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Berry JL, Pike S, Shah R, Reid MW, Peng CC, Wang Y, Yellapantula V, Biegel J, Kuhn P, Hicks J, Xu L. Aqueous Humor Liquid Biopsy as a Companion Diagnostic for Retinoblastoma: Implications for Diagnosis, Prognosis, and Therapeutic Options: Five Years of Progress. Am J Ophthalmol 2024; 263:188-205. [PMID: 38040321 PMCID: PMC11148850 DOI: 10.1016/j.ajo.2023.11.020] [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: 04/02/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
PURPOSE To define the prospective use of the aqueous humor (AH) as a molecular diagnostic and prognostic liquid biopsy for retinoblastoma (RB). METHODS This is a prospective, observational study wherein an AH liquid biopsy is performed at diagnosis and longitudinally through therapy for patients with RB. Tumor-derived cell-free DNA is isolated and sequenced for single nucleotide variant analysis of the RB1 gene and detection of somatic copy number alterations (SCNAs). The SCNAs are used to determine tumor fraction (TFx). Specific SCNAs, including 6p gain and focal MycN gain, along with TFx, are prospectively correlated with intraocular tumor relapse, response to therapy, and globe salvage. RESULTS A total of 26 eyes of 21 patients were included with AH taken at diagnosis. Successful ocular salvage was achieved in 19 of 26 (73.1%) eyes. Mutational analysis of 26 AH samples identified 23 pathogenic RB1 variants and 2 focal RB1 deletions; variant allele fraction ranged from 30.5% to 100% (median 93.2%). At diagnosis, SCNAs were detectable in 17 of 26 (65.4%) AH samples. Eyes with 6p gain and/or focal MycN gain had significantly greater odds of poor therapeutic outcomes (odds ratio = 6.75, 95% CI = 1.06-42.84, P = .04). Higher AH TFx was observed in eyes with vitreal progression (TFx = 46.0% ± 40.4) than regression (22.0 ± 29.1; difference: -24.0; P = .049). CONCLUSIONS Establishing an AH liquid biopsy for RB is aimed at addressing (1) our inability to biopsy tumor tissue and (2) the lack of molecular biomarkers for intraocular prognosis. Current management decisions for RB are made based solely on clinical features without objective molecular testing. This prognostic study shows great promise for using AH as a companion diagnostic. NOTE: Publication of this article is sponsored by the American Ophthalmological Society.
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Affiliation(s)
- Jesse L Berry
- From the Vision Center, Children's Hospital Los Angeles (J.L.B., S.P., M.W.R., C.-C.P., L.X.); USC Roski Eye Institute, Keck School of Medicine of the University of Southern California (J.L.B., S.P., M.W.R., C.-C.P., L.X.); the Saban Research Institute, Children's Hospital Los Angeles (J.L.B., V.Y., J.B., L.X.); Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California (J.L.B., P.K., J.H.).
| | - Sarah Pike
- From the Vision Center, Children's Hospital Los Angeles (J.L.B., S.P., M.W.R., C.-C.P., L.X.); USC Roski Eye Institute, Keck School of Medicine of the University of Southern California (J.L.B., S.P., M.W.R., C.-C.P., L.X.)
| | - Rachana Shah
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles (R.S.)
| | - Mark W Reid
- From the Vision Center, Children's Hospital Los Angeles (J.L.B., S.P., M.W.R., C.-C.P., L.X.); USC Roski Eye Institute, Keck School of Medicine of the University of Southern California (J.L.B., S.P., M.W.R., C.-C.P., L.X.)
| | - Chen-Ching Peng
- From the Vision Center, Children's Hospital Los Angeles (J.L.B., S.P., M.W.R., C.-C.P., L.X.); USC Roski Eye Institute, Keck School of Medicine of the University of Southern California (J.L.B., S.P., M.W.R., C.-C.P., L.X.)
| | - Yingfei Wang
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles (R.S.); Department of Quantitative and Computational Biology, University of Southern California (Y.W.)
| | - Venkata Yellapantula
- the Saban Research Institute, Children's Hospital Los Angeles (J.L.B., V.Y., J.B., L.X.); Center for Personalized Medicine, Children's Hospital Los Angeles (V.Y., J.B.)
| | - Jaclyn Biegel
- the Saban Research Institute, Children's Hospital Los Angeles (J.L.B., V.Y., J.B., L.X.)
| | - Peter Kuhn
- Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California (J.L.B., P.K., J.H.); USC Michelson Center for Convergent Biosciences and Department of Biological Sciences (P.K., J.H.), Los Angeles, California, USA
| | - James Hicks
- Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California (J.L.B., P.K., J.H.); USC Michelson Center for Convergent Biosciences and Department of Biological Sciences (P.K., J.H.), Los Angeles, California, USA
| | - Liya Xu
- From the Vision Center, Children's Hospital Los Angeles (J.L.B., S.P., M.W.R., C.-C.P., L.X.); USC Roski Eye Institute, Keck School of Medicine of the University of Southern California (J.L.B., S.P., M.W.R., C.-C.P., L.X.); the Saban Research Institute, Children's Hospital Los Angeles (J.L.B., V.Y., J.B., L.X.)
