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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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Nag A, Khetan V. Retinoblastoma - A comprehensive review, update and recent advances. Indian J Ophthalmol 2024; 72:778-788. [PMID: 38804799 PMCID: PMC11232864 DOI: 10.4103/ijo.ijo_2414_23] [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: 09/01/2023] [Revised: 11/28/2023] [Accepted: 12/02/2023] [Indexed: 05/29/2024] Open
Abstract
Retinoblastoma is the most common pediatric ocular malignancy. It is triggered by a biallelic mutation in the RB1 gene or MYCN oncogene amplification. Retinoblastomas can be unilateral (60%-70%) or bilateral (30%-40%); bilateral tumors are always heritable and present at an earlier age as compared to unilateral ones (18-24 months vs. 36 months in India). High prevalence rates, delayed presentation, and inaccessibility to healthcare lead to worse outcomes in developing countries. The past few decades have seen a paradigm change in the treatment of retinoblastomas, shifting from enucleation and external beam radiotherapy to less aggressive modalities for eye salvage. Multimodality treatment is now the standard of care and includes intraarterial or intravenous chemotherapy along with focal consolidation therapies such as transpupillary thermotherapy, cryotherapy, and laser photocoagulation. Intravitreal and intracameral chemotherapy can help in controlling intraocular seeds. Advanced extraocular or metastatic tumors still have a poor prognosis. Genetic testing, counseling, and screening of at-risk family members must be incorporated as essential parts of management. A better understanding of the genetics and molecular basis of retinoblastoma has opened up the path for potential targeted therapy in the future. Novel recent advances such as liquid biopsy, prenatal diagnosis, prognostic biomarkers, tylectomy, and chemoplaque point to promising future directions.
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Affiliation(s)
- Adwaita Nag
- Ocular Oncology Service, Department of Ophthalmology and Vision Sciences, University of Toronto, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Vikas Khetan
- Formerly at Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai, Tamil Nadu, India
- Professor, Department of Ophthalmology, Flaum Eye Institute, Rochester, NY, USA
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Kurzawa-Akanbi M, Tzoumas N, Corral-Serrano JC, Guarascio R, Steel DH, Cheetham ME, Armstrong L, Lako M. Pluripotent stem cell-derived models of retinal disease: Elucidating pathogenesis, evaluating novel treatments, and estimating toxicity. Prog Retin Eye Res 2024; 100:101248. [PMID: 38369182 DOI: 10.1016/j.preteyeres.2024.101248] [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: 12/07/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Blindness poses a growing global challenge, with approximately 26% of cases attributed to degenerative retinal diseases. While gene therapy, optogenetic tools, photosensitive switches, and retinal prostheses offer hope for vision restoration, these high-cost therapies will benefit few patients. Understanding retinal diseases is therefore key to advance effective treatments, requiring in vitro models replicating pathology and allowing quantitative assessments for drug discovery. Pluripotent stem cells (PSCs) provide a unique solution given their limitless supply and ability to differentiate into light-responsive retinal tissues encompassing all cell types. This review focuses on the history and current state of photoreceptor and retinal pigment epithelium (RPE) cell generation from PSCs. We explore the applications of this technology in disease modelling, experimental therapy testing, biomarker identification, and toxicity studies. We consider challenges in scalability, standardisation, and reproducibility, and stress the importance of incorporating vasculature and immune cells into retinal organoids. We advocate for high-throughput automation in data acquisition and analyses and underscore the value of advanced micro-physiological systems that fully capture the interactions between the neural retina, RPE, and choriocapillaris.
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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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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] [Grants] [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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Luo Y, Xu M, Yang L, Yao Y, Berry JL, Xu L, Wen X, He X, Han M, Fan X, Fan J, Jia R. Correlating somatic copy number alteration in aqueous humour cfDNA with chemotherapy history, eye salvage and pathological features in retinoblastoma. Br J Ophthalmol 2024; 108:449-456. [PMID: 36931696 PMCID: PMC10505245 DOI: 10.1136/bjo-2022-322866] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/24/2023] [Indexed: 03/19/2023]
Abstract
BackgroundThis study determined to probe the potential association between somatic copy number alteration (SCNA) in retinoblastoma (RB) aqueous humour (AH) and pathological high-risk factors, clinical features and previous chemotherapy history. METHODS Single-centre retrospective cohort study from including 58 AH samples collected from 58 patients diagnosed. Among them, 41 samples were collected after enucleation and 17 samples were collected before intravitreal chemotherapy. SCNAs were accessed by conducting shallow whole-genome sequencing in cell-free (cf) DNA of AH. HRs and ORs were applied to measure risk factors. RESULTS Canonical RB SCNAs including 1q gain (87%), 2p gain (50%), 6p gain (76%), 16q loss (69%) were frequently detected. Non-classical RB SCNAs in AH including 17q gain (53%), 19q loss (43%), 7q gain (35%) were also commonly observed. 19q loss was significantly more common in patients with cT3c or worse stage than others (p=0.034). 2p gain(p=0.001) and 7q gain(p=0.001) were both more common in patients with primary enucleation than those with previous chemotherapy. Interestingly, both 2p gain (HR=1.933, p=0.027) and 7q gain (HR=2.394, p=0.005) might predict enucleation. Correlation analysis with pathological features among enucleated eyes showed that 19q loss can predict a higher risk for both massive choroid invasion (OR=4.909, p=0.038) and postlaminar optic nerve invasion (OR=4.250, p=0.043). DISCUSSION Sequencing of AH cfDNA in RB can provide sufficient in vivo information. 19q loss was a potential signature of advanced cases clinically and pathologically.Repeated sampling from eyes receiving sequential chemotherapy should be conducted to evaluate fluctuation of SCNA in future study.
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Affiliation(s)
- Yingxiu Luo
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Mingpeng Xu
- Department of ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ludi Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Yiran Yao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jesse L Berry
- USC Roski Eye Institute,Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Vision Center at Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Liya Xu
- Vision Center at Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Xuyang Wen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Xiaoyu He
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Minglei Han
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Xianqun Fan
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jiayan Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
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Macke EL, Miller AR, Stonerock E, Olshefski R, Zajo K, Bedrosian TA, Mardis ER, Akkari YMN, Cottrell CE, Schieffer KM. A LINE-1 mediated deletion resulting in germline retinoblastoma predisposition. Neurooncol Adv 2024; 6:vdad163. [PMID: 38213835 PMCID: PMC10783486 DOI: 10.1093/noajnl/vdad163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024] Open
Abstract
Retinoblastoma is an ocular cancer associated with genomic variation in the RB1 gene. In individuals with bilateral retinoblastoma, a germline variant in RB1 is identified in virtually all cases. We describe herein an individual with bilateral retinoblastoma for whom multiple clinical lab assays performed by outside commercial laboratories failed to identify a germline RB1 variant. Paired tumor/normal exome sequencing, long-read whole genome sequencing, and long-read isoform sequencing was performed on a translational research basis ultimately identified a germline likely de novo Long Interspersed Nuclear Element (LINE)-1 mediated deletion resulting in a premature stop of translation of RB1 as the underlying genetic cause of retinoblastoma in this individual. Based on these research findings, the LINE-1 mediated deletion was confirmed via Sanger sequencing in our clinical laboratory, and results were reported in the patient's medical record to allow for appropriate genetic counseling.
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Affiliation(s)
- Erica L Macke
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Anthony R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Eileen Stonerock
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Randal Olshefski
- Division of Hematology/Oncology/BMT, Department of Pediatrics, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Kristin Zajo
- Division of Hematology/Oncology/BMT, Department of Pediatrics, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Tracy A Bedrosian
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Yassmine M N Akkari
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
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Choi S, Cho N, Kim EM, Kim KK. The role of alternative pre-mRNA splicing in cancer progression. Cancer Cell Int 2023; 23:249. [PMID: 37875914 PMCID: PMC10594706 DOI: 10.1186/s12935-023-03094-3] [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: 09/06/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023] Open
Abstract
Alternative pre-mRNA splicing is a critical mechanism that generates multiple mRNA from a single gene, thereby increasing the diversity of the proteome. Recent research has highlighted the significance of specific splicing isoforms in cellular processes, particularly in regulating cell numbers. In this review, we examine the current understanding of the role of alternative splicing in controlling cancer cell growth and discuss specific splicing factors and isoforms and their molecular mechanisms in cancer progression. These isoforms have been found to intricately control signaling pathways crucial for cell cycle progression, proliferation, and apoptosis. Furthermore, studies have elucidated the characteristics and functional importance of splicing factors that influence cell numbers. Abnormal expression of oncogenic splicing isoforms and splicing factors, as well as disruptions in splicing caused by genetic mutations, have been implicated in the development and progression of tumors. Collectively, these findings provide valuable insights into the complex interplay between alternative splicing and cell proliferation, thereby suggesting the potential of alternative splicing as a therapeutic target for cancer.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Eun-Mi Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea.
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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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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Rathore S, Verma A, Ratna R, Marwa N, Ghiya Y, Honavar SG, Tiwari A, Das S, Varshney A. Retinoblastoma: A review of the molecular basis of tumor development and its clinical correlation in shaping future targeted treatment strategies. Indian J Ophthalmol 2023; 71:2662-2676. [PMID: 37417104 PMCID: PMC10491038 DOI: 10.4103/ijo.ijo_3172_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 04/25/2023] [Accepted: 05/21/2023] [Indexed: 07/08/2023] Open
Abstract
Retinoblastoma is a retinal cancer that affects children and is the most prevalent intraocular tumor worldwide. Despite tremendous breakthroughs in our understanding of the fundamental mechanisms that regulate progression of retinoblastoma, the development of targeted therapeutics for retinoblastoma has lagged. Our review highlights the current developments in the genetic, epigenetic, transcriptomic, and proteomic landscapes of retinoblastoma. We also discuss their clinical relevance and potential implications for future therapeutic development, with the aim to create a frontline multimodal therapy for retinoblastoma.
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Affiliation(s)
- Shruti Rathore
- Ocular Oncology Services, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
| | - Aman Verma
- Ocular Oncology Services, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
| | - Ria Ratna
- Ocular Genetics Services, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
| | - Navjot Marwa
- Ocular Oncology Services, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
| | - Yagya Ghiya
- Ocular Oncology Services, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
| | - Santosh G Honavar
- Ophthalmic Plastic Surgery, Orbit and Ocular Oncology, Centre for Sight, Hyderbad, Telangana, India
| | - Anil Tiwari
- Ocular Oncology Services, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
| | - Sima Das
- Ocular Oncology Services, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
| | - Akhil Varshney
- Ocular Oncology Services, Dr. Shroff’s Charity Eye Hospital, New Delhi, India
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Tovini L, Johnson SC, Guscott MA, Andersen AM, Spierings DCJ, Wardenaar R, Foijer F, McClelland SE. Targeted assembly of ectopic kinetochores to induce chromosome-specific segmental aneuploidies. EMBO J 2023; 42:e111587. [PMID: 37063065 PMCID: PMC10183824 DOI: 10.15252/embj.2022111587] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/18/2023] Open
Abstract
Cancer cells display persistent underlying chromosomal instability, with individual tumour types intriguingly exhibiting characteristic subsets of whole, and subchromosomal aneuploidies. Few methods to induce specific aneuploidies will exist, hampering investigation of functional consequences of recurrent aneuploidies, as well as the acute consequences of specific chromosome mis-segregation. We therefore investigated the possibility of sabotaging the mitotic segregation of specific chromosomes using nuclease-dead CRISPR-Cas9 (dCas9) as a cargo carrier to specific genomic loci. We recruited the kinetochore-nucleating domain of centromere protein CENP-T to assemble ectopic kinetochores either near the centromere of chromosome 9, or the telomere of chromosome 1. Ectopic kinetochore assembly led to increased chromosome instability and partial aneuploidy of the target chromosomes, providing the potential to induce specific chromosome mis-segregation events in a range of cell types. We also provide an analysis of putative endogenous repeats that could support ectopic kinetochore formation. Overall, our findings provide new insights into ectopic kinetochore biology and represent an important step towards investigating the role of specific aneuploidy and chromosome mis-segregation events in diseases associated with aneuploidy.
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Affiliation(s)
| | - Sarah C Johnson
- Centre for Cancer Genomics and Computational BiologyBarts Cancer Institute, Queen Mary University of LondonLondonUK
| | - Molly A Guscott
- Centre for Cancer Genomics and Computational BiologyBarts Cancer Institute, Queen Mary University of LondonLondonUK
| | - Alexander M Andersen
- Centre for Cancer Genomics and Computational BiologyBarts Cancer Institute, Queen Mary University of LondonLondonUK
| | - Diana Carolina Johanna Spierings
- European Research Institute for the Biology of AgeingUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - René Wardenaar
- European Research Institute for the Biology of AgeingUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of AgeingUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Sarah E McClelland
- Centre for Cancer Genomics and Computational BiologyBarts Cancer Institute, Queen Mary University of LondonLondonUK
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12
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Stachelek K, Harutyunyan N, Lee S, Beck A, Kim J, Xu L, Berry JL, Nagiel A, Reynolds CP, Murphree AL, Lee TC, Aparicio JG, Cobrinik D. Non-synonymous, synonymous, and non-coding nucleotide variants contribute to recurrently altered biological processes during retinoblastoma progression. Genes Chromosomes Cancer 2023; 62:275-289. [PMID: 36550020 PMCID: PMC10006380 DOI: 10.1002/gcc.23120] [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: 10/12/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Retinoblastomas form in response to biallelic RB1 mutations or MYCN amplification and progress to more aggressive and therapy-resistant phenotypes through accumulation of secondary genomic changes. Progression-related changes include recurrent somatic copy number alterations and typically non-recurrent nucleotide variants, including synonymous and non-coding variants, whose significance has been unclear. To determine if nucleotide variants recurrently affect specific biological processes, we identified altered genes and over-represented variant gene ontologies in 168 exome or whole-genome-sequenced retinoblastomas and 12 tumor-matched cell lines. In addition to RB1 mutations, MYCN amplification, and established retinoblastoma somatic copy number alterations, the analyses revealed enrichment of variant genes related to diverse biological processes including histone monoubiquitination, mRNA processing (P) body assembly, and mitotic sister chromatid segregation and cytokinesis. Importantly, non-coding and synonymous variants increased the enrichment significance of each over-represented biological process term. To assess the effects of such mutations, we examined the consequences of a 3' UTR variant of PCGF3 (a BCOR-binding component of Polycomb repressive complex I), dual 3' UTR variants of CDC14B (a regulator of sister chromatid segregation), and a synonymous variant of DYNC1H1 (a regulator of P-body assembly). One PCGF3 and one of two CDC14B 3' UTR variants impaired gene expression whereas a base-edited DYNC1H1 synonymous variant altered protease sensitivity and stability. Retinoblastoma cell lines retained only ~50% of variants detected in tumors and enriched for new variants affecting p53 signaling. These findings reveal potentially important differences in retinoblastoma cell lines and tumors and implicate synonymous and non-coding variants, along with non-synonymous variants, in retinoblastoma oncogenesis.
