPs) surrounding the gene of interest in the parents and an affected or unaffected offspring to conduct haplotype phasing of the high- and low-risk alleles. NGS is carried out in parallel on the maternal cell-free DNA, and fetal inheritance is predicted using sensitive dosage calculations performed at sites where the parental genotypes differ. RHDO is not currently offered to consanguineous couples owing to the shared haplotype between parents. Here we test the expansion of RHDO for AR monogenic conditions to include consanguineous couples. METHODS The existing sequential probability ratio test analysis pipeline was modified to apply to SNPs where both parents are heterozygous for the same genotype. Quality control thresholds were developed using 33 nonconsanguineous cases. The performance of the adapted RHDO pipeline was tested on 8 consanguineous cases. RESULTS The correct fetal genotype was predicted by our revised RHDO approach in all conclusive cases with known genotypes (n = 5). Haplotype block classification accuracies of 94.5% and 93.9% were obtained for the nonconsanguineous and consanguineous case cohorts, respectively. CONCLUSIONS Our modified RHDO pipeline correctly predicts the genotype in fetuses from consanguineous families, allowing the potential to expand access to NIPD services for these families.
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Affiliation(s)
- Britt Hanson
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, United Kingdom
| | - Joe Shaw
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, United Kingdom
| | - Nikita Povarnitsyn
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, United Kingdom
| | - Benjamin Bowns
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom
| | - Elizabeth Young
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom
| | - Amy Gerrish
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, United Kingdom
| | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, United Kingdom
- Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Natalie J Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, United Kingdom
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Rodriguez A, Kelley C, Patel A, Ramasubramanian A. Prenatal Diagnosis of Retinoblastomas: A Scoping Review. Int J Gen Med 2023; 16:1101-1110. [PMID: 37007908 PMCID: PMC10064871 DOI: 10.2147/ijgm.s380634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Purpose The objective of this review is to explore the prenatal diagnosis of retinoblastoma and the recommended screening practices. Patients and Methods An electronic literature search on prenatal diagnosis of retinoblastoma was conducted on the PubMed database. Publications within the last 20 years that matched the inclusion criteria were selected. The literature search included the following keywords: retinoblastoma, prenatal, diagnosis, screening, and associated synonyms to increase search sensitivity. Nine studies were included for investigation and extracted to identify prenatal diagnostic and screening techniques for retinoblastoma, their associated impact, and the target population that should receive prenatal screening for retinoblastoma. Results Familial retinoblastoma has an autosomal inheritance pattern and 90% penetrance. Therefore, future parents with a family history of retinoblastoma are strongly advised to get tested for retinoblastoma (Rb) gene mutations; if one of the parents is positive for a mutated allele of the RB1 gene, there is a 45% chance that their child will inherit a mutated allele of the retinoblastoma gene, rendering the allele non-functional in all of the cells of the individual and predisposing the child to a higher risk of developing retinoblastoma as well as other secondary cancers. Thus, prenatal screening and diagnosis of retinoblastoma is crucial for early diagnosis and optimal treatment. Conclusion Prenatal testing for retinoblastoma in high-risk families is important for everyone in the family. For the parents, prenatal screening has been shown to improve their family planning decisions and psychological well-being as they can mentally prepare beforehand and make informed decisions. More importantly, these practices have shown to yield better treatment and vision outcomes in the newborn.