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Daniels AB, Sishtla KL, Bogan CM, Pierce JM, Chen SC, Xu L, Berry JL, Corson TW. Aqueous VEGF-A Levels as a Liquid Biopsy Biomarker of Retinoblastoma Vitreous Seed Response to Therapy. Invest Ophthalmol Vis Sci 2024; 65:18. [PMID: 38861274 PMCID: PMC11174092 DOI: 10.1167/iovs.65.6.18] [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: 04/02/2023] [Accepted: 01/31/2024] [Indexed: 06/12/2024] Open
Abstract
Purpose Regression of retinoblastoma vitreous seeds (VS) during intravitreal chemotherapy can be delayed, resulting in supernumerary injections. Similarly, VS relapse may not be clinically evident at first. A predictive biomarker of tumor regression and relapse could help guide real-time clinical decision making. Retinoblastoma is an oxygen-sensitive tumor; paradoxically, VS survive in the hypoxic vitreous. We hypothesized that VS elaborate pro-angiogenic cytokines. The purpose was to determine if pro-angiogenic cytokine signatures from aqueous humor could serve as a biomarker of VS response to treatment. Methods Multiplex ELISA was performed on aqueous from rabbit eyes with human retinoblastoma VS xenografts to identify expressed proangiogenic cytokines and changes in aqueous cytokine levels during intravitreal treatment were determined. Confirmatory RNAscope in situ hybridization for VEGF-A was performed on human retinoblastoma tumor sections and VS xenografts from rabbits. For human eyes undergoing intravitreal chemotherapy, serial aqueous VEGF-A levels measured via VEGF-A-specific ELISA were compared to clinical response. Results VEGF-A was highly expressed in human retinoblastoma VS in the xenograft model, and was the only proangiogenic cytokine that correlated with VS disease burden. In rabbits, aqueous VEGF-A levels decreased in response to therapy, consistent with quantitative VS reduction. In patients, aqueous VEGF-A levels associated with clinical changes in disease burden (regression, stability, or relapse), with changes in VEGF-A levels correlating with clinical response. Conclusions Aqueous VEGF-A levels correlate with extent of retinoblastoma VS, suggesting that aqueous VEGF-A may serve as a predictive molecular biomarker of treatment response.
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Affiliation(s)
- Anthony B. Daniels
- Division of Ocular Oncology and Pathology, Department of Ophthalmology and Visual Sciences, and Department of Radiation Oncology, Vanderbilt Eye Institute and Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Kamakshi L. Sishtla
- Department of Pharmacology and Toxicology, Department of Ophthalmology, Department of Biochemistry and Molecular Biology, and Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Carley M. Bogan
- Division of Ocular Oncology and Pathology, Department of Ophthalmology and Visual Sciences, and Department of Radiation Oncology, Vanderbilt Eye Institute and Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Janene M. Pierce
- Division of Ocular Oncology and Pathology, Department of Ophthalmology and Visual Sciences, and Department of Radiation Oncology, Vanderbilt Eye Institute and Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Sheau-Chiann Chen
- Center for Quantitative Sciences, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Liya Xu
- Children's Hospital - Los Angeles, University of Southern California, Los Angeles, California, United States
| | - Jesse L. Berry
- Children's Hospital - Los Angeles, University of Southern California, Los Angeles, California, United States
| | - Timothy W. Corson
- Department of Pharmacology and Toxicology, Department of Ophthalmology, Department of Biochemistry and Molecular Biology, and Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana, United States
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3
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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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Goldberg DC, Cloud C, Lee SM, Barnes B, Gruber S, Kim E, Pottekat A, Westphal M, McAuliffe L, Majournie E, KalayilManian M, Zhu Q, Tran C, Hansen M, Parker JB, Kohli RM, Porecha R, Renke N, Zhou W. MSA: scalable DNA methylation screening BeadChip for high-throughput trait association studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594606. [PMID: 38826316 PMCID: PMC11142114 DOI: 10.1101/2024.05.17.594606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The Infinium DNA Methylation BeadChips have significantly contributed to population-scale epigenetics research by enabling epigenome-wide trait association discoveries. Here, we design, describe, and experimentally verify a new iteration of this technology, the Methylation Screening Array (MSA), to focus on human trait screening and discovery. This array utilizes extensive data from previous Infinium platform-based epigenome-wide association studies (EWAS). It incorporates knowledge from the latest single-cell and cell type-resolution whole genome methylome profiles. The MSA is engineered to achieve scalable screening of epigenetics-trait association in an ultra-high sample throughput. Our design encompassed diverse human trait associations, including those with genetic, cellular, environmental, and demographical variables and human diseases such as genetic, neurodegenerative, cardiovascular, infectious, and immune diseases. We comprehensively evaluated this array's reproducibility, accuracy, and capacity for cell-type deconvolution and supporting 5-hydroxymethylation profiling in diverse human tissues. Our first atlas data using this platform uncovered the complex chromatin and tissue contexts of DNA modification variations and genetic variants linked to human phenotypes.
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Affiliation(s)
- David C Goldberg
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Cameron Cloud
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Sol Moe Lee
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | | | | | - Elliot Kim
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | | | | | | | | | | | | | | | | | - Jared B Parker
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | | | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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Tang J, Liu Y, Wang Y, Zhang Z, Nie J, Wang X, Ai S, Li J, Gao Y, Li C, Cheng C, Su S, Chen S, Zhang P, Lu R. Deciphering metabolic heterogeneity in retinoblastoma unravels the role of monocarboxylate transporter 1 in tumor progression. Biomark Res 2024; 12:48. [PMID: 38730450 PMCID: PMC11088057 DOI: 10.1186/s40364-024-00596-8] [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: 04/03/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Tumors exhibit metabolic heterogeneity, influencing cancer progression. However, understanding metabolic diversity in retinoblastoma (RB), the primary intraocular malignancy in children, remains limited. METHODS The metabolic landscape of RB was constructed based on single-cell transcriptomic sequencing from 11 RB and 5 retina samples. Various analyses were conducted, including assessing overall metabolic activity, metabolic heterogeneity, and the correlation between hypoxia and metabolic pathways. Additionally, the expression pattern of the monocarboxylate transporter (MCT) family in different cell clusters was examined. Validation assays of MCT1 expression and function in RB cell lines were performed. The therapeutic potential of targeting MCT1 was evaluated using an orthotopic xenograft model. A cohort of 47 RB patients was analyzed to evaluate the relationship between MCT1 expression and tumor invasion. RESULTS Distinct metabolic patterns in RB cells, notably increased glycolysis, were identified. This metabolic heterogeneity correlated closely with hypoxia. MCT1 emerged as the primary monocarboxylate transporter in RB cells. Disrupting MCT1 altered cell viability and energy metabolism. In vivo studies using the MCT1 inhibitor AZD3965 effectively suppressed RB tumor growth. Additionally, a correlation between MCT1 expression and optic nerve invasion in RB samples suggested prognostic implications. CONCLUSIONS This study enhances our understanding of RB metabolic characteristics at the single-cell level, highlighting the significance of MCT1 in RB pathogenesis. Targeting MCT1 holds promise as a therapeutic strategy for combating RB, with potential prognostic implications.