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Affiliation(s)
- Kevin Stachelek
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Cancer Biology and Genomics Program, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Narine Harutyunyan
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - Susan Lee
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - Assaf Beck
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - Jonathan Kim
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Liya Xu
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jesse L. Berry
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Aaron Nagiel
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - C. Patrick Reynolds
- Department of Pediatrics and Cancer Center, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX
| | - A. Linn Murphree
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Thomas C. Lee
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jennifer G. Aparicio
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - David Cobrinik
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
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13
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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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14
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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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15
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Sirivolu S, Xu L, Warren M, Prabakar RK, Shah R, Kuhn P, Hicks J, Berry JL. Chromosome 6p amplification detected in blood cell-free DNA in advanced intraocular retinoblastoma. Ophthalmic Genet 2022; 43:866-870. [PMID: 36342106 PMCID: PMC9877166 DOI: 10.1080/13816810.2022.2142246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND In patients with retinoblastoma, gains of chromosome 6p have been associated with less differentiated tumors. In cell-free DNA from the aqueous humor (AH), 6p gain has been associated with an increased risk of enucleation. While the identification of somatic copy number alterations (SCNAs) via the AH has been well established, these alterations are not routinely identified in the blood due to low tumor fraction. MATERIALS AND METHODS SCNAs were considered positive at 20% deflection from the baseline. Somatic RB1 pathogenic variants were identified with targeted sequencing using a panel including all RB1 exons. RESULTS A 24-month-old patient presented with unilateral retinoblastoma (Group D/AJCC Stage cT2B) and was treated with primary enucleation. In the peripheral blood, a heterozygous mutation (c.3920T>A) in the APC gene was reported. Genomic analysis of the tumor and AH revealed two novel somatic RB1 mutations (c.1589_1590del and c.2330dupC). Both also demonstrated highly recurrent RB-related SCNAs. Chromosome 6p gain was detected in the blood with an amplitude suggesting approximately 12% tumor fraction. At a follow-up of 24 months, there has been no evidence of metastatic disease. CONCLUSIONS To our knowledge, this is the first time an SCNA has been detected in the blood of an RB patient, suggesting in some advanced eyes there may be a high enough tumor fraction to detect these alterations (>5% needed). It remains unclear whether 6p gain or increased tumor fraction in the blood is indicative of increased risk of metastatic disease or new primary cancer; studies to address this are ongoing.
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Affiliation(s)
- Shreya Sirivolu
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, Califorina, USA,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Liya Xu
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, Califorina, USA,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Mikako Warren
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Rishvanth K. Prabakar
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Rachana Shah
- Cancer and Blood Disease Institute at Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Peter Kuhn
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, Califorina, USA,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA,Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA,Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | - James Hicks
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, Califorina, USA,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jesse L. Berry
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, Califorina, USA,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA,The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, Califorina, USA
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16
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Pike S, Iyengar R, Peng CC, Chevez-Barrios P, Brown B, Shah R, Biegel J, Yellapantula V, Nagiel A, Reiser BJ, Xu L, Berry JL. Malignant teratoid intraocular ciliary body medulloepithelioma in a 5-year-old male with corresponding somatic copy number alteration profile of aqueous humor cell-free DNA. Ophthalmic Genet 2022; 43:855-861. [PMID: 36314385 PMCID: PMC9877122 DOI: 10.1080/13816810.2022.2138457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Intraocular, ciliary body, medulloepithelioma (CBME) is a rare tumor of the nonpigmented ciliary body epithelium, typically presenting in childhood. We describe a case of CBME. MATERIALS AND METHODS Ocular examination and imaging guided diagnostic and treatment decisions. Aqueous humor (AH) liquid biopsy was collected from the affected eye at eventual enucleation. Whole genome sequencing (WGS) was employed to determine somatic copy number alterations (SCNA) in AH cell-free DNA (cfDNA). Tumor sample was analyzed using various assays to evaluate for oncogenic mutations and SCNAs. Histopathology determined diagnosis. RESULTS A 5-year-old male with glaucoma and cataract in the left eye (OS) experienced worsening left eye pain and redness. There was no light perception OS and the eye was hypotonus. Anterior segment exam showed complete cataract and rubeosis iridis. Ocular B-scan ultrasound OS revealed an intraocular lesion with calcifications and retinal detachment. Orbital MRI suggested left globe hypercellularity. An infiltrative lesion involving the ciliary body was seen in the left eye on examination under anesthesia. Left eye enucleation was performed in the setting of pain, blindness, and tumor, with anterior chamber paracentesis for AH liquid biopsy collection. SCNA profile of AH cfDNA demonstrated loss of copy of chromosomes 4, 6, and 9. Tumor was negative for clinically significant mutations or SCNAs. Histopathology diagnosed malignant teratoid CBME. CONCLUSIONS We present a case of CBME and include the unique SCNA profile of AH cfDNA from the enucleated eye. This case suggests utility of AH liquid biopsy in distinguishing between differential diagnoses for intraocular mass lesions.
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Affiliation(s)
- Sarah Pike
- The Vision Center, Children’s Hospital Los Angeles, Los Angeles, CA, USA,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Rahul Iyengar
- The Vision Center, Children’s Hospital Los Angeles, Los Angeles, CA, USA,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Chen-Ching Peng
- The Vision Center, Children’s Hospital Los Angeles, Los Angeles, CA, USA,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | | | - Brianne Brown
- The Vision Center, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Rachana Shah
- Cancer and Blood Disease Institute Retinoblastoma Program, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Jaclyn Biegel
- Center for Personalized Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Venkata Yellapantula
- Center for Personalized Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Aaron Nagiel
- The Vision Center, Children’s Hospital Los Angeles, Los Angeles, CA, USA,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA,The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Bibiana Jin Reiser
- The Vision Center, Children’s Hospital Los Angeles, Los Angeles, CA, USA,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA,The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Liya Xu
- The Vision Center, Children’s Hospital Los Angeles, Los Angeles, CA, USA,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Jesse L. Berry
- The Vision Center, Children’s Hospital Los Angeles, Los Angeles, CA, USA,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA,The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA, USA,Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
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17
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Field MG, Kuznetsoff JN, Zhang MG, Dollar JJ, Durante MA, Sayegh Y, Decatur CL, Kurtenbach S, Pelaez D, Harbour JW. RB1 loss triggers dependence on ESRRG in retinoblastoma. SCIENCE ADVANCES 2022; 8:eabm8466. [PMID: 35984874 PMCID: PMC9390996 DOI: 10.1126/sciadv.abm8466] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 07/08/2022] [Indexed: 05/10/2023]
Abstract
Retinoblastoma (Rb) is a deadly childhood eye cancer that is classically initiated by inactivation of the RB1 tumor suppressor. Clinical management continues to rely on nonspecific chemotherapeutic agents that are associated with treatment resistance and toxicity. Here, we analyzed 103 whole exomes, 20 whole transcriptomes, 5 single-cell transcriptomes, and 4 whole genomes from primary Rb tumors to identify previously unknown Rb dependencies. Several recurrent genomic aberrations implicate estrogen-related receptor gamma (ESRRG) in Rb pathogenesis. RB1 directly interacts with and inhibits ESRRG, and RB1 loss uncouples ESRRG from negative regulation. ESRRG regulates genes involved in retinogenesis and oxygen metabolism in Rb cells. ESRRG is preferentially expressed in hypoxic Rb cells in vivo. Depletion or inhibition of ESRRG causes marked Rb cell death, which is exacerbated in hypoxia. These findings reveal a previously unidentified dependency of Rb cells on ESRRG, and they implicate ESRRG as a potential therapeutic vulnerability in Rb.
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Affiliation(s)
- Matthew G. Field
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center, and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Jeffim N. Kuznetsoff
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center, and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michelle G. Zhang
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center, and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - James J. Dollar
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center, and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael A. Durante
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center, and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Yoseph Sayegh
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center, and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Christina L. Decatur
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center, and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Stefan Kurtenbach
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center, and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Daniel Pelaez
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center, and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - J. William Harbour
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center, and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Ophthalmology and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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18
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An immature, dedifferentiated, and lineage-deconstrained cone precursor origin of N-Myc-initiated retinoblastoma. Proc Natl Acad Sci U S A 2022; 119:e2200721119. [PMID: 35867756 PMCID: PMC9282279 DOI: 10.1073/pnas.2200721119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Most retinoblastomas develop from maturing cone precursors in response to biallelic RB1 loss and are dependent on cone maturation-related signaling. Additionally, ∼2% lack RB1 mutations but have MYCN amplification (MYCNA), N-Myc protein overexpression, and more rapid and invasive growth, yet the MYCNA retinoblastoma cell of origin and basis for its responses to deregulated N-Myc are unknown. Here, using explanted cultured retinae, we show that ectopic N-Myc induces cell cycle entry in cells expressing markers of several retinal types yet induces continuous proliferation and tumorigenesis only in cone precursors. Unlike the response to RB1 loss, both immature cone arrestin-negative (ARR3-) and maturing ARR3+ cone precursors proliferate, and maturing cone precursors rapidly dedifferentiate, losing ARR3 as well as L/M-opsin expression. N-Myc-overexpressing retinal cells also lose cell lineage constraints, occasionally coexpressing the cone-specific RXRγ with the rod-specific NRL or amacrine-specific AP2α and widely coexpressing RXRγ with the progenitor and Müller cell-specific SOX9 and retinal ganglion cell-specific BRN3 and GAP43. Mechanistically, N-Myc induced Cyclin D2 and CDK4 overexpression, pRB phosphorylation, and SOX9-dependent proliferation without a retinoma-like stage that characterizes pRB-deficient retinoblastoma, despite continuous p16INK4A expression. Orthotopic xenografts of N-Myc-overexpressing retinal cells formed tumors with retinal cell marker expression similar to those in MYCN-transduced retinae and MYCNA retinoblastomas in patients. These findings demonstrate the MYCNA retinoblastoma origin from immature and lineage-deconstrained cone precursors, reveal their opportunistic use of an undifferentiated retinal progenitor cell feature, and illustrate that different cancer-initiating mutations cooperate with distinct developmental stage-specific cell signaling circuitries to drive retinoblastoma tumorigenesis.
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19
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In Mitosis You Are Not: The NIMA Family of Kinases in Aspergillus, Yeast, and Mammals. Int J Mol Sci 2022; 23:ijms23074041. [PMID: 35409400 PMCID: PMC8999480 DOI: 10.3390/ijms23074041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/17/2022] Open
Abstract
The Never in mitosis gene A (NIMA) family of serine/threonine kinases is a diverse group of protein kinases implicated in a wide variety of cellular processes, including cilia regulation, microtubule dynamics, mitotic processes, cell growth, and DNA damage response. The founding member of this family was initially identified in Aspergillus and was found to play important roles in mitosis and cell division. The yeast family has one member each, Fin1p in fission yeast and Kin3p in budding yeast, also with functions in mitotic processes, but, overall, these are poorly studied kinases. The mammalian family, the main focus of this review, consists of 11 members named Nek1 to Nek11. With the exception of a few members, the functions of the mammalian Neks are poorly understood but appear to be quite diverse. Like the prototypical NIMA, many members appear to play important roles in mitosis and meiosis, but their functions in the cell go well beyond these well-established activities. In this review, we explore the roles of fungal and mammalian NIMA kinases and highlight the most recent findings in the field.
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Liu J, Ottaviani D, Sefta M, Desbrousses C, Chapeaublanc E, Aschero R, Sirab N, Lubieniecki F, Lamas G, Tonon L, Dehainault C, Hua C, Fréneaux P, Reichman S, Karboul N, Biton A, Mirabal-Ortega L, Larcher M, Brulard C, Arrufat S, Nicolas A, Elarouci N, Popova T, Némati F, Decaudin D, Gentien D, Baulande S, Mariani O, Dufour F, Guibert S, Vallot C, Rouic LLL, Matet A, Desjardins L, Pascual-Pasto G, Suñol M, Catala-Mora J, Llano GC, Couturier J, Barillot E, Schaiquevich P, Gauthier-Villars M, Stoppa-Lyonnet D, Golmard L, Houdayer C, Brisse H, Bernard-Pierrot I, Letouzé E, Viari A, Saule S, Sastre-Garau X, Doz F, Carcaboso AM, Cassoux N, Pouponnot C, Goureau O, Chantada G, de Reyniès A, Aerts I, Radvanyi F. A high-risk retinoblastoma subtype with stemness features, dedifferentiated cone states and neuronal/ganglion cell gene expression. Nat Commun 2021; 12:5578. [PMID: 34552068 PMCID: PMC8458383 DOI: 10.1038/s41467-021-25792-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 08/26/2021] [Indexed: 02/06/2023] Open
Abstract
Retinoblastoma is the most frequent intraocular malignancy in children, originating from a maturing cone precursor in the developing retina. Little is known on the molecular basis underlying the biological and clinical behavior of this cancer. Here, using multi-omics data, we demonstrate the existence of two retinoblastoma subtypes. Subtype 1, of earlier onset, includes most of the heritable forms. It harbors few genetic alterations other than the initiating RB1 inactivation and corresponds to differentiated tumors expressing mature cone markers. By contrast, subtype 2 tumors harbor frequent recurrent genetic alterations including MYCN-amplification. They express markers of less differentiated cone together with neuronal/ganglion cell markers with marked inter- and intra-tumor heterogeneity. The cone dedifferentiation in subtype 2 is associated with stemness features including low immune and interferon response, E2F and MYC/MYCN activation and a higher propensity for metastasis. The recognition of these two subtypes, one maintaining a cone-differentiated state, and the other, more aggressive, associated with cone dedifferentiation and expression of neuronal markers, opens up important biological and clinical perspectives for retinoblastomas.