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Affiliation(s)
| | - Caitlin Kelley
- School of Medicine, Creighton University, Phoenix, AZ, USA
| | - Anjali Patel
- School of Medicine, Creighton University, Phoenix, AZ, USA
| | - Aparna Ramasubramanian
- Ophthalmology Department, Phoenix Children’s Hospital, Phoenix, AZ, USA
- Correspondence: Aparna Ramasubramanian, Ophthalmology Department, Phoenix Children’s Hospital, 1919 E Thomas Road, Phoenix, AZ, 85016, USA, Tel +1 602-933-3937, Fax +1 602-933-2409, Email
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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: 0] [Impact Index Per Article: 0] [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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Hanson B, Scotchman E, Chitty LS, Chandler NJ. Non-invasive prenatal diagnosis (NIPD): how analysis of cell-free DNA in maternal plasma has changed prenatal diagnosis for monogenic disorders. Clin Sci (Lond) 2022; 136:1615-1629. [PMID: 36383187 PMCID: PMC9670272 DOI: 10.1042/cs20210380] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 07/30/2023]
Abstract
Cell-free fetal DNA (cffDNA) is released into the maternal circulation from trophoblastic cells during pregnancy, is detectable from 4 weeks and is representative of the entire fetal genome. The presence of this cffDNA in the maternal bloodstream has enabled clinical implementation of non-invasive prenatal diagnosis (NIPD) for monogenic disorders. Detection of paternally inherited and de novo mutations is relatively straightforward, and several methods have been developed for clinical use, including quantitative polymerase chain reaction (qPCR), and PCR followed by restriction enzyme digest (PCR-RED) or next-generation sequencing (NGS). A greater challenge has been in the detection of maternally inherited variants owing to the high background of maternal cell-free DNA (cfDNA). Molecular counting techniques have been developed to measure subtle changes in allele frequency. For instance, relative haplotype dosage analysis (RHDO), which uses single nucleotide polymorphisms (SNPs) for phasing of high- and low-risk alleles, is clinically available for several monogenic disorders. A major drawback is that RHDO requires samples from both parents and an affected or unaffected proband, therefore alternative methods, such as proband-free RHDO and relative mutation dosage (RMD), are being investigated. cffDNA was thought to exist only as short fragments (<500 bp); however, long-read sequencing technologies have recently revealed a range of sizes up to ∼23 kb. cffDNA also carries a specific placental epigenetic mark, and so fragmentomics and epigenetics are of interest for targeted enrichment of cffDNA. Cell-based NIPD approaches are also currently under investigation as a means to obtain a pure source of intact fetal genomic DNA.
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Affiliation(s)
- Britt Hanson
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| | - Lyn S. Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
- Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, U.K
| | - Natalie J. Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
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Abstract
PURPOSE Retinoblastoma (RB) is the most common intraocular malignancy in children. The diagnosis of RB is mainly based on clinical features and imaging characteristics. Prognosis is based on stage of disease and response to treatment. In salvaged globes, direct tumor biopsy for genetic analysis and prognostication is an absolute contraindication at this point of time for the fear of extraocular tumor spread. Currently, there is a search for surrogate markers to allow accurate diagnosis and for prognostication, to predict the chances of globe salvage in RB. Therefore, biofluids such as plasma or aqueous humor have been studied to detect circulating tumor DNA (ctDNA) or cell-free DNA (cfDNA), respectively, to allow for treatment decision making, monitoring treatment response, and prognostic counselling. METHODS A search of electronic databases (PubMed, Google Scholar and MEDLINE) of all articles on liquid biopsy in retinoblastoma published in English was performed. The keywords used for the search included "retinoblastoma", "liquid biopsy", "aqueous humor" "circulating tumor cells", "cell-free DNA", "cfDNA", "circulating tumor DNA", "ctDNA", "tumor fraction", "RB1 mutation" and "SNCA". Additionally, historic articles on the advent of liquid biopsy in medicine were also reviewed. Pertinent cross-references from the studies were reviewed. Retrospective interventional and observational case series, observational case series, prospective cohort studies, reviews, case reports, surgical techniques, invited commentary and letters were included. RESULTS A total of 40 relevant articles were selected. Biomarkers in aqueous humor, serum and cerebrospinal fluid and their clinical applications are discussed. CONCLUSION Harvesting aqueous humor from eyes with retinoblastoma has been found safe and superior to blood for the detection of chromosomal changes. cfDNA from aqueous can be a surrogate marker to detect somatic copy number alterations and other genetic alterations in RB. ctDNA in plasma also has potential to help in diagnosis and prognosis of RB. Liquid biopsy in RB is an emerging topic, which could pave way for a better understanding of mechanisms for treatment response, resistance and recurrence in RB as well as possibly provide specific therapeutic targets to improve globe salvage.
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Affiliation(s)
- Neha Ghose
- Operation Eyesight Universal Institute for Eye Cancer, LV Prasad Eye Institute, Hyderabad, India
| | - Swathi Kaliki
- Operation Eyesight Universal Institute for Eye Cancer, LV Prasad Eye Institute, Hyderabad, India
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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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