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Affiliation(s)
- Junjie Tang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yaoming Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yinghao Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Zhihui Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Jiahe Nie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Xinyue Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Siming Ai
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Jinmiao Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yang Gao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Cheng Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Chao Cheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Shicai Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Shuxia Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Ping Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Rong Lu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
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Lee SM, Loo C, Prasasya R, Bartolomei M, Kohli R, Zhou W. Low-input and single-cell methods for Infinium DNA methylation BeadChips. Nucleic Acids Res 2024; 52:e38. [PMID: 38407446 PMCID: PMC11040145 DOI: 10.1093/nar/gkae127] [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: 09/11/2023] [Revised: 01/29/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
The Infinium BeadChip is the most widely used DNA methylome assay technology for population-scale epigenome profiling. However, the standard workflow requires over 200 ng of input DNA, hindering its application to small cell-number samples, such as primordial germ cells. We developed experimental and analysis workflows to extend this technology to suboptimal input DNA conditions, including ultra-low input down to single cells. DNA preamplification significantly enhanced detection rates to over 50% in five-cell samples and ∼25% in single cells. Enzymatic conversion also substantially improved data quality. Computationally, we developed a method to model the background signal's influence on the DNA methylation level readings. The modified detection P-value calculation achieved higher sensitivities for low-input datasets and was validated in over 100 000 public diverse methylome profiles. We employed the optimized workflow to query the demethylation dynamics in mouse primordial germ cells available at low cell numbers. Our data revealed nuanced chromatin states, sex disparities, and the role of DNA methylation in transposable element regulation during germ cell development. Collectively, we present comprehensive experimental and computational solutions to extend this widely used methylation assay technology to applications with limited DNA.
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Affiliation(s)
- Sol Moe Lee
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA 19104, USA
| | - Christian E Loo
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rexxi D Prasasya
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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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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8
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Cobrinik D. Retinoblastoma Origins and Destinations. N Engl J Med 2024; 390:1408-1419. [PMID: 38631004 DOI: 10.1056/nejmra1803083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Affiliation(s)
- David Cobrinik
- From the Vision Center, Department of Surgery, and Saban Research Institute, Children's Hospital Los Angeles, and the Departments of Ophthalmology and Biochemistry and Molecular Medicine, Roski Eye Institute, and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California - both in Los Angeles
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9
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Joseph S, Pike S, Peng CC, Brown B, Xu L, Berry JL, Chévez-Barrios P, Hubbard GB, Grossniklaus HE. Retinoblastoma with MYCN Amplification Diagnosed from Cell-Free DNA in the Aqueous Humor. Ocul Oncol Pathol 2024; 10:15-24. [PMID: 38751495 PMCID: PMC11095586 DOI: 10.1159/000533311] [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: 05/17/2023] [Accepted: 07/26/2023] [Indexed: 05/18/2024] Open
Abstract
Introduction The objective of this study was to report the clinicopathologic features of three cases of MYCN-amplified retinoblastoma identified genetically by aqueous humor sampling. Methods Whole-genome sequencing was performed using isolated cell-free DNA (cfDNA) from aqueous humor of 3 retinoblastoma patients. We analyzed genomic copy number and mutational alterations, histologic and pathologic features, and clinical data. Results The most common genetic alteration identified in these three retinoblastoma cases was a focal MYCN amplification on 2p. All tumors showed an early age of diagnosis with a median of 9 months. The tumor histopathologic features included neovascularization and subretinal seeding in case 1, diffuse nature with choroidal and prelaminar optic nerve invasion in case 2, and complete vitreous seeding in case 3. Case 1 expressed RB protein and had no RB1 mutation, case 2 did not express RB protein and had an RB1 mutation, and case 3 did not express RB protein and likely had an epigenetic effect on RB expression. Conclusions Our report shows 3 cases of unilateral retinoblastomas diagnosed in patients ranging from 4 months to 18 months old. Genomic analysis from AH cfDNA revealed MYCN amplification with intact RB protein staining in case 1 and lack of RB staining in cases 2 and 3. RB1 mutational analysis in the AH confirmed a pathogenic variant in case 2. Clinical pathology showed features requiring aggressive treatment, specifically enucleation. Importance MYCN-amplified retinoblastomas demonstrate unique pathogenesis and aggressive behavior, regardless if MYCN is a primary or secondary driver of disease. Genomic analysis from aqueous humor may be useful when deciding to enucleate as opposed to treating conservatively. Focal MYCN amplification on 2p might be relevant for tumor growth in this subset of the retinoblastoma population in terms of targeted therapeutics.