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Affiliation(s)
- Jing Liu
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France ,grid.452770.30000 0001 2226 6748Programme Cartes d’Identité des Tumeurs, Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Daniela Ottaviani
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France ,grid.414531.60000 0001 0695 6255Precision Medicine, Hospital J.P. Garrahan, Buenos Aires, Argentina
| | - Meriem Sefta
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Céline Desbrousses
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Elodie Chapeaublanc
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Rosario Aschero
- grid.414531.60000 0001 0695 6255Pathology Service, Hospital J.P. Garrahan, Buenos Aires, Argentina
| | - Nanor Sirab
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Fabiana Lubieniecki
- grid.414531.60000 0001 0695 6255Pathology Service, Hospital J.P. Garrahan, Buenos Aires, Argentina
| | - Gabriela Lamas
- grid.414531.60000 0001 0695 6255Pathology Service, Hospital J.P. Garrahan, Buenos Aires, Argentina
| | - Laurie Tonon
- grid.418116.b0000 0001 0200 3174Synergie Lyon Cancer, Plateforme de Bioinformatique “Gilles Thomas”, Centre Léon Bérard, 69008 Lyon, France
| | - Catherine Dehainault
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Service de Génétique, Institut Curie, 75005 Paris, France
| | - Clément Hua
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Paul Fréneaux
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France
| | - Sacha Reichman
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 75012 Paris, France
| | - Narjesse Karboul
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Anne Biton
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM, U900, 75005 Paris, France ,Ecole des Mines ParisTech, 77305 Fontainebleau, France ,grid.428999.70000 0001 2353 6535Present Address: Institut Pasteur – Hub Bioinformatique et Biostatistique – C3BI, USR 3756 IP CNRS, 75015 Paris, France
| | - Liliana Mirabal-Ortega
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR3347, PSL Research University, 91405 Orsay, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM, U1021, 91405 Orsay, France ,grid.460789.40000 0004 4910 6535Université Paris-Saclay, 91405 Orsay, France
| | - Magalie Larcher
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR3347, PSL Research University, 91405 Orsay, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM, U1021, 91405 Orsay, France ,grid.460789.40000 0004 4910 6535Université Paris-Saclay, 91405 Orsay, France
| | - Céline Brulard
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France ,grid.411777.30000 0004 1765 1563Present Address: INSERM U930, CHU Bretonneau, 37000 Tours, France
| | - Sandrine Arrufat
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France
| | - André Nicolas
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France
| | - Nabila Elarouci
- grid.452770.30000 0001 2226 6748Programme Cartes d’Identité des Tumeurs, Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Tatiana Popova
- grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM U830, 75005 Paris, France
| | - Fariba Némati
- grid.418596.70000 0004 0639 6384Département de Recherche Translationnelle, Institut Curie, 75005 Paris, France
| | - Didier Decaudin
- grid.418596.70000 0004 0639 6384Département de Recherche Translationnelle, Institut Curie, 75005 Paris, France
| | - David Gentien
- grid.418596.70000 0004 0639 6384Département de Recherche Translationnelle, Institut Curie, 75005 Paris, France
| | - Sylvain Baulande
- grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, NGS Platform, 75005 Paris, France
| | - Odette Mariani
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France
| | - Florent Dufour
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Sylvain Guibert
- grid.425132.3GeCo Genomics Consulting, Integragen, 91000 Evry, France
| | - Céline Vallot
- grid.425132.3GeCo Genomics Consulting, Integragen, 91000 Evry, France
| | - Livia Lumbroso-Le Rouic
- grid.418596.70000 0004 0639 6384Département de Chirurgie, Service d’Ophtalmologie, Institut Curie, 75005 Paris, France
| | - Alexandre Matet
- grid.418596.70000 0004 0639 6384Département de Chirurgie, Service d’Ophtalmologie, Institut Curie, 75005 Paris, France ,grid.508487.60000 0004 7885 7602Université de Paris, Paris, France
| | - Laurence Desjardins
- grid.418596.70000 0004 0639 6384Département de Chirurgie, Service d’Ophtalmologie, Institut Curie, 75005 Paris, France
| | - Guillem Pascual-Pasto
- grid.411160.30000 0001 0663 8628Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain ,grid.411160.30000 0001 0663 8628Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Mariona Suñol
- grid.411160.30000 0001 0663 8628Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain ,grid.411160.30000 0001 0663 8628Department of Pathology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Jaume Catala-Mora
- grid.411160.30000 0001 0663 8628Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain ,grid.411160.30000 0001 0663 8628Department of Ophthalmology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Genoveva Correa Llano
- grid.411160.30000 0001 0663 8628Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain ,grid.411160.30000 0001 0663 8628Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Jérôme Couturier
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France
| | - Emmanuel Barillot
- grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM, U900, 75005 Paris, France ,Ecole des Mines ParisTech, 77305 Fontainebleau, France
| | - Paula Schaiquevich
- grid.414531.60000 0001 0695 6255Pathology Service, Hospital J.P. Garrahan, Buenos Aires, Argentina ,grid.423606.50000 0001 1945 2152National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
| | - Marion Gauthier-Villars
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Service de Génétique, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM U830, 75005 Paris, France
| | - Dominique Stoppa-Lyonnet
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Service de Génétique, Institut Curie, 75005 Paris, France ,grid.508487.60000 0004 7885 7602Université de Paris, Paris, France
| | - Lisa Golmard
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Service de Génétique, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM U830, 75005 Paris, France
| | - Claude Houdayer
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Service de Génétique, Institut Curie, 75005 Paris, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM U830, 75005 Paris, France ,grid.41724.34Present Address: Department of Genetics, Rouen University Hospital, 76000 Rouen, France
| | - Hervé Brisse
- grid.418596.70000 0004 0639 6384Département d’Imagerie Médicale, Institut Curie, 75005 Paris, France
| | - Isabelle Bernard-Pierrot
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
| | - Eric Letouzé
- grid.417925.cCentre de Recherche des Cordeliers, Sorbonne Universités, INSERM, 75006 Paris, France ,grid.508487.60000 0004 7885 7602Functional Genomics of Solid Tumors, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, France
| | - Alain Viari
- grid.418116.b0000 0001 0200 3174Synergie Lyon Cancer, Plateforme de Bioinformatique “Gilles Thomas”, Centre Léon Bérard, 69008 Lyon, France
| | - Simon Saule
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR3347, PSL Research University, 91405 Orsay, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM, U1021, 91405 Orsay, France ,grid.460789.40000 0004 4910 6535Université Paris-Saclay, 91405 Orsay, France
| | - Xavier Sastre-Garau
- grid.418596.70000 0004 0639 6384Département de Biologie des Tumeurs, Institut Curie, 75005 Paris, France ,grid.414145.10000 0004 1765 2136Present Address: Department of Pathology, Centre Hospitalier Intercommunal de Créteil, 94000 Créteil, France
| | - François Doz
- grid.508487.60000 0004 7885 7602Université de Paris, Paris, France ,grid.418596.70000 0004 0639 6384SIREDO Center (Care, Innovation and Research in Pediatric Adolescent and Young Adult Oncology), Institut Curie, 75005 Paris, France
| | - Angel M. Carcaboso
- grid.411160.30000 0001 0663 8628Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain ,grid.411160.30000 0001 0663 8628Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Nathalie Cassoux
- grid.418596.70000 0004 0639 6384Département de Chirurgie, Service d’Ophtalmologie, Institut Curie, 75005 Paris, France ,grid.508487.60000 0004 7885 7602Université de Paris, Paris, France
| | - Celio Pouponnot
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR3347, PSL Research University, 91405 Orsay, France ,grid.418596.70000 0004 0639 6384Institut Curie, PSL Research University, INSERM, U1021, 91405 Orsay, France ,grid.460789.40000 0004 4910 6535Université Paris-Saclay, 91405 Orsay, France
| | - Olivier Goureau
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 75012 Paris, France
| | - Guillermo Chantada
- grid.414531.60000 0001 0695 6255Precision Medicine, Hospital J.P. Garrahan, Buenos Aires, Argentina ,grid.411160.30000 0001 0663 8628Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain ,grid.411160.30000 0001 0663 8628Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain ,grid.423606.50000 0001 1945 2152National Scientific and Technical Research Council, CONICET, Buenos Aires, Argentina
| | - Aurélien de Reyniès
- grid.452770.30000 0001 2226 6748Programme Cartes d’Identité des Tumeurs, Ligue Nationale Contre le Cancer, 75013 Paris, France
| | - Isabelle Aerts
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France ,grid.418596.70000 0004 0639 6384SIREDO Center (Care, Innovation and Research in Pediatric Adolescent and Young Adult Oncology), Institut Curie, 75005 Paris, France
| | - François Radvanyi
- grid.4444.00000 0001 2112 9282Institut Curie, CNRS, UMR144, Equipe Labellisée Ligue contre le Cancer, PSL Research University, 75005 Paris, France ,grid.462844.80000 0001 2308 1657Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005 Paris, France
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Gargallo P, Oltra S, Balaguer J, Barranco H, Yáñez Y, Segura V, Juan-Ribelles A, Calabria I, Llavador M, Castel V, Cañete A. Retinoblastoma and mosaic 13q deletion: a case report. Int J Retina Vitreous 2021; 7:50. [PMID: 34479642 PMCID: PMC8418035 DOI: 10.1186/s40942-021-00321-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Patients with 13q-syndrome are at risk of retinoblastoma when the RB1 gene, located in the chromosomal band 13q14.2, is deleted. This syndrome is frequently associated with congenital malformations and developmental delay, although these signs could be mild. Mosaic 13q-deletion patients have been previously reported in the literature; their phenotype is variable, and they may not be recognized. CASE PRESENTATION Retinoblastoma diagnosed in a child with 13q-mosaicism confirmed in blood, oral mucosa, healthy retina and retinoblastoma. A second RB1 hit is present exclusively in the retinoblastoma sample (RB1 c.958C>T p.Arg320Ter). Other detected molecular events in retinoblastoma are 6p12.3pter gain and 6q25.3qter loss. Clinical examination is unremarkable except for clinodactyly of the right fifth finger. DISCUSSION AND CONCLUSIONS We describe a case of mosaic 13q deletion syndrome affected by retinoblastoma. Molecular data obtained from the tumor analysis are similar to previous data available about this malignancy. High clinical suspicion is essential for an adequate diagnosis of mosaic cases.
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Affiliation(s)
- Pablo Gargallo
- Clinical and Translational Research in Cancer, Health Research Institute La Fe (IIS La Fe), Valencia, Spain. .,Oncology Department, Imegen-Health in Code Group, Valencia, Spain.
| | - Silvestre Oltra
- Genetics Unit, La Fe Hospital, Valencia, Spain.,Genetics Department, Valencia University, Valencia, Spain
| | - Julia Balaguer
- Clinical and Translational Research in Cancer, Health Research Institute La Fe (IIS La Fe), Valencia, Spain.,Oncology Department, Imegen-Health in Code Group, Valencia, Spain.,Genetics Unit, La Fe Hospital, Valencia, Spain.,Genetics Department, Valencia University, Valencia, Spain.,Pediatric Oncology and Hematology Unit, University Hospital La Fe, Valencia, Spain
| | - Honorio Barranco
- Pediatric Ophthalmology Unit, University Hospital La Fe Hospital, Valencia, Spain
| | - Yania Yáñez
- Clinical and Translational Research in Cancer, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
| | - Vanessa Segura
- Clinical and Translational Research in Cancer, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
| | - Antonio Juan-Ribelles
- Clinical and Translational Research in Cancer, Health Research Institute La Fe (IIS La Fe), Valencia, Spain.,Oncology Department, Imegen-Health in Code Group, Valencia, Spain.,Genetics Unit, La Fe Hospital, Valencia, Spain.,Genetics Department, Valencia University, Valencia, Spain.,Pediatric Oncology and Hematology Unit, University Hospital La Fe, Valencia, Spain
| | - Inés Calabria
- Oncology Department, Imegen-Health in Code Group, Valencia, Spain
| | | | - Victoria Castel
- Clinical and Translational Research in Cancer, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
| | - Adela Cañete
- Clinical and Translational Research in Cancer, Health Research Institute La Fe (IIS La Fe), Valencia, Spain.,Oncology Department, Imegen-Health in Code Group, Valencia, Spain.,Genetics Unit, La Fe Hospital, Valencia, Spain.,Genetics Department, Valencia University, Valencia, Spain.,Pediatric Oncology and Hematology Unit, University Hospital La Fe, Valencia, Spain
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22
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Kim ME, Polski A, Xu L, Prabakar RK, Peng CC, Reid MW, Shah R, Kuhn P, Cobrinik D, Hicks J, Berry JL. Comprehensive Somatic Copy Number Analysis Using Aqueous Humor Liquid Biopsy for Retinoblastoma. Cancers (Basel) 2021; 13:cancers13133340. [PMID: 34283049 PMCID: PMC8268955 DOI: 10.3390/cancers13133340] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Aqueous humor (AH) liquid biopsy is an enriched source of cell-free circulating tumor-derived DNA for retinoblastoma (RB). The use of this AH liquid biopsy allows for genomic analysis of eyes in the absence of tumor tissue. Development of this platform was critical because direct tumor biopsy is prohibited in RB due to risk of extraocular tumor spread. In this retrospective study, we provide comprehensive, whole-genome analysis of the somatic copy number alterations (SCNAs) in 68 eyes of 64 RB patients. We show that the prevalence of specific SCNAs differ between eyes that required immediate enucleation (surgical removal) and eyes that were attempted to be saved but subsequently failed treatment, requiring secondary enucleation. Increases in chromosomal instability, or higher number of broad genomic alterations, predict higher risk clinical and biomarker features in these eyes. Prospective analyses are needed to further determine the clinical relevance and application of these findings. Abstract Aqueous humor (AH) liquid biopsy has been established as a surrogate tumor biopsy for retinoblastoma (RB). Previous AH studies have focused on highly recurrent RB somatic copy number alterations (SCNAs) including gain of 1q, 2p, 6p, and loss of 13q and 16q. In this retrospective study, we provide a comprehensive, whole-genome analysis of RB SCNAs and evaluate associated clinical features for 68 eyes of 64 RB patients from whom AH was obtained between December 2014 and October 2020. Shallow whole-genome sequencing of AH cell-free DNA was performed to assess for SCNAs. The prevalence of specific non-highly recurrent SCNAs, such as 20q gain and 8p loss, differed between primarily and secondarily enucleated eyes. Increases in chromosomal instability predict more advanced seeding morphology (p = 0.015); later age of diagnosis (p < 0.0001); greater odds of an endophytic tumor growth pattern (without retinal detachment; p = 0.047); tumor heights >10 mm (p = 0.09); and containing 6p gain, a biomarker of poor ocular prognosis (p = 0.004). The AH liquid biopsy platform is a high-yield method of whole-genome RB SCNA analysis, and SCNAs are associated with numerous clinical findings in RB eyes. Prospective analyses are encouraged to further elucidate the clinical relevance of specific SCNAs in RB.
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Affiliation(s)
- Mary E. Kim
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (M.E.K.); (A.P.); (L.X.); (C.-C.P.); (M.W.R.); (D.C.)
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Ashley Polski
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (M.E.K.); (A.P.); (L.X.); (C.-C.P.); (M.W.R.); (D.C.)
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Liya Xu
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (M.E.K.); (A.P.); (L.X.); (C.-C.P.); (M.W.R.); (D.C.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90007, USA; (P.K.); (J.H.)
| | - Rishvanth K. Prabakar
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90007, USA;
| | - Chen-Ching Peng
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (M.E.K.); (A.P.); (L.X.); (C.-C.P.); (M.W.R.); (D.C.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90007, USA; (P.K.); (J.H.)
| | - Mark W. Reid
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (M.E.K.); (A.P.); (L.X.); (C.-C.P.); (M.W.R.); (D.C.)
| | - Rachana Shah
- Cancer and Blood Disease Institute at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA;
| | - Peter Kuhn
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90007, USA; (P.K.); (J.H.)
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90007, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90007, USA
| | - David Cobrinik
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (M.E.K.); (A.P.); (L.X.); (C.-C.P.); (M.W.R.); (D.C.)
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - James Hicks
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90007, USA; (P.K.); (J.H.)
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jesse L. Berry
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (M.E.K.); (A.P.); (L.X.); (C.-C.P.); (M.W.R.); (D.C.)
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA
- Correspondence: ; Tel.: +1-323-442-6335
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23
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Dutta A, Dutreux F, Schacherer J. Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds. eLife 2021; 10:70339. [PMID: 34159898 PMCID: PMC8245132 DOI: 10.7554/elife.70339] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/11/2021] [Indexed: 12/12/2022] Open
Abstract
The dynamics and diversity of the appearance of genetic variants play an essential role in the evolution of the genome and the shaping of biodiversity. Recent population-wide genome sequencing surveys have highlighted the importance of loss of heterozygosity (LOH) events and have shown that they are a neglected part of the genetic diversity landscape. To assess the extent, variability, and spectrum, we explored the accumulation of LOH events in 169 heterozygous diploid Saccharomyces cerevisiae mutation accumulation lines across nine genetic backgrounds. In total, we detected a large set of 22,828 LOH events across distinct genetic backgrounds with a heterozygous level ranging from 0.1% to 1%. LOH events are very frequent with a rate consistently much higher than the mutation rate, showing their importance for genome evolution. We observed that the interstitial LOH (I-LOH) events, resulting in internal short LOH tracts, were much frequent (n = 19,660) than the terminal LOH (T-LOH) events, that is, tracts extending to the end of the chromosome (n = 3168). However, the spectrum, the rate, and the fraction of the genome under LOH vary across genetic backgrounds. Interestingly, we observed that the more the ancestors were heterozygous, the more they accumulated T-LOH events. In addition, frequent short I-LOH tracts are a signature of the lines derived from hybrids with low spore fertility. Finally, we found lines showing almost complete homozygotization during vegetative progression. Overall, our results highlight that the variable dynamics of the LOH accumulation across distinct genetic backgrounds might lead to rapid differential genome evolution during vegetative growth.
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Affiliation(s)
- Abhishek Dutta
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF), Paris, France
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24
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Price EA, Patel R, Scheimberg I, Kotiloglu Karaa E, Sagoo MS, Reddy MA, Onadim Z. MYCN amplification levels in primary retinoblastoma tumors analyzed by Multiple Ligation-dependent Probe Amplification. Ophthalmic Genet 2021; 42:604-611. [PMID: 34003079 DOI: 10.1080/13816810.2021.1923038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Background: Retinoblastoma (Rb) is a childhood tumor of the developing retina where predisposition is caused by RB1 pathogenic variants. MYCN amplification (MYCNA) has been implicated in around 2% of sporadic unilateral Rb tumors with no detectable RB1 variants. We audited data from tumors collected between 1993 and 2019 to determine if this is the case for patients treated at Barts Health NHS Trust, and how often it occurred alongside RB1 variants. Materials and methods: Screening for MYCNA was carried out by Multiple Ligation Probe Analysis of tumor and blood samples collected for RB1 genetic screening. The cohort consisted of 149 tumors, of which 114 had matched blood samples. Results: 10/149 (6.7%) tumors were positive for MYCNA in a population containing a disproportionate number of cases negative for RB1 pathogenic variants. Of 65 unbiased tumors collected from 2014 to 2019, 2 (3.1%) had MYCNA. All MYCNA samples were from sporadic, unilateral patients and 3/10 (30%) had RB1 pathogenic variants. MYCNA was not detected in any blood sample. No MYCNA tumor had 6p gain which is usually a common alteration in Rbs. Conclusions: MYCNA occurs in a small fraction of Rbs and can occur in the presence of pathogenic RB1 variants. However, where it occurs alongside RB1 alterations, the age of onset appears to be later. MYCNA has yet to be seen as a heritable change. In sporadic cases with early diagnosis, Rbs with no RB1 pathogenic variant identified should be tested for MYCNA. Conversely, tumors with MYCNA should still be screened for RB1 pathogenic variants.
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Affiliation(s)
- Elizabeth A Price
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, London, UK
| | - Roopal Patel
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, London, UK
| | | | | | - Mandeep S Sagoo
- Retinoblastoma Service, Royal London Hospital, Barts Health NHS Trust, London, UK.,NIHR Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, UK
| | - M Ashwin Reddy
- Retinoblastoma Service, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Zerrin Onadim
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, London, UK
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25
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Gerrish A, Jenkinson H, Cole T. The Impact of Cell-Free DNA Analysis on the Management of Retinoblastoma. Cancers (Basel) 2021; 13:cancers13071570. [PMID: 33805427 PMCID: PMC8037190 DOI: 10.3390/cancers13071570] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Retinoblastoma is a childhood eye cancer, mainly caused by mutations in the RB1 gene, which can be somatic or constitutional. Unlike many other cancers, tumour biopsies are not performed due to the risk of tumour dissemination. As a result, until recently, somatic genetic analysis was only possible if an affected eye was removed as part of a treatment. Several recent proof of principle studies have demonstrated that the analysis of tumour-derived cell-free DNA, either obtained from ocular fluid or blood plasma, has the potential to advance the diagnosis and influence the prognosis of retinoblastoma patients. It has been shown that a confirmed diagnosis is possible in retinoblastoma patients undergoing conservative treatment. In vivo genetic analysis of retinoblastoma tumours is also now possible, allowing the potential identification of secondary genetic events as prognostic biomarkers. In addition, noninvasive prenatal diagnosis in children at risk of inheriting retinoblastoma has been developed. Here, we review the current literature and discuss the potential impact of cell-free DNA analysis on both the diagnosis and treatment of retinoblastoma patients and their families.
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Affiliation(s)
- Amy Gerrish
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK;
- Correspondence:
| | - Helen Jenkinson
- Department of Paediatric Oncology, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B4 6NH, UK;
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK;
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26
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Xu L, Kim ME, Polski A, Prabakar RK, Shen L, Peng CC, Reid MW, Chévez-Barrios P, Kim JW, Shah R, Jubran R, Kuhn P, Cobrinik D, Biegel JA, Gai X, Hicks J, Berry JL. Establishing the Clinical Utility of ctDNA Analysis for Diagnosis, Prognosis, and Treatment Monitoring of Retinoblastoma: The Aqueous Humor Liquid Biopsy. Cancers (Basel) 2021; 13:1282. [PMID: 33805776 PMCID: PMC8001323 DOI: 10.3390/cancers13061282] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/05/2021] [Accepted: 03/11/2021] [Indexed: 12/23/2022] Open
Abstract
Because direct tumor biopsy is prohibited for retinoblastoma (RB), eye-specific molecular biomarkers are not used in clinical practice for RB. Recently, we demonstrated that the aqueous humor (AH) is a rich liquid biopsy source of cell-free tumor DNA. Herein, we detail clinically-relevant molecular biomarkers from the first year of prospective validation data. Seven eyes from 6 RB patients who had AH sampled at diagnosis and throughout therapy with ≥12 months of follow-up were included. Cell-free DNA (cfDNA) from each sample was isolated and sequenced to assess genome-wide somatic copy number alterations (SCNAs), followed by targeted resequencing for pathogenic variants using a RB1 and MYCN custom hybridization panel. Tumoral genomic information was detected in 100% of diagnostic AH samples. Of the seven diagnostic AH samples, 5/7 were positive for RB SCNAs. Mutational analysis identified RB1 variants in 5/7 AH samples, including the 2 samples in which no SCNAs were detected. Two eyes failed therapy and required enucleation; both had poor prognostic biomarkers (chromosome 6p gain or MYCN amplification) present in the AH at the time of diagnosis. In the context of previously established pre-analytical, analytical, and clinical validity, this provides evidence for larger, prospective studies to further establish the clinical utility of the AH liquid biopsy and its applications to precision oncology for RB.
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Affiliation(s)
- Liya Xu
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (L.X.); (M.E.K.); (A.P.); (C.-C.P.); (M.W.R.); (J.W.K.); (D.C.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90007, USA; (P.K.); (J.H.)
| | - Mary E. Kim
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (L.X.); (M.E.K.); (A.P.); (C.-C.P.); (M.W.R.); (J.W.K.); (D.C.)
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Ashley Polski
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (L.X.); (M.E.K.); (A.P.); (C.-C.P.); (M.W.R.); (J.W.K.); (D.C.)
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Rishvanth K. Prabakar
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90007, USA;
| | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (L.S.); (J.A.B.); (X.G.)
| | - Chen-Ching Peng
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (L.X.); (M.E.K.); (A.P.); (C.-C.P.); (M.W.R.); (J.W.K.); (D.C.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90007, USA; (P.K.); (J.H.)
| | - Mark W. Reid
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (L.X.); (M.E.K.); (A.P.); (C.-C.P.); (M.W.R.); (J.W.K.); (D.C.)
| | - Patricia Chévez-Barrios
- Ophthalmic Pathology, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA;
| | - Jonathan W. Kim
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (L.X.); (M.E.K.); (A.P.); (C.-C.P.); (M.W.R.); (J.W.K.); (D.C.)
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Rachana Shah
- Cancer and Blood Disease Institute at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (R.S.); (R.J.)
| | - Rima Jubran
- Cancer and Blood Disease Institute at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (R.S.); (R.J.)
| | - Peter Kuhn
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90007, USA; (P.K.); (J.H.)
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90007, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90007, USA
| | - David Cobrinik
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (L.X.); (M.E.K.); (A.P.); (C.-C.P.); (M.W.R.); (J.W.K.); (D.C.)
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Jaclyn A. Biegel
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (L.S.); (J.A.B.); (X.G.)
- Department of Pathology and Laboratory Medicine, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (L.S.); (J.A.B.); (X.G.)
- Department of Pathology and Laboratory Medicine, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - James Hicks
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90007, USA; (P.K.); (J.H.)
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jesse L. Berry
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (L.X.); (M.E.K.); (A.P.); (C.-C.P.); (M.W.R.); (J.W.K.); (D.C.)
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA
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27
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Davies HR, Broad KD, Onadim Z, Price EA, Zou X, Sheriff I, Karaa EK, Scheimberg I, Reddy MA, Sagoo MS, Ohnuma SI, Nik-Zainal S. Whole-Genome Sequencing of Retinoblastoma Reveals the Diversity of Rearrangements Disrupting RB1 and Uncovers a Treatment-Related Mutational Signature. Cancers (Basel) 2021; 13:754. [PMID: 33670346 PMCID: PMC7918943 DOI: 10.3390/cancers13040754] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/02/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
The development of retinoblastoma is thought to require pathological genetic changes in both alleles of the RB1 gene. However, cases exist where RB1 mutations are undetectable, suggesting alternative pathways to malignancy. We used whole-genome sequencing (WGS) and transcriptomics to investigate the landscape of sporadic retinoblastomas derived from twenty patients, sought RB1 and other driver mutations and investigated mutational signatures. At least one RB1 mutation was identified in all retinoblastomas, including new mutations in addition to those previously identified by clinical screening. Ten tumours carried structural rearrangements involving RB1 ranging from relatively simple to extremely complex rearrangement patterns, including a chromothripsis-like pattern in one tumour. Bilateral tumours obtained from one patient harboured conserved germline but divergent somatic RB1 mutations, indicating independent evolution. Mutational signature analysis showed predominance of signatures associated with cell division, an absence of ultraviolet-related DNA damage and a profound platinum-related mutational signature in a chemotherapy-exposed tumour. Most RB1 mutations are identifiable by clinical screening. However, the increased resolution and ability to detect otherwise elusive rearrangements by WGS have important repercussions on clinical management and advice on recurrence risks.
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Affiliation(s)
- Helen R. Davies
- Academic Department of Medical Genetics, University of Cambridge, Addenbrooke’s Treatment Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (H.R.D.); (X.Z.)
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Kevin D. Broad
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
| | - Zerrin Onadim
- Retinoblastoma Genetic Screening Unit, The Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (Z.O.); (E.A.P.)
| | - Elizabeth A. Price
- Retinoblastoma Genetic Screening Unit, The Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (Z.O.); (E.A.P.)
| | - Xueqing Zou
- Academic Department of Medical Genetics, University of Cambridge, Addenbrooke’s Treatment Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (H.R.D.); (X.Z.)