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Affiliation(s)
- Sarah Joseph
- Department of Ophthalmology, Emory University School of Medicine, Los Angeles, CA, USA
| | - Sarah Pike
- Children’s Hospital Los Angeles and the USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chen-Ching Peng
- Children’s Hospital Los Angeles and the USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Brianne Brown
- Children’s Hospital Los Angeles and the USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Liya Xu
- Children’s Hospital Los Angeles and the USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Jesse L. Berry
- Children’s Hospital Los Angeles and the USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - G. Baker Hubbard
- Department of Ophthalmology, Emory University School of Medicine, Los Angeles, CA, USA
| | - Hans E. Grossniklaus
- Department of Ophthalmology, Emory University School of Medicine, Los Angeles, CA, USA
- Department of Pathology, Emory University School of Medicine, Los Angeles, CA, USA
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10
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Zhou M, Tang J, Fan J, Wen X, Shen J, Jia R, Chai P, Fan X. Recent progress in retinoblastoma: Pathogenesis, presentation, diagnosis and management. Asia Pac J Ophthalmol (Phila) 2024; 13:100058. [PMID: 38615905 DOI: 10.1016/j.apjo.2024.100058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 04/16/2024] Open
Abstract
Retinoblastoma, the primary ocular malignancy in pediatric patients, poses a substantial threat to mortality without prompt and effective management. The prognosis for survival and preservation of visual acuity hinges upon the disease severity at the time of initial diagnosis. Notably, retinoblastoma has played a crucial role in unraveling the genetic foundations of oncogenesis. The process of tumorigenesis commonly begins with the occurrence of biallelic mutation in the RB1 tumor suppressor gene, which is then followed by a cascade of genetic and epigenetic alterations that correspond to the clinical stage and pathological features of the tumor. The RB1 gene, recognized as a tumor suppressor, encodes the retinoblastoma protein, which plays a vital role in governing cellular replication through interactions with E2F transcription factors and chromatin remodeling proteins. The diagnosis and treatment of retinoblastoma necessitate consideration of numerous factors, including disease staging, germline mutation status, family psychosocial factors, and the resources available within the institution. This review has systematically compiled and categorized the latest developments in the diagnosis and treatment of retinoblastoma which enhanced the quality of care for this pediatric malignancy.
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Affiliation(s)
- Min Zhou
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China
| | - Jieling Tang
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China
| | - Jiayan Fan
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China
| | - Xuyang Wen
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China
| | - Jianfeng Shen
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China
| | - Renbing Jia
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China
| | - Peiwei Chai
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China.
| | - Xianqun Fan
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 20025, People's Republic of China.
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11
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Tonti E, Dell'Omo R, Filippelli M, Spadea L, Salati C, Gagliano C, Musa M, Zeppieri M. Exploring Epigenetic Modifications as Potential Biomarkers and Therapeutic Targets in Glaucoma. Int J Mol Sci 2024; 25:2822. [PMID: 38474069 DOI: 10.3390/ijms25052822] [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: 02/07/2024] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Glaucoma, a complex and multifactorial neurodegenerative disorder, is a leading cause of irreversible blindness worldwide. Despite significant advancements in our understanding of its pathogenesis and management, early diagnosis and effective treatment of glaucoma remain major clinical challenges. Epigenetic modifications, encompassing deoxyribonucleic acid (DNA) methylation, histone modifications, and non-coding RNAs, have emerged as critical regulators of gene expression and cellular processes. The aim of this comprehensive review focuses on the emerging field of epigenetics and its role in understanding the complex genetic and molecular mechanisms underlying glaucoma. The review will provide an overview of the pathophysiology of glaucoma, emphasizing the intricacies of intraocular pressure regulation, retinal ganglion cell dysfunction, and optic nerve damage. It explores how epigenetic modifications, such as DNA methylation and histone modifications, can influence gene expression, and how these mechanisms are implicated in glaucomatous neurodegeneration and contribute to glaucoma pathogenesis. The manuscript discusses evidence from both animal models and human studies, providing insights into the epigenetic alterations associated with glaucoma onset and progression. Additionally, it discusses the potential of using epigenetic modifications as diagnostic biomarkers and therapeutic targets for more personalized and targeted glaucoma treatment.
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Affiliation(s)
- Emanuele Tonti
- Eye Clinic, Policlinico Umberto I University Hospital, 00142 Rome, Italy
| | - Roberto Dell'Omo
- Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Via Francesco De Sanctis 1, 86100 Campobasso, Italy
| | - Mariaelena Filippelli
- Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Via Francesco De Sanctis 1, 86100 Campobasso, Italy
| | - Leopoldo Spadea
- Eye Clinic, Policlinico Umberto I University Hospital, 00142 Rome, Italy
| | - Carlo Salati
- Department of Ophthalmology, University Hospital of Udine, 33100 Udine, Italy
| | - Caterina Gagliano
- Faculty of Medicine and Surgery, University of Enna "Kore", Piazza dell'Università, 94100 Enna, Italy
- Eye Clinic, Catania University, San Marco Hospital, Viale Carlo Azeglio Ciampi, 95121 Catania, Italy
| | - Mutali Musa
- Department of Optometry, University of Benin, Benin City 300238, Nigeria
| | - Marco Zeppieri
- Department of Ophthalmology, University Hospital of Udine, 33100 Udine, Italy
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12
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Wolf J, Franco JA, Yip R, Dabaja MZ, Velez G, Liu F, Bassuk AG, Mruthyunjaya P, Dufour A, Mahajan VB. Liquid Biopsy Proteomics in Ophthalmology. J Proteome Res 2024; 23:511-522. [PMID: 38171013 PMCID: PMC10845144 DOI: 10.1021/acs.jproteome.3c00756] [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: 11/11/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024]
Abstract
Minimally invasive liquid biopsies from the eye capture locally enriched fluids that contain thousands of proteins from highly specialized ocular cell types, presenting a promising alternative to solid tissue biopsies. The advantages of liquid biopsies include sampling the eye without causing irreversible functional damage, potentially better reflecting tissue heterogeneity, collecting samples in an outpatient setting, monitoring therapeutic response with sequential sampling, and even allowing examination of disease mechanisms at the cell level in living humans, an approach that we refer to as TEMPO (Tracing Expression of Multiple Protein Origins). Liquid biopsy proteomics has the potential to transform molecular diagnostics and prognostics and to assess disease mechanisms and personalized therapeutic strategies in individual patients. This review addresses opportunities, challenges, and future directions of high-resolution liquid biopsy proteomics in ophthalmology, with particular emphasis on the large-scale collection of high-quality samples, cutting edge proteomics technology, and artificial intelligence-supported data analysis.