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Ibrahim Sheriff
- Retinoblastoma Service, Royal London Hospital, Barts Health Trust, London E1 1FR, UK; (I.S.); (M.A.R.)
| | - Esin Kotiloğlu Karaa
- Pathology Department, Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (E.K.K.); (I.S.)
| | - Irene Scheimberg
- Pathology Department, Royal London Hospital, Barts Health NHS Trust, London E1 1FR, UK; (E.K.K.); (I.S.)
| | - M. Ashwin Reddy
- Retinoblastoma Service, Royal London Hospital, Barts Health Trust, London E1 1FR, UK; (I.S.); (M.A.R.)
- NIHR Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital, Institute of Ophthalmology, University College London, London EC1V 2PD, UK
| | - Mandeep S. Sagoo
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
- Retinoblastoma Service, Royal London Hospital, Barts Health Trust, London E1 1FR, UK; (I.S.); (M.A.R.)
- NIHR Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital, Institute of Ophthalmology, University College London, London EC1V 2PD, UK
| | - Shin-ichi Ohnuma
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, University of Cambridge, Addenbrooke’s Treatment Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (H.R.D.); (X.Z.)
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XZ, UK
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28
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Aschero R, Francis JH, Ganiewich D, Gomez-Gonzalez S, Sampor C, Zugbi S, Ottaviani D, Lemelle L, Mena M, Winter U, Correa Llano G, Lamas G, Lubieniecki F, Szijan I, Mora J, Podhajcer O, Doz F, Radvanyi F, Abramson DH, Llera AS, Schaiquevich PS, Lavarino C, Chantada GL. Recurrent Somatic Chromosomal Abnormalities in Relapsed Extraocular Retinoblastoma. Cancers (Basel) 2021; 13:cancers13040673. [PMID: 33567541 PMCID: PMC7915502 DOI: 10.3390/cancers13040673] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Relapse outside the eye of retinoblastoma (the most common eye cancer in children) is an uncommon event in developed countries, however it is the main cause of death in patients with retinoblastoma worldwide. The genomic features of this population are not known. We studied 23 cases from four countries and found a characteristic pattern in chromosomal copy number alterations that could help guide future clinical management of these patients. Abstract Most reports about copy number alterations (CNA) in retinoblastoma relate to patients with intraocular disease and features of children with extraocular relapse remain unknown, so we aimed to describe the CNA in this population. We evaluated 23 patients and 27 specimens from 4 centers. Seventeen cases had extraocular relapse after initial enucleation and six cases after an initial preservation attempt. We performed an analysis of CNA and BCOR gene alteration by SNP array (Single Nucleotide Polymorfism array), whole-exome sequencing, IMPACT panel and CGH array (Array-based comparative genomic hybridization). All cases presented CNA at a higher prevalence than those reported in previously published studies for intraocular cases. CNA previously reported for intraocular retinoblastoma were found at a high frequency in our cohort: gains in 1q (69.5%), 2p (60.9%) and 6p (86.9%), and 16q loss (78.2%). Other, previously less-recognized, CNA were found including loss of 11q (34.8%), gain of 17q (56.5%), loss of 19q (30.4%) and BCOR alterations were present in 72.7% of our cases. A high number of CNA including 11q deletions, 17q gains, 19q loss, and BCOR alterations, are more common in extraocular retinoblastoma. Identification of these features may be correlated with a more aggressive tumor warranting consideration for patient management.
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Affiliation(s)
- Rosario Aschero
- Pathology Service, Hospital de Pediatría JP Garrahan, Buenos Aires 1245, Argentina; (R.A.); (U.W.); (G.L.); (F.L.)
- National Scientific and Technical Research Council, CONICET, Buenos Aires 1425, Argentina; (S.Z.); (O.P.); (A.S.L.); (P.S.S.)
| | - Jasmine H. Francis
- Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (J.H.F.); (D.H.A.)
| | - Daiana Ganiewich
- Laboratory of Molecular and Cellular Therapy, Instituto Leloir-Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Buenos Aires 1405, Argentina;
| | - Soledad Gomez-Gonzalez
- Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (S.G.-G.); (J.M.); (C.L.)
| | - Claudia Sampor
- Hematology-Oncology Service, Hospital de Pediatría JP Garrahan, Buenos Aires 1245, Argentina;
| | - Santiago Zugbi
- National Scientific and Technical Research Council, CONICET, Buenos Aires 1425, Argentina; (S.Z.); (O.P.); (A.S.L.); (P.S.S.)
- Innovative Treatments Unit, Hospital de Pediatría JP Garrahan, Buenos Aires 1245, Argentina;
| | - Daniela Ottaviani
- University of Paris and Institut Curie (SIREDO Center: Care, Innovation and Reserach in pediatric, Adolescent and Young Adults Oncology), CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France; (D.O.); (L.L.); (F.D.); (F.R.)
| | - Lauriane Lemelle
- University of Paris and Institut Curie (SIREDO Center: Care, Innovation and Reserach in pediatric, Adolescent and Young Adults Oncology), CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France; (D.O.); (L.L.); (F.D.); (F.R.)
| | - Marcela Mena
- Innovative Treatments Unit, Hospital de Pediatría JP Garrahan, Buenos Aires 1245, Argentina;
| | - Ursula Winter
- Pathology Service, Hospital de Pediatría JP Garrahan, Buenos Aires 1245, Argentina; (R.A.); (U.W.); (G.L.); (F.L.)
| | - Genoveva Correa Llano
- Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Gabriela Lamas
- Pathology Service, Hospital de Pediatría JP Garrahan, Buenos Aires 1245, Argentina; (R.A.); (U.W.); (G.L.); (F.L.)
| | - Fabiana Lubieniecki
- Pathology Service, Hospital de Pediatría JP Garrahan, Buenos Aires 1245, Argentina; (R.A.); (U.W.); (G.L.); (F.L.)
| | - Irene Szijan
- Genetic and Molecular Biology, University of Buenos Aires, Buenos Aires 1113, Argentina;
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (S.G.-G.); (J.M.); (C.L.)
- Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Osvaldo Podhajcer
- National Scientific and Technical Research Council, CONICET, Buenos Aires 1425, Argentina; (S.Z.); (O.P.); (A.S.L.); (P.S.S.)
- Laboratory of Molecular and Cellular Therapy, Instituto Leloir-Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Buenos Aires 1405, Argentina;
| | - François Doz
- University of Paris and Institut Curie (SIREDO Center: Care, Innovation and Reserach in pediatric, Adolescent and Young Adults Oncology), CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France; (D.O.); (L.L.); (F.D.); (F.R.)
| | - François Radvanyi
- University of Paris and Institut Curie (SIREDO Center: Care, Innovation and Reserach in pediatric, Adolescent and Young Adults Oncology), CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, 75005 Paris, France; (D.O.); (L.L.); (F.D.); (F.R.)
| | - David H. Abramson
- Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (J.H.F.); (D.H.A.)
| | - Andrea S. Llera
- National Scientific and Technical Research Council, CONICET, Buenos Aires 1425, Argentina; (S.Z.); (O.P.); (A.S.L.); (P.S.S.)
- Laboratory of Molecular and Cellular Therapy, Instituto Leloir-Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Buenos Aires 1405, Argentina;
| | - Paula S. Schaiquevich
- National Scientific and Technical Research Council, CONICET, Buenos Aires 1425, Argentina; (S.Z.); (O.P.); (A.S.L.); (P.S.S.)
- Innovative Treatments Unit, Hospital de Pediatría JP Garrahan, Buenos Aires 1245, Argentina;
| | - Cinzia Lavarino
- Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (S.G.-G.); (J.M.); (C.L.)
- Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Guillermo L. Chantada
- National Scientific and Technical Research Council, CONICET, Buenos Aires 1425, Argentina; (S.Z.); (O.P.); (A.S.L.); (P.S.S.)
- Pediatric Hematology and Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain;
- Correspondence:
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Wani K, AlHarthi H, Alghamdi A, Sabico S, Al-Daghri NM. Role of NLRP3 Inflammasome Activation in Obesity-Mediated Metabolic Disorders. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:E511. [PMID: 33435142 PMCID: PMC7826517 DOI: 10.3390/ijerph18020511] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/22/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022]
Abstract
NLRP3 inflammasome is one of the multimeric protein complexes of the nucleotide-binding domain, leucine-rich repeat (NLR)-containing pyrin and HIN domain family (PYHIN). When activated, NLRP3 inflammasome triggers the release of pro-inflammatory interleukins (IL)-1β and IL-18, an essential step in innate immune response; however, defective checkpoints in inflammasome activation may lead to autoimmune, autoinflammatory, and metabolic disorders. Among the consequences of NLRP3 inflammasome activation is systemic chronic low-grade inflammation, a cardinal feature of obesity and insulin resistance. Understanding the mechanisms involved in the regulation of NLRP3 inflammasome in adipose tissue may help in the development of specific inhibitors for the treatment and prevention of obesity-mediated metabolic diseases. In this narrative review, the current understanding of NLRP3 inflammasome activation and regulation is highlighted, including its putative roles in adipose tissue dysfunction and insulin resistance. Specific inhibitors of NLRP3 inflammasome activation which can potentially be used to treat metabolic disorders are also discussed.
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Affiliation(s)
| | | | | | | | - Nasser M. Al-Daghri
- Biochemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (K.W.); (H.A.); (A.A.); (S.S.)
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30
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Sun Z, Gong W, Zhang Y, Jia Z. Physiological and Pathological Roles of Mammalian NEK7. Front Physiol 2020; 11:606996. [PMID: 33364979 PMCID: PMC7750478 DOI: 10.3389/fphys.2020.606996] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
NEK7 is the smallest NIMA-related kinase (NEK) in mammals. The pathological and physiological roles of NEK7 have been widely reported in many studies. To date, the major function of NEK7 has been well documented in mitosis and NLRP3 inflammasome activation, but the detailed mechanisms of its regulation remain unclear. This review summarizes current advances in NEK7 research involving mitotic regulation, NLRP3 inflammasome activation, related diseases and potential inhibitors, which may provide new insights into the understanding and therapy of the diseases associated with NEK7, as well as the subsequent studies in the future.
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Affiliation(s)
- Zhenzhen Sun
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China.,Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Wei Gong
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China.,Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Yue Zhang
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China.,Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Zhanjun Jia
- Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, China.,Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
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31
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Zhou Z, Gong Q, Lin Z, Wang Y, Li M, Wang L, Ding H, Li P. Emerging Roles of SRSF3 as a Therapeutic Target for Cancer. Front Oncol 2020; 10:577636. [PMID: 33072610 PMCID: PMC7544984 DOI: 10.3389/fonc.2020.577636] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022] Open
Abstract
Ser/Arg-rich (SR) proteins are RNA-binding proteins known as constitutive and alternative splicing (AS) regulators that regulate multiple aspects of the gene expression program. Ser/Arg-rich splicing factor 3 (SRSF3) is the smallest member of the SR protein family, and its level is controlled by multiple factors and involves complex mechanisms in eukaryote cells, whereas the aberrant expression of SRSF3 is associated with many human diseases, including cancer. Here, we review state-of-the-art research on SRSF3 in terms of its function, expression, and misregulation in human cancers. We emphasize the negative consequences of the overexpression of the SRSF3 oncogene in cancers, the pathways underlying SRSF3-mediated transformation, and implications of potential anticancer drugs by downregulation of SRSF3 expression for cancer therapy. Cumulative research on SRSF3 provides critical insight into its essential part in maintaining cellular processes, offering potential new targets for anti-cancer therapy.
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Affiliation(s)
- Zhixia Zhou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Qi Gong
- Departments of Pediatrics, Second Clinical Medical College of Qingdao University, Qingdao, China
| | - Zhijuan Lin
- Key Laboratory for Immunology in Universities of Shandong Province, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Mengkun Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lu Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Hongfei Ding
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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32
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Xu L, Shen L, Polski A, Prabakar RK, Shah R, Jubran R, Kim JW, Biegel J, Kuhn P, Cobrinik D, Hicks J, Gai X, Berry JL. Simultaneous identification of clinically relevant RB1 mutations and copy number alterations in aqueous humor of retinoblastoma eyes. Ophthalmic Genet 2020; 41:526-532. [PMID: 32799607 DOI: 10.1080/13816810.2020.1799417] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND Detection of germline RB1 mutations is critical for risk assessment of retinoblastoma (RB) patients. Assessment of somatic copy number alterations (SCNAs) is also critically important because of their prognostic significance. Herein we present a refined approach for the simultaneous identification of RB1 variants and SCNAs in the aqueous humor (AH) of RB eyes. MATERIALS AND METHODS Subjects included 7 eyes of 6 RB patients that underwent AH extraction, and 4 matched tumor samples. Cell-free DNA (cfDNA) was isolated and sequenced to assess genome-wide SCNAs. The same sequencing libraries then underwent targeted resequencing and mutation detection using a custom hybridization panel that targets RB1 and MYCN. Illumina paired-end 2x150bp sequencing was used to characterize single-nucleotide variants (SNVs) and loss of heterozygosity (LOH). Results were compared to peripheral blood RB1 testing. Tumor fraction (TFx) was calculated using ichorCNA. RESULTS Four of 7 AH samples contained clinically significant SCNAs. Of the 3 other samples, 1 showed focal MYCN amplification and 1 showed focal RB1 deletion. All 4 enucleated tumors contained SCNAs. Mutational analysis of tumor DNA identified all first hits (2 germline RB1 SNVs, 2 germline CNAs) and second hits (4 RB1 SNVs). RB1 variants in AH were concordant with those obtained from corresponding tumor tissue and blood. In AH samples without paired tumor, both RB1 hits were identified with high variant allele frequency, even in the absence of SCNAs. CONCLUSIONS AH liquid biopsy is a minimally invasive, in vivo alternative to tissue analysis for the simultaneous identification of RB1 variants and SCNAs in RB eyes.
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Affiliation(s)
- Liya Xu
- The Vision Center, Children's Hospital Los Angeles , Los Angeles, California, USA.,Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California , Los Angeles, California, USA
| | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles , Los Angeles, California, USA
| | - Ashley Polski
- The Vision Center, Children's Hospital Los Angeles , Los Angeles, California, USA.,USC Roski Eye Institute, Keck School of Medicine of USC , Los Angeles, California, USA
| | - Rishvanth K Prabakar
- Department of Molecular and Computational Biology, University of Southern California , Los Angeles, California, USA
| | - Rachana Shah
- Center for Blood Disorders, Children's Hospital Los Angeles , Los Angeles, California, USA
| | - Rima Jubran
- Center for Blood Disorders, Children's Hospital Los Angeles , Los Angeles, California, USA
| | - Jonathan W Kim
- The Vision Center, Children's Hospital Los Angeles , Los Angeles, California, USA.,USC Roski Eye Institute, Keck School of Medicine of USC , Los Angeles, California, USA
| | - Jacklyn Biegel
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles , Los Angeles, California, USA
| | - Peter Kuhn
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California , Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine of USC , Los Angeles, California, USA.,Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California , Los Angeles, California, USA.,Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California , Los Angeles, California, USA
| | - David Cobrinik
- The Vision Center, Children's Hospital Los Angeles , Los Angeles, California, USA.,USC Roski Eye Institute, Keck School of Medicine of USC , Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine of USC , Los Angeles, California, USA.,The Saban Research Institute, Children's Hospital Los Angeles , Los Angeles, California, USA
| | - James Hicks
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California , Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine of USC , Los Angeles, California, USA.,Department of Biochemistry and Molecular Medicine, Keck School of Medicine of USC , Los Angeles, California, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles , Los Angeles, California, USA
| | - Jesse L Berry
- The Vision Center, Children's Hospital Los Angeles , Los Angeles, California, USA.,USC Roski Eye Institute, Keck School of Medicine of USC , Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine of USC , Los Angeles, California, USA.,The Saban Research Institute, Children's Hospital Los Angeles , Los Angeles, California, USA
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Retinoblastoma: Etiology, Modeling, and Treatment. Cancers (Basel) 2020; 12:cancers12082304. [PMID: 32824373 PMCID: PMC7465685 DOI: 10.3390/cancers12082304] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/03/2020] [Accepted: 08/12/2020] [Indexed: 12/19/2022] Open
Abstract
Retinoblastoma is a retinal cancer that is initiated in response to biallelic loss of RB1 in almost all cases, together with other genetic/epigenetic changes culminating in the development of cancer. RB1 deficiency makes the retinoblastoma cell-of-origin extremely susceptible to cancerous transformation, and the tumor cell-of-origin appears to depend on the developmental stage and species. These are important to establish reliable preclinical models to study the disease and develop therapies. Although retinoblastoma is the most curable pediatric cancer with a high survival rate, advanced tumors limit globe salvage and are often associated with high-risk histopathological features predictive of dissemination. The advent of chemotherapy has improved treatment outcomes, which is effective for globe preservation with new routes of targeted drug delivery. However, molecularly targeted therapeutics with more effectiveness and less toxicity are needed. Here, we review the current knowledge concerning retinoblastoma genesis with particular attention to the genomic and transcriptomic landscapes with correlations to clinicopathological characteristics, as well as the retinoblastoma cell-of-origin and current disease models. We further discuss current treatments, clinicopathological correlations, which assist in guiding treatment and may facilitate globe preservation, and finally we discuss targeted therapeutics for future treatments.
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34
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Xu L, Polski A, Prabakar RK, Reid MW, Chevez-Barrios P, Jubran R, Kim JW, Kuhn P, Cobrinik D, Hicks J, Berry JL. Chromosome 6p Amplification in Aqueous Humor Cell-Free DNA Is a Prognostic Biomarker for Retinoblastoma Ocular Survival. Mol Cancer Res 2020; 18:1166-1175. [PMID: 32434859 PMCID: PMC7415535 DOI: 10.1158/1541-7786.mcr-19-1262] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/10/2020] [Accepted: 05/18/2020] [Indexed: 11/16/2022]
Abstract
Aqueous humor contains tumor-derived cell-free DNA (cfDNA) and can serve as a liquid biopsy for retinoblastoma. We previously associated somatic copy-number alteration (SCNA) 6p gain with a 10-fold increased risk of enucleation. Here we provide a 2-year update to further explore 6p gain as a prognostic biomarker for ocular survival. Patients diagnosed with retinoblastoma from December 2014 to July 2019 from whom aqueous humor was sampled were included. cfDNA was extracted and shallow whole-genome sequencing performed to identify highly recurrent retinoblastoma SCNAs (gain of 1q, 2p, 6p, loss of 13q, 16q). 116 aqueous humor samples from 50 eyes of 46 patients were included: 27 eyes were salvaged, 23 were enucleated. Highly recurrent retinoblastoma SCNAs were found in 66% eyes. 6p gain was the most prevalent SCNA (50% eyes). It was particularly more prevalent in enucleated eyes (73.9%) than in salvaged eyes (29.6%; P = 0.004). 6p gain in aqueous humor cfDNA portended nearly 10-fold increased odds of enucleation (OR = 9.87; 95% confidence interval = 1.75-55.65; P = 0.009). In the enucleated eyes, 6p gain was associated with aggressive histopathologic features, including necrosis, higher degrees of anaplasia, and focal invasion of ocular structures. With extended follow-up and nearly double the aqueous humor samples, we continue to demonstrate 6p gain as a potential prognostic biomarker for retinoblastoma. IMPLICATIONS: Aqueous humor is a high-yield source of tumor-derived DNA in retinoblastoma eyes. Detection of 6p gain in the aqueous humor allows for targeted, patient-centered therapies based on this molecular prognostic marker. Prospective, multicenter studies with aqueous humor sampled from all eyes at diagnosis are warranted to validate these findings.
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Affiliation(s)
- Liya Xu
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - Ashley Polski
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck Medical School of the University of Southern California, Los Angeles, California
| | - Rishvanth K Prabakar
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California
| | - Mark W Reid
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California
| | - Patricia Chevez-Barrios
- Departments of Pathology and Genomic Medicine and Ophthalmology, Houston Methodist, Weill Cornell Medical College, Houston, Texas
| | - Rima Jubran
- Department of Hematology-Oncology, Children's Hospital Los Angeles, Los Angeles, California
| | - Jonathan W Kim
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck Medical School of the University of Southern California, Los Angeles, California
| | - Peter Kuhn
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California
| | - David Cobrinik
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck Medical School of the University of Southern California, Los Angeles, California
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - James Hicks
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jesse L Berry
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California.
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
- USC Roski Eye Institute, Keck Medical School of the University of Southern California, Los Angeles, California
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
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Özdemir Özdoğan G, Kaya H. Next-Generation Sequencing Data Analysis on Pool-Seq and Low-Coverage Retinoblastoma Data. Interdiscip Sci 2020; 12:302-310. [PMID: 32519123 DOI: 10.1007/s12539-020-00374-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 04/26/2020] [Accepted: 05/22/2020] [Indexed: 12/31/2022]
Abstract
Next-generation sequencing (NGS) is related to massively parallel or deep deoxyribonucleic acid (DNA) sequencing technology which has revolutionized genomic researches in recent years. Although the cost of generating NGS data was decreased compared to the one at the time of emerging this technology, its cost might still be somewhat a problem. Hence, new strategies as pool-seq and low-coverage NGS data have been developed to overcome the cost problem. Despite decreasing cost, it is important to elucidate whether they are efficient in NGS studies. We applied a bioinformatics pipeline on pool-seq and low-coverage retinoblastoma data retrieved from only tumor data. Retinoblastoma is an eye malignancy in childhood that is initiated by RB1 mutation or MYCN amplification and can lead to the loss of vision of eye(s), and even sometimes life. We applied our pipeline on both retinoblastoma disease data and two other particular data to testify the validity and also for comparison purposes in the aspect of performance. High-confidence variant calls from Genome in a Bottle Consortium were used for fulfilling these purposes. We observed that our pipeline successfully called higher number of variants than a standard pipeline for all these three different data. Besides, the recall and F-score values were quite better in our pipeline as being noteworthy. We further presented our results on disease data in the aspects of the variants, variant types and disease-related genes. This study provides a guideline for performing NGS data analysis pipeline on pool-seq and low-coverage sequencing data in conjunction. To get more conclusive outcomes of these two strategies, we recommend using cancer data having higher mutation rates and larger pools.
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Affiliation(s)
| | - Hilal Kaya
- Department of Computer Engineering, Ankara Yildirim Beyazit University, 06010, Ankara, Turkey.
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36
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Polski A, Xu L, Prabakar RK, Gai X, Kim JW, Shah R, Jubran R, Kuhn P, Cobrinik D, Hicks J, Berry JL. Variability in retinoblastoma genome stability is driven by age and not heritability. Genes Chromosomes Cancer 2020; 59:584-590. [PMID: 32390242 DOI: 10.1002/gcc.22859] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023] Open
Abstract
Retinoblastoma (RB) is a childhood intraocular cancer initiated by biallelic inactivation of the RB tumor suppressor gene (RB1-/- ). RB can be hereditary (germline RB1 pathogenic allele is present) or non-hereditary. Somatic copy number alterations (SCNAs) contribute to subsequent tumorigenesis. Previous studies of only enucleated RB eyes have reported associations between heritability status and the prevalence of SCNAs. Herein, we use an aqueous humor (AH) liquid biopsy to investigate RB genomic profiles in the context of germline RB1 status, age, and International Intraocular Retinoblastoma Classification (IIRC) clinical grouping for both enucleated and salvaged eyes. Between 2014 and 2019, AH was sampled from a total of 54 eyes of 50 patients. Germline RB1 status was determined from clinical blood testing, and cell-free DNA from AH was analyzed for SCNAs. Of the 50 patients, 23 (46.0%; 27 eyes) had hereditary RB, and 27 (54.0%, 27 eyes) had non-hereditary RB. Median age at diagnosis was comparable between hereditary (13 ± 10 months) and non-hereditary (13 ± 8 months) eyes (P = 0.818). There was no significant difference in the prevalence or number of SCNAs based on (1) hereditary status (P > 0.56) or (2) IIRC grouping (P > 0.47). There was, however, a significant correlation between patient age at diagnosis, and (1) number of total SCNAs (r[52] = 0.672, P < 0.00001) and (2) number of highly-recurrent RB SCNAs (r[52] = 0.616, P < 0.00001). This evidence does not support the theory that specific molecular or genomic subtypes exist between hereditary and non-hereditary RB; rather, the prevalence of genomic alterations in RB eyes is strongly related to patient age at diagnosis.
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Affiliation(s)
- Ashley Polski
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California, USA.,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Liya Xu
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California, USA.,Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California, USA
| | - Rishvanth K Prabakar
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Jonathan W Kim
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California, USA.,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Rachana Shah
- Cancer and Blood Disease Institute at Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Rima Jubran
- Cancer and Blood Disease Institute at Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Peter Kuhn
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.,Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA.,Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | - David Cobrinik
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California, USA.,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.,Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.,The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - James Hicks
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jesse L Berry
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California, USA.,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
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Liu G, Chen X, Wang Q, Yuan L. NEK7: a potential therapy target for NLRP3-related diseases. Biosci Trends 2020; 14:74-82. [PMID: 32295992 DOI: 10.5582/bst.2020.01029] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
NLRP3 inflammasome plays an essential role in innate immunity, yet the activation mechanism of NLRP3 inflammasome is not clear. In human or animal models, inappropriate NLRP3 inflammasome activation is implicated in many NLRP3-related diseases, such as tumors, inflammatory diseases and autoimmune diseases. Until now, a great number of inhibitors have been used to disturb the related signaling pathways, such as IL-1β blockade, IL-18 blockade and caspase-1 inhibitors. Unfortunately, most of these inhibitors just disturb the signaling pathways after the activation of NLRP3 inflammasome. Inhibitors that directly regulate NLRP3 to abolish the inflammation response may be more effective. NEK7 is a multifunctional kinase affecting centrosome duplication, mitochondrial regulation, intracellular protein transport, DNA repair and mitotic spindle assembly. Researchers have made significant observations on the regulation of gene transcription or protein expression of the NLRP3 inflammasome signaling pathway by NEK7. Those signaling pathways include ROS signaling, potassium efflux, lysosomal destabilization, and NF-κB signaling. Furthermore, NEK7 has been proved to be involved in many NLRP3-related diseases in humans or in animal models. Inhibitors focused on NEK7 may regulate NLRP3 to abolish the inflammation response and NEK7 may be a potential therapeutic target for NLRP3-related diseases.
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Affiliation(s)
- Ganglei Liu
- Department of Geriatrics Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xueliang Chen
- Department of Geriatrics Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qianqian Wang
- Department of Oncology, The Affiliated Zhuzhou Hospital of Xiangya Medical College, Central South University, Zhuzhou, Hunan, China
| | - Lianwen Yuan
- Department of Geriatrics Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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Wang Y, Sun D, Sheng Y, Guo H, Meng F, Song T. XIST promotes cell proliferation and invasion by regulating miR-140-5p and SOX4 in retinoblastoma. World J Surg Oncol 2020; 18:49. [PMID: 32127028 PMCID: PMC7055023 DOI: 10.1186/s12957-020-01825-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 02/19/2020] [Indexed: 12/13/2022] Open
Abstract
Background Retinoblastoma (RB) is the most common intraocular malignancy in children. Long non-coding RNA X-inactive specific transcript (lncRNA XIST) has been reported to be associated with RB, but research on the mechanism of XIST is not well studied. Methods Expressions of XIST, microRNA-140-5p (miR-140-5p), and sex-determining region Y-related high-mobility group box 4 (SOX4) were analyzed by qRT-PCR or Western blot. Relationships of XIST, SOX4, and miR-140-5p were evaluated by dual-luciferase reporter assay and Spearman’s analysis. Cell Counting Kit-8 (CCK-8) and Transwell assay were performed to assess the function of XIST on RB cell proliferation and invasion. Results In RB tissues, XIST and SOX4 expressions were obviously increased, but the miR-140-5p expression was markedly reduced. XIST expression was positively related to SOX4 expression while negatively correlated with miR-140-5p expression, and negative correlation was exhibited between miR-140-5p and SOX4 expression in RB tissues. XIST was confirmed to directly bind to miR-140-5p, and SOX4 was one target of miR-140-5p. XIST knockdown could impede RB cell proliferation and invasion, while miR-140-5p inhibition reversed the effects. In addition, XIST overexpression or miR-140-5p inhibition could abrogate the inhibition of SOX4 silencing on cell proliferation and invasion of RB cells. Conclusions XIST was obviously increased in RB tissues and cells, and XIST inhibition repressed the proliferation and invasion of RB cells by miR-140-5p/SOX4 axis, which may provide new understandings of the XIST molecular mechanism in RB.