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Affiliation(s)
- Julian Wolf
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Joel A. Franco
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Rui Yip
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Mohamed Ziad Dabaja
- Departments
of Physiology and Pharmacology & Biochemistry and Molecular Biology,
Cumming School of Medicine, University of
Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Gabriel Velez
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Fei Liu
- Department
of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Alexander G. Bassuk
- Department
of Pediatrics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Prithvi Mruthyunjaya
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Antoine Dufour
- Departments
of Physiology and Pharmacology & Biochemistry and Molecular Biology,
Cumming School of Medicine, University of
Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Vinit B. Mahajan
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
- Veterans
Affairs Palo Alto Health Care System, Palo Alto, California 94304, United States
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13
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Muniyandi A, Jensen NR, Devanathan N, Dimaras H, Corson TW. The Potential of Aqueous Humor Sampling in Diagnosis, Prognosis, and Treatment of Retinoblastoma. Invest Ophthalmol Vis Sci 2024; 65:18. [PMID: 38180770 PMCID: PMC10774694 DOI: 10.1167/iovs.65.1.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 11/27/2023] [Indexed: 01/06/2024] Open
Abstract
Retinoblastoma (RB) is a rare malignant tumor that arises in the developing retina in one or both eyes of children. Pathogenic variants of the RB1 tumor suppressor gene drive the majority of germline and sporadic RB tumors. Considering the risk of tumor spread, the biopsy of RB tumor tissue is contraindicated. Advancement of chemotherapy has led to preservation of more eye globes. However, this has reduced access to tumor material from enucleation specimens. Recently, liquid biopsy of aqueous humor (AH) has advanced the RB tumor- or eye-specific genetic analysis. In particular, nucleic acid analysis of AH demonstrates the genomic copy number profiles and RB1 pathogenic variants akin to that of enucleated RB eye tissue. This advance reduces the previous limitation that genetic assessment of the primary tumor could be done only after enucleation of the eye. Additionally, nucleic acid evaluation of AH allows the exploration of the genomic landscape of RB tumors at diagnosis and during and after treatment. This review explores how AH sampling and AH nucleic acid analysis in RB patients assist in diagnosis, prognosis, and comprehending the pathophysiology of RB, which will ultimately benefit individualized treatment decisions to carefully manage this ocular cancer in children.
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Affiliation(s)
- Anbukkarasi Muniyandi
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Nathan R. Jensen
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Department of Ophthalmology, University of Utah, Salt Lake City, Utah, United States
| | - Nirupama Devanathan
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Helen Dimaras
- Department of Ophthalmology and Vision Sciences, Hospital for Sick Children, Toronto, Ontario, Canada
- Child Health Evaluative Sciences Program, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario
- Division of Clinical Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Timothy W. Corson
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, United States
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
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14
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Tang J, Liu Y, Zhang Z, Ren Y, Ma Y, Wang Y, Li J, Gao Y, Li C, Cheng C, Su S, Chen S, Zhang P, Lu R. Heterogeneous Expression Patterns of the Minichromosome Maintenance Complex Members in Retinoblastoma Unveil Its Clinical Significance. Invest Ophthalmol Vis Sci 2024; 65:31. [PMID: 38231525 PMCID: PMC10795548 DOI: 10.1167/iovs.65.1.31] [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: 10/10/2023] [Accepted: 12/28/2023] [Indexed: 01/18/2024] Open
Abstract
Purpose To explore the expression patterns and clinical significance of minichromosome maintenance (MCM) complex members in retinoblastoma (RB). Methods Single-cell RNA sequencing datasets from five normal retina, six intraocular, and five extraocular RB samples were integrated to characterize the expression patterns of MCM complex members at the single-cell level. Western blot and quantitative PCR were used to detect the expression of MCM complex members in RB cell lines. Immunohistochemistry was conducted to validate the expression of MCM complex members in RB patient samples and a RB mouse model. Results The expression of MCM2-7 is increased in RB tissue, with MCM2/3/7 showing particularly higher levels in extraocular RB. MCM3/7 are abundantly detected in cell types associated with oncogenesis. Both mRNA and protein levels of MCM3/4/6/7 are increased in RB cell lines. Immunohistochemistry further confirmed the elevated expression of MCM3 in extraocular RB, with MCM6 being the most abundantly expressed MCM in RB. Conclusions The distinct MCM expression patterns across various RB cell types suggest diverse functional roles, offering valuable insights for targeted therapeutic strategies. The upregulation of MCM3, MCM4, MCM6, and MCM7 in RB, with a specific emphasis on MCM6 as a notable marker, highlights their potential significance.
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Affiliation(s)
- Junjie Tang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yaoming Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhihui Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yi Ren
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yujun Ma
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yinghao Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jinmiao Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yang Gao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Cheng Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Chao Cheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Shicai Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Shuxia Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Ping Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Rong Lu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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15
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Velez G, Wolf J, Dufour A, Mruthyunjaya P, Mahajan VB. Cross-Platform Identification and Validation of Uveal Melanoma Vitreous Protein Biomarkers. Invest Ophthalmol Vis Sci 2023; 64:14. [PMID: 37955612 PMCID: PMC10653261 DOI: 10.1167/iovs.64.14.14] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Purpose The purpose of this study was to profile protein expression liquid vitreous biopsies from patients with uveal melanoma (UM) using mass spectrometry to identify prognostic biomarkers, signaling pathways, and therapeutic targets. Methods Vitreous biopsies were collected from two cohorts in a pilot study: comparative control eyes with epiretinal membranes (ERM; n = 3) and test eyes with UM (n = 8). Samples were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Identified proteins were compared to data from a targeted multiplex ELISA proteomics platform. Results A total of 69 significantly elevated proteins were detected in the UM vitreous, including LYVE-1. LC-MS/MS identified 62 significantly upregulated proteins in UM vitreous that were not previously identified by ELISA. Analysis of differential protein expression by tumor molecular classification (gene expression profiling [GEP] and preferentially expressed antigen in melanoma [PRAME]) further identified proteins that correlated with these classifications. Patients with high-risk GEP tumors displayed elevated vitreous expression of HGFR (fold-change [FC] = 2.66E + 03, P value = 0.003) and PYGL (FC = 1.02E + 04, P = 1.72E-08). Patients with PRAME positive tumors displayed elevated vitreous expression of ENPP-2 (FC = 3.21, P = 0.04), NEO1 (FC = 2.65E + 03, P = 0.002), and LRP1 (FC = 5.59E + 02, P value = 0.01). IGF regulatory effectors were highly represented (P value = 1.74E-16). Cross-platform analysis validated seven proteins identified by ELISA and LC-MS/MS. Conclusions Proteomic analysis of liquid biopsies may provide prognostic information supporting gene expression of tumor biopsies. The use of multiple protein detection platforms in the same patient samples increases the sensitivity of candidate biomarker detection and allows for precise characterization of the vitreous proteome.
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Affiliation(s)
- Gabriel Velez
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, United States
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, United States
| | - Julian Wolf
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, United States
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, United States
| | - Antoine Dufour
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Prithvi Mruthyunjaya
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, United States
| | - Vinit B. Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, United States
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, United States
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California, United States
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16
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Lee SM, Loo CE, Prasasya RD, Bartolomei MS, Kohli RM, Zhou W. Low-input and single-cell methods for Infinium DNA methylation BeadChips. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558252. [PMID: 37786695 PMCID: PMC10541608 DOI: 10.1101/2023.09.18.558252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The Infinium BeadChip is the most widely used DNA methylome assay technology for population-scale epigenome profiling. However, the standard workflow requires over 200 ng of input DNA, hindering its application to small cell-number samples, such as primordial germ cells. We developed experimental and analysis workflows to extend this technology to suboptimal input DNA conditions, including ultra-low input down to single cells. DNA preamplification significantly enhanced detection rates to over 50% in five-cell samples and ∼25% in single cells. Enzymatic conversion also substantially improved data quality. Computationally, we developed a method to model the background signal's influence on the DNA methylation level readings. The modified detection p -values calculation achieved higher sensitivities for low-input datasets and was validated in over 100,000 public datasets with diverse methylation profiles. We employed the optimized workflow to query the demethylation dynamics in mouse primordial germ cells available at low cell numbers. Our data revealed nuanced chromatin states, sex disparities, and the role of DNA methylation in transposable element regulation during germ cell development. Collectively, we present comprehensive experimental and computational solutions to extend this widely used methylation assay technology to applications with limited DNA.
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17
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Herrgott GA, Snyder JM, She R, Malta TM, Sabedot TS, Lee IY, Pawloski J, Podolsky-Gondim GG, Asmaro KP, Zhang J, Cannella CE, Nelson K, Thomas B, deCarvalho AC, Hasselbach LA, Tundo KM, Newaz R, Transou A, Morosini N, Francisco V, Poisson LM, Chitale D, Mukherjee A, Mosella MS, Robin AM, Walbert T, Rosenblum M, Mikkelsen T, Kalkanis S, Tirapelli DPC, Weisenberger DJ, Carlotti CG, Rock J, Castro AV, Noushmehr H. Detection of diagnostic and prognostic methylation-based signatures in liquid biopsy specimens from patients with meningiomas. Nat Commun 2023; 14:5669. [PMID: 37704607 PMCID: PMC10499807 DOI: 10.1038/s41467-023-41434-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
Recurrence of meningiomas is unpredictable by current invasive methods based on surgically removed specimens. Identification of patients likely to recur using noninvasive approaches could inform treatment strategy, whether intervention or monitoring. In this study, we analyze the DNA methylation levels in blood (serum and plasma) and tissue samples from 155 meningioma patients, compared to other central nervous system tumor and non-tumor entities. We discover DNA methylation markers unique to meningiomas and use artificial intelligence to create accurate and universal models for identifying and predicting meningioma recurrence, using either blood or tissue samples. Here we show that liquid biopsy is a potential noninvasive and reliable tool for diagnosing and predicting outcomes in meningioma patients. This approach can improve personalized management strategies for these patients.
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Affiliation(s)
- Grayson A Herrgott
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - James M Snyder
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Ruicong She
- Department of Public Health, Biostatistics, Henry Ford Health, Detroit, MI, USA
| | - Tathiane M Malta
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Thais S Sabedot
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Ian Y Lee
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Jacob Pawloski
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Guilherme G Podolsky-Gondim
- Department of Neurosurgery, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Karam P Asmaro
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Jiaqi Zhang
- Department of Public Health, Biostatistics, Henry Ford Health, Detroit, MI, USA
| | - Cara E Cannella
- Department of Public Health, Biostatistics, Henry Ford Health, Detroit, MI, USA
| | - Kevin Nelson
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Bartow Thomas
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Ana C deCarvalho
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Laura A Hasselbach
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Kelly M Tundo
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Rehnuma Newaz
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Andrea Transou
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Natalia Morosini
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Victor Francisco
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Laila M Poisson
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
- Department of Public Health, Biostatistics, Henry Ford Health, Detroit, MI, USA
| | | | - Abir Mukherjee
- Department of Pathology, Henry Ford Health, Detroit, MI, USA
| | - Maritza S Mosella
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Adam M Robin
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Tobias Walbert
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Mark Rosenblum
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Tom Mikkelsen
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Steven Kalkanis
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Daniela P C Tirapelli
- Department of Neurosurgery, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Carlos G Carlotti
- Department of Neurosurgery, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Jack Rock
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Ana Valeria Castro
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA.
- Department of Physiology, Michigan State University, E. Lansing, MI, USA.
| | - Houtan Noushmehr
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA.
- Department of Physiology, Michigan State University, E. Lansing, MI, USA.
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18
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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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19
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Schultz KAP, Chintagumpala M, Piao J, Chen KS, Gartrell R, Christison-Lagay E, Berry JL, Shah R, Laetsch TW. Children's Oncology Group's 2023 blueprint for research: Rare tumors. Pediatr Blood Cancer 2023; 70 Suppl 6:e30574. [PMID: 37458616 PMCID: PMC10529839 DOI: 10.1002/pbc.30574] [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: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/22/2023]
Abstract
The Children's Oncology Group (COG) Rare Tumor Committee includes the Infrequent Tumor and Retinoblastoma subcommittees, encompassing a wide range of extracranial solid tumors that do not fall within another COG disease committee. Current therapeutic trial development focuses on nasopharyngeal carcinoma, adrenocortical carcinoma, pleuropulmonary blastoma, colorectal carcinoma, melanoma, and thyroid carcinoma. Given the rarity of these tumors, novel strategies and international collaborative efforts are necessary to advance research and improve outcomes.