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Affiliation(s)
- Yuhui Wang
- Department of Clinical Laboratory, Affiliated Hospital of Beihua University, Jilin, 132011, China
| | - Dahong Sun
- Department of Pediatrics, The Third People's Hospital of Qingdao, Qingdao, 266041, China
| | - Ying Sheng
- Department of Pediatrics, The Third People's Hospital of Qingdao, Qingdao, 266041, China
| | - Hong Guo
- Health Management Center, The People's Hospital of Zhangqiu Area, Jinan, 250200, China
| | - Fanchun Meng
- Delivery Room, The People's Hospital of Zhangqiu Area, Jinan, 250200, China
| | - Tingting Song
- No. 2 Department of Oncology, Qingdao Central Hospital, Qingdao Tumor Hospital, 127 Siliu South Road, Shibei District, Qingdao, 266042, China.
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Afshar AR, Pekmezci M, Bloomer MM, Cadenas NJ, Stevers M, Banerjee A, Roy R, Olshen AB, Van Ziffle J, Onodera C, Devine WP, Grenert JP, Bastian BC, Solomon DA, Damato BE. Next-Generation Sequencing of Retinoblastoma Identifies Pathogenic Alterations beyond RB1 Inactivation That Correlate with Aggressive Histopathologic Features. Ophthalmology 2019; 127:804-813. [PMID: 32139107 DOI: 10.1016/j.ophtha.2019.12.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/20/2022] Open
Abstract
PURPOSE To determine the usefulness of a comprehensive, targeted-capture next-generation sequencing (NGS) assay for the clinical management of children undergoing enucleation for retinoblastoma. DESIGN Cohort study. PARTICIPANTS Thirty-two children with retinoblastoma. METHODS We performed targeted NGS using the UCSF500 Cancer Panel (University of California, San Francisco, San Francisco, CA) on formalin-fixed, paraffin-embedded tumor tissue along with constitutional DNA isolated from peripheral blood, buccal swab, or uninvolved optic nerve. Peripheral blood samples were also sent to a commercial laboratory for germline RB1 mutation testing. MAIN OUTCOME MEASURES Presence or absence of germline RB1 mutation or deletion, tumor genetic profile, and association of genetic alterations with clinicopathologic features. RESULTS Germline mutation or deletion of the RB1 gene was identified in all children with bilateral retinoblastoma (n = 12), and these NGS results were 100% concordant with commercial germline RB1 mutation analysis. In tumor tissue tested with NGS, biallelic inactivation of RB1 was identified in 28 tumors and focal MYCN amplification was identified in 4 tumors (2 with wild-type RB1 and 2 with biallelic RB1 inactivation). Additional likely pathogenic alterations beyond RB1 were identified in 13 tumors (41%), several of which have not been reported previously in retinoblastoma. These included focal amplifications of MDM4 and RAF1, as well as damaging mutations involving BCOR, ARID1A, MGA, FAT1, and ATRX. The presence of additional likely pathogenetic mutations beyond RB1 inactivation was associated with aggressive histopathologic features, including higher histologic grade and anaplasia, and also with both unilateral and sporadic disease. CONCLUSIONS Comprehensive NGS analysis reliably detects relevant mutations, amplifications, and chromosomal copy number changes in retinoblastoma. The presence of genetic alterations beyond RB1 inactivation correlates with aggressive histopathologic features.
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Affiliation(s)
- Armin R Afshar
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California.
| | - Melike Pekmezci
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Department of Pathology, University of California, San Francisco, San Francisco, California
| | - Michele M Bloomer
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California; Department of Pathology, University of California, San Francisco, San Francisco, California
| | - Nicola J Cadenas
- Cancer Genetics and Prevention Program, University of California, San Francisco, San Francisco, California
| | - Meredith Stevers
- Department of Pathology, University of California, San Francisco, San Francisco, California
| | - Anuradha Banerjee
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Division of Hematology-Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Computational Biology and Informatics, University of California, San Francisco, San Francisco, California
| | - Adam B Olshen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Computational Biology and Informatics, University of California, San Francisco, San Francisco, California; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Jessica Van Ziffle
- Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California
| | - Courtney Onodera
- Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California
| | - W Patrick Devine
- Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California
| | - James P Grenert
- Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California
| | - Boris C Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California; Department of Dermatology, University of California, San Francisco, San Francisco, California
| | - David A Solomon
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California
| | - Bertil E Damato
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
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40
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Non-random Mis-segregation of Human Chromosomes. Cell Rep 2019; 23:3366-3380. [PMID: 29898405 PMCID: PMC6019738 DOI: 10.1016/j.celrep.2018.05.047] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/25/2018] [Accepted: 05/14/2018] [Indexed: 02/07/2023] Open
Abstract
A common assumption is that human chromosomes carry equal chances of mis-segregation during compromised cell division. Human chromosomes vary in multiple parameters that might generate bias, but technological limitations have precluded a comprehensive analysis of chromosome-specific aneuploidy. Here, by imaging specific centromeres coupled with high-throughput single-cell analysis as well as single-cell sequencing, we show that aneuploidy occurs non-randomly following common treatments to elevate chromosome mis-segregation. Temporary spindle disruption leads to elevated mis-segregation and aneuploidy of a subset of chromosomes, particularly affecting chromosomes 1 and 2. Unexpectedly, we find that a period of mitotic delay weakens centromeric cohesion and promotes chromosome mis-segregation and that chromosomes 1 and 2 are particularly prone to suffer cohesion fatigue. Our findings demonstrate that inherent properties of individual chromosomes can bias chromosome mis-segregation and aneuploidy rates, with implications for studies on aneuploidy in human disease.
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Donnaloja F, Jacchetti E, Soncini M, Raimondi MT. Mechanosensing at the Nuclear Envelope by Nuclear Pore Complex Stretch Activation and Its Effect in Physiology and Pathology. Front Physiol 2019; 10:896. [PMID: 31354529 PMCID: PMC6640030 DOI: 10.3389/fphys.2019.00896] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/27/2019] [Indexed: 02/03/2023] Open
Abstract
Cell fate is correlated to mechanotransduction, in which forces transmitted by the cytoskeleton filaments alter the nuclear shape, affecting transcription factor import/export, cells transcription activity and chromatin distribution. There is in fact evidence that stem cells cultured in 3D environments mimicking the native niche are able to maintain their stemness or modulate their cellular function. However, the molecular and biophysical mechanisms underlying cellular mechanosensing are still largely unclear. The propagation of mechanical stimuli via a direct pathway from cell membrane integrins to SUN proteins residing in the nuclear envelop has been demonstrated, but we suggest that the cells’ fate is mainly affected by the force distribution at the nuclear envelope level, where the SUN protein transmits the stimuli via its mechanical connection to several cell structures such as chromatin, lamina and the nuclear pore complex (NPC). In this review, we analyze the NPC structure and organization, which have not as yet been fully investigated, and its plausible involvement in cell fate. NPC is a multiprotein complex that spans the nuclear envelope, and is involved in several key cellular processes such as bidirectional nucleocytoplasmic exchange, cell cycle regulation, kinetochore organization, and regulation of gene expression. As several connections between the NPC and the nuclear envelope, chromatin and other transmembrane proteins have been identified, it is reasonable to suppose that nuclear deformations can alter the NPC structure. We provide evidence that the transmission of mechanical forces may significantly affects the basket conformation via the Nup153-SUN1 connection, both altering the passage of molecules through it and influencing the state of chromatin packing. Finally, we review the known correlations between a pathological NPC structure and diseases such as cancer, autoimmune disease, aging and laminopathies.
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Affiliation(s)
- F Donnaloja
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta," Politecnico di Milano, Milan, Italy
| | - E Jacchetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta," Politecnico di Milano, Milan, Italy
| | - M Soncini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, Italy
| | - M T Raimondi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta," Politecnico di Milano, Milan, Italy
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Munier FL, Beck-Popovic M, Chantada GL, Cobrinik D, Kivelä TT, Lohmann D, Maeder P, Moll AC, Carcaboso AM, Moulin A, Schaiquevich P, Bergin C, Dyson PJ, Houghton S, Puccinelli F, Vial Y, Gaillard MC, Stathopoulos C. Conservative management of retinoblastoma: Challenging orthodoxy without compromising the state of metastatic grace. "Alive, with good vision and no comorbidity". Prog Retin Eye Res 2019; 73:100764. [PMID: 31173880 DOI: 10.1016/j.preteyeres.2019.05.005] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/25/2019] [Accepted: 05/29/2019] [Indexed: 12/21/2022]
Abstract
Retinoblastoma is lethal by metastasis if left untreated, so the primary goal of therapy is to preserve life, with ocular survival, visual preservation and quality of life as secondary aims. Historically, enucleation was the first successful therapeutic approach to decrease mortality, followed over 100 years ago by the first eye salvage attempts with radiotherapy. This led to the empiric delineation of a window for conservative management subject to a "state of metastatic grace" never to be violated. Over the last two decades, conservative management of retinoblastoma witnessed an impressive acceleration of improvements, culminating in two major paradigm shifts in therapeutic strategy. Firstly, the introduction of systemic chemotherapy and focal treatments in the late 1990s enabled radiotherapy to be progressively abandoned. Around 10 years later, the advent of chemotherapy in situ, with the capitalization of new routes of targeted drug delivery, namely intra-arterial, intravitreal and now intracameral injections, allowed significant increase in eye preservation rate, definitive eradication of radiotherapy and reduction of systemic chemotherapy. Here we intend to review the relevant knowledge susceptible to improve the conservative management of retinoblastoma in compliance with the "state of metastatic grace", with particular attention to (i) reviewing how new imaging modalities impact the frontiers of conservative management, (ii) dissecting retinoblastoma genesis, growth patterns, and intraocular routes of tumor propagation, (iii) assessing major therapeutic changes and trends, (iv) proposing a classification of relapsing retinoblastoma, (v) examining treatable/preventable disease-related or treatment-induced complications, and (vi) appraising new therapeutic targets and concepts, as well as liquid biopsy potentiality.
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Affiliation(s)
- Francis L Munier
- Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, Lausanne, Switzerland.
| | - Maja Beck-Popovic
- Unit of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Guillermo L Chantada
- Hemato-Oncology Service, Hospital JP Garrahan, Buenos Aires, Argentina; Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, Barcelona, Spain; Institut de Recerca Sant Joan de Deu, Barcelona, Spain
| | - David Cobrinik
- The Vision Center and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA; USC Roski Eye Institute, Department of Biochemistry & Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Tero T Kivelä
- Department of Ophthalmology, Ocular Oncology and Pediatric Ophthalmology Services, Helsinki University Hospital, Helsinki, Finland
| | - Dietmar Lohmann
- Eye Oncogenetics Research Group, Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Philippe Maeder
- Unit of Neuroradiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Annette C Moll
- UMC, Vrije Universiteit Amsterdam, Department of Ophthalmology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Angel Montero Carcaboso
- Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, Barcelona, Spain; Institut de Recerca Sant Joan de Deu, Barcelona, Spain
| | - Alexandre Moulin
- Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, Lausanne, Switzerland
| | - Paula Schaiquevich
- Unit of Clinical Pharmacokinetics, Hospital de Pediatria JP Garrahan, Buenos Aires, Argentina; National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
| | - Ciara Bergin
- Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, Lausanne, Switzerland
| | - Paul J Dyson
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Susan Houghton
- Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, Lausanne, Switzerland
| | - Francesco Puccinelli
- Interventional Neuroradiology Unit, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Yvan Vial
- Materno-Fetal Medicine Unit, Woman-Mother-Child Department, University Hospital of Lausanne, Switzerland
| | - Marie-Claire Gaillard
- Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, Lausanne, Switzerland
| | - Christina Stathopoulos
- Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, Lausanne, Switzerland
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43
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Dimaras H, Corson TW. Retinoblastoma, the visible CNS tumor: A review. J Neurosci Res 2019; 97:29-44. [PMID: 29314142 PMCID: PMC6034991 DOI: 10.1002/jnr.24213] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/02/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022]
Abstract
The pediatric ocular cancer retinoblastoma is the only central nervous system (CNS) tumor readily observed without specialized equipment: it can be seen by, and in, the naked eye. This accessibility enables unique imaging modalities. Here, we review this cancer for a neuroscience audience, highlighting these clinical and research imaging options, including fundus imaging, optical coherence tomography, ultrasound, and magnetic resonance imaging. We also discuss the subtype of retinoblastoma driven by the MYCN oncogene more commonly associated with neuroblastoma, and consider trilateral retinoblastoma, in which an intracranial tumor arises along with ocular tumors in patients with germline RB1 gene mutations. Retinoblastoma research and clinical care can offer insights applicable to CNS malignancies, and also benefit from approaches developed elsewhere in the CNS.
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Affiliation(s)
- Helen Dimaras
- Department of Ophthalmology and Vision Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Division of Clinical Public Health, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Child Health Evaluative Sciences Program, SickKids Research Institute, Toronto, ON, M5G 1X8, Canada
- Department of Human Pathology, College of Health Sciences, University of Nairobi, Nairobi, Kenya
| | - Timothy W. Corson
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, 46202, USA
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44
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Saengwimol D, Rojanaporn D, Chaitankar V, Chittavanich P, Aroonroch R, Boontawon T, Thammachote W, Jinawath N, Hongeng S, Kaewkhaw R. A three-dimensional organoid model recapitulates tumorigenic aspects and drug responses of advanced human retinoblastoma. Sci Rep 2018; 8:15664. [PMID: 30353124 PMCID: PMC6199308 DOI: 10.1038/s41598-018-34037-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/10/2018] [Indexed: 02/07/2023] Open
Abstract
Persistent or recurrent retinoblastoma (RB) is associated with the presence of vitreous or/and subretinal seeds in advanced RB and represents a major cause of therapeutic failure. This necessitates the development of novel therapies and thus requires a model of advanced RB for testing candidate therapeutics. To this aim, we established and characterized a three-dimensional, self-organizing organoid model derived from chemotherapy-naïve tumors. The responses of organoids to drugs were determined and compared to relate organoid model to advanced RB, in terms of drug sensitivities. We found that organoids had histological features resembling retinal tumors and seeds and retained DNA copy-number alterations as well as gene and protein expression of the parental tissue. Cone signal circuitry (M/L+ cells) and glial tumor microenvironment (GFAP+ cells) were primarily present in organoids. Topotecan alone or the combined drug regimen of topotecan and melphalan effectively targeted proliferative tumor cones (RXRγ+ Ki67+) in organoids after 24-h drug exposure, blocking mitotic entry. In contrast, methotrexate showed the least efficacy against tumor cells. The drug responses of organoids were consistent with those of tumor cells in advanced disease. Patient-derived organoids enable the creation of a faithful model to use in examining novel therapeutics for RB.