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Affiliation(s)
| | - Murali Chintagumpala
- Division of Hematology-Oncology, Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Jin Piao
- University of Southern California Keck School of Medicine, Los Angeles, CA
| | - Kenneth S. Chen
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX
| | - Robyn Gartrell
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Emily Christison-Lagay
- Division of Pediatric Surgery, Yale School of Medicine, Yale New-Haven Children’s Hospital, New Haven, CT
| | - Jesse L. Berry
- The Vision Center, Children's Hospital Los Angeles, The Saban Research Institute, Children's Hospital Los Angeles, USC Roski Eye Institute, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Rachana Shah
- Division of Hematology-Oncology, Department of Pediatrics, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Theodore W. Laetsch
- Division of Oncology, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA
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20
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He LF, Mou P, Yang CH, Huang C, Shen Y, Zhang JD, Wei RL. Single-cell sequencing in primary intraocular tumors: understanding heterogeneity, the microenvironment, and drug resistance. Front Immunol 2023; 14:1194590. [PMID: 37359513 PMCID: PMC10287964 DOI: 10.3389/fimmu.2023.1194590] [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: 03/27/2023] [Accepted: 05/02/2023] [Indexed: 06/28/2023] Open
Abstract
Retinoblastoma (RB) and uveal melanoma (UM) are the most common primary intraocular tumors in children and adults, respectively. Despite continued increases in the likelihood of salvaging the eyeball due to advancements in local tumor control, prognosis remains poor once metastasis has occurred. Traditional sequencing technology obtains averaged information from pooled clusters of diverse cells. In contrast, single-cell sequencing (SCS) allows for investigations of tumor biology at the resolution of the individual cell, providing insights into tumor heterogeneity, microenvironmental properties, and cellular genomic mutations. SCS is a powerful tool that can help identify new biomarkers for diagnosis and targeted therapy, which may in turn greatly improve tumor management. In this review, we focus on the application of SCS for evaluating heterogeneity, microenvironmental characteristics, and drug resistance in patients with RB and UM.
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Affiliation(s)
- Lin-feng He
- Department of Ophthalmology, Changzheng Hospital of Naval Medical University, Shanghai, China
| | - Pei Mou
- Department of Ophthalmology, Changzheng Hospital of Naval Medical University, Shanghai, China
| | - Chun-hui Yang
- Department of Ophthalmology, Changzheng Hospital of Naval Medical University, Shanghai, China
| | - Cheng Huang
- 92882 Troops of the Chinese People’s Liberation Army, Qingdao, China
| | - Ya Shen
- Department of Ophthalmology, Changzheng Hospital of Naval Medical University, Shanghai, China
| | - Jin-di Zhang
- Department of Ophthalmology, Changzheng Hospital of Naval Medical University, Shanghai, China
| | - Rui-li Wei
- Department of Ophthalmology, Changzheng Hospital of Naval Medical University, Shanghai, China
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21
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Schmidt MJ, Prabakar RK, Pike S, Yellapantula V, Peng CC, Kuhn P, Hicks J, Xu L, Berry JL. Simultaneous Copy Number Alteration and Single-Nucleotide Variation Analysis in Matched Aqueous Humor and Tumor Samples in Children with Retinoblastoma. Int J Mol Sci 2023; 24:ijms24108606. [PMID: 37239954 DOI: 10.3390/ijms24108606] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/09/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Retinoblastoma (RB) is a childhood cancer that forms in the developing retina of young children; this tumor cannot be biopsied due to the risk of provoking extraocular tumor spread, which dramatically alters the treatment and survival of the patient. Recently, aqueous humor (AH), the clear fluid in the anterior chamber of the eye, has been developed as an organ-specific liquid biopsy for investigation of in vivo tumor-derived information found in the cell-free DNA (cfDNA) of the biofluid. However, identifying somatic genomic alterations, including both somatic copy number alterations (SCNAs) and single nucleotide variations (SNVs) of the RB1 gene, typically requires either: (1) two distinct experimental protocols-low-pass whole genome sequencing for SCNAs and targeted sequencing for SNVs-or (2) expensive deep whole genome or exome sequencing. To save time and cost, we applied a one-step targeted sequencing method to identify both SCNAs and RB1 SNVs in children with RB. High concordance (median = 96.2%) was observed in comparing SCNA calls derived from targeted sequencing to the traditional low-pass whole genome sequencing method. We further applied this method to investigate the degree of concordance of genomic alterations between paired tumor and AH samples from 11 RB eyes. We found 11/11 AH samples (100%) had SCNAs, and 10 of them (90.1%) with recurrent RB-SCNAs, while only nine out of 11 tumor samples (81.8%) had positive RB-SCNA signatures in both low-pass and targeted methods. Eight out of the nine (88.9%) detected SNVs were shared between AH and tumor samples. Ultimately, 11/11 cases have somatic alterations identified, including nine RB1 SNVs and 10 recurrent RB-SCNAs with four focal RB1 deletions and one MYCN gain. The results presented show the feasibility of utilizing one sequencing approach to obtain SCNA and targeted SNV data to capture a broad genomic scope of RB disease, which may ultimately expedite clinical intervention and be less expensive than other methods.
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Affiliation(s)
- 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, CA 90089, 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, CA 90089, USA
| | - Sarah Pike
- The Vision Center, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Venkata Yellapantula
- The Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Chen-Ching Peng
- The Vision Center, Children's Hospital Los Angeles, Los Angeles, CA 90027, 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, CA 90089, 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, CA 90089, USA
| | - Liya Xu
- The Vision Center, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jesse L Berry
- The Vision Center, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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22
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Im DH, Pike S, Reid MW, Peng CC, Sirivolu S, Grossniklaus HE, Hubbard GB, Skalet AH, Bellsmith KN, Shields CL, Lally SE, Stacey AW, Reiser BJ, Nagiel A, Shah R, Xu L, Berry JL. A multicenter analysis of nucleic acid quantification using aqueous humor liquid biopsy in retinoblastoma – Implications for clinical testing. OPHTHALMOLOGY SCIENCE 2023; 3:100289. [PMID: 37025945 PMCID: PMC10070901 DOI: 10.1016/j.xops.2023.100289] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023]
Abstract
Purpose Retinoblastoma (RB) is most often diagnosed with clinical features and not diagnosed with tumor biopsy. This study describes tumor-derived analyte concentrations from aqueous humor (AH) liquid biopsy and its use in clinical assays. Design Case series study. Participants Sixty-two RB eyes from 55 children and 14 control eyes from 12 children from 4 medical centers. Methods This study included 128 RB AH samples including: diagnostic (DX) samples, samples from eyes undergoing treatment (TX), samples after completing treatment (END), and during bevacizumab injection for radiation therapy after completing RB treatment (BEV). Fourteen-control AH were analyzed for unprocessed analytes (double-stranded DNA [dsDNA], single-stranded DNA [ssDNA], micro-RNA [miRNA], RNA, and protein) with Qubit fluorescence assays. Double-stranded DNA from 2 RB AH samples underwent low-pass whole-genome sequencing to detect somatic copy number alterations. Logistic regression was used to predict disease burden given analyte concentrations. Main Outcome Measures Unprocessed analyte (dsDNA, ssDNA, miRNA, RNA and protein) concentrations. Results Results revealed dsDNA, ssDNA, miRNA, and proteins, but not RNA, were quantifiable in most samples (up to 98%) with Qubit fluorescence assays. Median dsDNA concentration was significantly higher in DX (3.08 ng/μl) compared to TX (0.18 ng/μl; P < 0.0001) at an order of 17 times greater and 20 times greater than END samples (0.15 ng/μl; P = 0.001). Using logistic regression, nucleic acid concentrations were useful in predicting higher versus lower RB disease burden. Retinoblastoma somatic copy number alterations were identified in a TX, but not in a BEV sample, indicating the correlation with RB activity. Conclusions Aqueous humor liquid biopsy in RB is a high-yield source of dsDNA, ssDNA, miRNA, and protein. Diagnostic samples are most useful for RB 1 gene mutational analyses. Genomic analysis may be more informative of tumor activity status than quantification alone and can be performed even with smaller analyte concentrations obtained from TX samples. Financial Disclosures Proprietary or commercial disclosure may be found after the references.
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Affiliation(s)
- Deborah H. Im
- Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Sarah Pike
- Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Mark W. Reid
- Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California
| | - Chen-Ching Peng
- Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Shreya Sirivolu
- Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | | | - G. Baker Hubbard
- Emory Eye Center, Emory University School of Medicine, Atlanta, Georgia
| | - Alison H. Skalet
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, Oregon
| | - Kellyn N. Bellsmith
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, Oregon
| | - Carol L. Shields
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Sara E. Lally
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Andrew W. Stacey
- Division of Ophthalmology, Department of Ophthalmology, Seattle Children’s Hospital, University of Washington, Seattle, Washington
| | - Bibiana J. Reiser
- Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Aaron Nagiel
- Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Rachana Shah
- Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Los Angeles, California
| | - Liya Xu
- Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Jesse L. Berry
- Department of Surgery, Division of Ophthalmology, The Vision Center at Children’s Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
- The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, California
- Correspondence: Jesse L. Berry, MD, Director of Ocular Oncology, Children’s Hospital Los Angeles, 4650 Sunset Blvd, Los Angeles, CA 90027.
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23
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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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24
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Nakamichi K, Stacey A, Mustafi D. Targeted long-read sequencing allows for rapid identification of pathogenic disease-causing variants in retinoblastoma. Ophthalmic Genet 2022; 43:762-770. [PMID: 36325802 DOI: 10.1080/13816810.2022.2141797] [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: 11/06/2022]
Abstract
BACKGROUND Identification of disease-causing variants of the retinoblastoma gene (RB1), the predominant cause of retinoblastoma, is challenging. Targeted long-read genome sequencing offers a novel approach to resolve the diverse range of pathogenic variants in RB1 and provides haplotype information rapidly. MATERIALS AND METHODS Genomic DNA was isolated from a venipuncture blood draw of a retinoblastoma patient. Whole genome sequencing (WGS) was carried out using the short-read Ilumina platform. WGS and targeted sequencing of RB1 was accomplished using the long-read Oxford Nanopore Technologies (ONT) platform. Deep-learning frameworks allowed haplotagging, variant calling, and variant annotation of both short- and long-read data. RESULTS Targeted long-read sequencing of the RB1 gene allowed for enhanced depth of read coverage for discovery of rare variants and haplotype analysis. A duplication leading to a frameshift and early termination in RB1 was identified as the most deleterious variant by all sequencing methods, with long-read technology providing additional information of methylation signal and haplotype information. More importantly, there was greater than 98% concordance of RB1 variants identified between short-read and targeted long-read sequencing modalities. CONCLUSIONS Targeted long-read technology allows for focused sequencing effort for variant discovery. Application of this for the first time in a retinoblastoma patient allowed haplotagged variant identification and demonstrated excellent concordance with benchmark short-read sequencing. The added benefit of targeted long-read sequencing to resolve disease-causing genomic variation in RB1 rapidly from a blood draw will provide a more definitive diagnosis of heritable RB and guide management decisions for patients and their families.
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Affiliation(s)
- Kenji Nakamichi
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, USA
| | - Andrew Stacey
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, USA.,Department of Ophthalmology, Seattle Children's Hospital, Seattlees, WA, USA
| | - Debarshi Mustafi
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, USA.,Department of Ophthalmology, Seattle Children's Hospital, Seattlees, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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