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Affiliation(s)
- Duangporn Saengwimol
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Duangnate Rojanaporn
- Department of Ophthalmology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Vijender Chaitankar
- Bioinformatics Computational Biology Core, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, USA
| | - Pamorn Chittavanich
- Section for Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Rangsima Aroonroch
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Tatpong Boontawon
- Section for Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Weerin Thammachote
- Section for Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Natini Jinawath
- Section for Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Rossukon Kaewkhaw
- Section for Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
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45
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Berry JL, Xu L, Kooi I, Murphree AL, Prabakar RK, Reid M, Stachelek K, Le BHA, Welter L, Reiser BJ, Chévez-Barrios P, Jubran R, Lee TC, Kim JW, Kuhn P, Cobrinik D, Hicks J. Genomic cfDNA Analysis of Aqueous Humor in Retinoblastoma Predicts Eye Salvage: The Surrogate Tumor Biopsy for Retinoblastoma. Mol Cancer Res 2018; 16:1701-1712. [PMID: 30061186 DOI: 10.1158/1541-7786.mcr-18-0369] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 06/28/2018] [Accepted: 07/18/2018] [Indexed: 01/29/2023]
Abstract
Tumor-derived cell-free DNA (cfDNA) has biomarker potential; therefore, this study aimed to identify cfDNA in the aqueous humor (AH) of retinoblastoma eyes and correlate somatic chromosomal copy-number alterations (SCNA) with clinical outcomes, specifically eye salvage. AH was extracted via paracentesis during intravitreal injection of chemotherapy or enucleation. Shallow whole-genome sequencing was performed using isolated cfDNA to assess for highly recurrent SCNAs in retinoblastoma including gain of 1q, 2p, 6p, loss of 13q, 16q, and focal MYCN amplification. Sixty-three clinical specimens of AH from 29 eyes of 26 patients were evaluated; 13 eyes were enucleated and 16 were salvaged (e.g., saved). The presence of detectable SCNAs was 92% in enucleated eyes versus 38% in salvaged eyes (P = 0.006). Gain of chromosome 6p was the most common SCNA found in 77% of enucleated eyes, compared with 25% of salvaged eyes (P = 0.0092), and associated with a 10-fold increased odds of enucleation (OR, 10; 95% CI, 1.8-55.6). The median amplitude of 6p gain was 1.47 in enucleated versus 1.07 in salvaged eyes (P = 0.001). The presence of AH SCNAs was correlated retrospectively with eye salvage. The probability of ocular salvage was higher in eyes without detectable SCNAs in the AH (P = 0.0028), specifically 6p gain. This is the first study to correlate clinical outcomes with SCNAs in the AH from retinoblastoma eyes, as such these findings indicate that 6p gain in the aqueous humor is a potential prognostic biomarker for poor clinical response to therapy.Implications: The correlation of clinical outcomes and SCNAs in the AH identified in the current study requires prospective studies to validate these finding before SCNAs, like 6p gain, can be used to predict clinical outcomes at diagnosis. Mol Cancer Res; 16(11); 1701-12. ©2018 AACR.
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Affiliation(s)
- Jesse L Berry
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California. .,USC Roski Eye Institute, Keck Medical School of the University of Southern CA, Los Angeles, California
| | - Liya Xu
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California
| | | | - A Linn Murphree
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California.,USC Roski Eye Institute, Keck Medical School of the University of Southern CA, Los Angeles, California
| | - Rishvanth K Prabakar
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California
| | - Mark Reid
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California
| | - Kevin Stachelek
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California
| | - Bao Han A Le
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California.,USC Roski Eye Institute, Keck Medical School of the University of Southern CA, Los Angeles, California
| | - Lisa Welter
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California
| | - Bibiana J Reiser
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California.,USC Roski Eye Institute, Keck Medical School of the University of Southern CA, Los Angeles, California
| | - Patricia Chévez-Barrios
- Departments of Pathology and Genomic Medicine and Ophthalmology, Houston Methodist, Weill Cornell Medical College, Houston, Texas
| | - Rima Jubran
- The Children's Center for Cancer and Blood Diseases, Children's Hospital Los Angeles, Los Angeles, California
| | - Thomas C Lee
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California.,USC Roski Eye Institute, Keck Medical School of the University of Southern CA, Los Angeles, California
| | - Jonathan W Kim
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California.,USC Roski Eye Institute, Keck Medical School of the University of Southern CA, Los Angeles, California
| | - Peter Kuhn
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California.,Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California.,Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California
| | - David Cobrinik
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California.,USC Roski Eye Institute, Keck Medical School of the University of Southern CA, Los Angeles, California.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California.,Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.,The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - James Hicks
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
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46
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Elchuri SV, Rajasekaran S, Miles WO. RNA-Sequencing of Primary Retinoblastoma Tumors Provides New Insights and Challenges Into Tumor Development. Front Genet 2018; 9:170. [PMID: 29868118 PMCID: PMC5966869 DOI: 10.3389/fgene.2018.00170] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/26/2018] [Indexed: 12/17/2022] Open
Abstract
Retinoblastoma is rare tumor of the retina caused by the homozygous loss of the Retinoblastoma 1 tumor suppressor gene (RB1). Loss of the RB1 protein, pRB, results in de-regulated activity of the E2F transcription factors, chromatin changes and developmental defects leading to tumor development. Extensive microarray profiles of these tumors have enabled the identification of genes sensitive to pRB disruption, however, this technology has a number of limitations in the RNA profiles that they generate. The advent of RNA-sequencing has enabled the global profiling of all of the RNA within the cell including both coding and non-coding features and the detection of aberrant RNA processing events. In this perspective, we focus on discussing how RNA-sequencing of rare Retinoblastoma tumors will build on existing data and open up new area's to improve our understanding of the biology of these tumors. In particular, we discuss how the RB-research field may be to use this data to determine how RB1 loss results in the expression of; non-coding RNAs, causes aberrant RNA processing events and how a deeper analysis of metabolic RNA changes can be utilized to model tumor specific shifts in metabolism. Each section discusses new opportunities and challenges associated with these types of analyses and aims to provide an honest assessment of how understanding these different processes may contribute to the treatment of Retinoblastoma.
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Affiliation(s)
- Sailaja V. Elchuri
- Department of Nanotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Swetha Rajasekaran
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States
| | - Wayne O. Miles
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH, United States
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States
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Zhang J, Wang L, Zhang Y. Downregulation of NIMA-related kinase-7 inhibits cell proliferation by inducing cell cycle arrest in human retinoblastoma cells. Exp Ther Med 2017; 15:1360-1366. [PMID: 29434721 PMCID: PMC5774400 DOI: 10.3892/etm.2017.5558] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 05/05/2017] [Indexed: 12/20/2022] Open
Abstract
NIMA-related kinase-7 (Nek7) is a centrosomal kinase involved in various types of cancer, including gallbladder cancer and hepatocellular carcinoma. However, the biological function and the potential underlying mechanism of Nek7 in retinoblastoma remain largely unknown. Therefore, the present study investigated the effects of Nek7 in retinoblastoma cells. The expression of Nek7 was initially determined and observed to be commonly upregulated in retinoblastoma cell lines (Y79, SO-RB50 and WERI-RB1) as compared with that in normal retinal pigment epithelium cells. Next, the endogenous expression of Nek7 was efficiently knocked down in Y79 and SO-RB50 cells using a lentivirus-mediated RNA interference approach, as confirmed by reverse transcription-quantitative polymerase chain reaction and western blot analysis. Loss-of-function assays, including MTT, colony formation and flow cytometry, indicated that knockdown of Nek7 significantly inhibited cell growth, impaired the colony formation ability and induced cell cycle arrest at G0/G1 phase. Furthermore, mechanistic studies demonstrated that silencing of Nek7 resulted in reduced cyclin-dependent kinase 2, cyclin D1 and cyclin E levels in vitro. In conclusion, the present study highlights the crucial role of Nek7 in promoting retinoblastoma cell proliferation, and Nek7-silencing may serve as a novel therapeutic target for retinoblastoma.
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Affiliation(s)
- Jian Zhang
- Department of Ophthalmology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi 710068, P.R. China
| | - Li Wang
- Department of Ophthalmology, Ankang City Central Hospital, Ankang, Shaanxi 725000, P.R. China
| | - Yongkang Zhang
- Department of Ophthalmology, Shaanxi Provincial Rehabilitation Hospital, Xi'an, Shaanxi 710065, P.R. China
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Berry JL, Xu L, Murphree AL, Krishnan S, Stachelek K, Zolfaghari E, McGovern K, Lee TC, Carlsson A, Kuhn P, Kim JW, Cobrinik D, Hicks J. Potential of Aqueous Humor as a Surrogate Tumor Biopsy for Retinoblastoma. JAMA Ophthalmol 2017; 135:1221-1230. [PMID: 29049475 DOI: 10.1001/jamaophthalmol.2017.4097] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Importance Retinoblastoma (Rb) is one of the first tumors to have a known genetic etiology. However, because biopsy of this tumor is contraindicated, it has not been possible to define the effects of secondary genetic changes on the disease course. Objective To investigate whether the aqueous humor (AH) of Rb eyes has sufficient tumor-derived DNA to perform genetic analysis of the tumor, including DNA copy number alterations. Design, Setting, and Participants This investigation was a case series study at a tertiary care hospital (Children's Hospital Los Angeles) with a large Rb treatment center. Cell-free DNA (cfDNA) was isolated from 6 AH samples from 3 children with Rb, including 2 after primary enucleation and 1 undergoing multiple intravitreous injections of melphalan for vitreous seeding. Samples were taken between December 2014 and September 2015. Main Outcomes and Measures Measurable levels of nucleic acids in the AH and identification of tumor-derived DNA copy number variation in the AH. The AH was analyzed for DNA, RNA, and micro-RNA using Qubit high-sensitivity kits. Cell-free DNA was isolated from the AH, and sequencing library protocols were optimized. Shallow whole-genome sequencing was performed on an Illumina platform, followed by genome-wide chromosomal copy number variation profiling to assess the presence of tumor DNA fractions in the AH cfDNA of the 3 patients. One child's cfDNA from the AH and tumor DNA were subjected to Sanger sequencing to isolate the RB1 mutation. Results Six AH samples were obtained from 3 Rb eyes in 3 children (2 male and 1 female; diagnosed at ages 7, 20, and 28 months). A corroborative pattern between the chromosomal copy number variation profiles of the AH cfDNA and tumor-derived DNA from the enucleated samples was identified. In addition, a nonsense RB1 mutation (Lys→STOP) from 1 child was also identified from the AH samples obtained during intravitreous injection of melphalan, which matched the tumor sample postsecondary enucleation. Sanger sequencing of the AH cfDNA and tumor DNA with polymerase chain reaction primers targeting RB1 gene c.1075A demonstrated this same RB1 mutation. Conclusions and Relevance In this study evaluating nucleic acids in the AH from Rb eyes undergoing salvage therapy with intravitreous injection of melphalan, the results suggest that the AH can serve as a surrogate tumor biopsy when Rb tumor tissue is not available. This novel method will allow for analyses of tumor-derived DNA in Rb eyes undergoing salvage therapy that have not been enucleated.
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Affiliation(s)
- Jesse L Berry
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California.,USC Roski Eye Institute, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles
| | - Liya Xu
- Department of Biological Sciences, USC Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles
| | - A Linn Murphree
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California.,USC Roski Eye Institute, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles
| | | | - Kevin Stachelek
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California
| | - Emily Zolfaghari
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California.,USC Roski Eye Institute, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles
| | - Kathleen McGovern
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California
| | - Thomas C Lee
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California.,USC Roski Eye Institute, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles
| | - Anders Carlsson
- Department of Biological Sciences, USC Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles
| | - Peter Kuhn
- Department of Biological Sciences, USC Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles.,Norris Comprehensive Cancer Center, Keck School of Medicine of USC, University of Southern California, Los Angeles.,Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles.,Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles
| | - Jonathan W Kim
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California.,USC Roski Eye Institute, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles
| | - David Cobrinik
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, California.,USC Roski Eye Institute, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles.,Norris Comprehensive Cancer Center, Keck School of Medicine of USC, University of Southern California, Los Angeles.,Department of Biochemistry and Molecular Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles.,The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California
| | - James Hicks
- Department of Biological Sciences, USC Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles.,Norris Comprehensive Cancer Center, Keck School of Medicine of USC, University of Southern California, Los Angeles
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Tomar S, Sethi R, Sundar G, Quah TC, Quah BL, Lai PS. Mutation spectrum of RB1 mutations in retinoblastoma cases from Singapore with implications for genetic management and counselling. PLoS One 2017; 12:e0178776. [PMID: 28575107 PMCID: PMC5456385 DOI: 10.1371/journal.pone.0178776] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 05/18/2017] [Indexed: 12/21/2022] Open
Abstract
Retinoblastoma (RB) is a rare childhood malignant disorder caused by the biallelic inactivation of RB1 gene. Early diagnosis and identification of carriers of heritable RB1 mutations can improve disease outcome and management. In this study, mutational analysis was conducted on fifty-nine matched tumor and peripheral blood samples from 18 bilateral and 41 unilateral unrelated RB cases by a combinatorial approach of Multiplex Ligation-dependent Probe Amplification (MLPA) assay, deletion screening, direct sequencing, copy number gene dosage analysis and methylation assays. Screening of both blood and tumor samples yielded a mutation detection rate of 94.9% (56/59) while only 42.4% (25/59) of mutations were detected if blood samples alone were analyzed. Biallelic mutations were observed in 43/59 (72.9%) of tumors screened. There were 3 cases (5.1%) in which no mutations could be detected and germline mutations were detected in 19.5% (8/41) of unilateral cases. A total of 61 point mutations were identified, of which 10 were novel. There was a high incidence of previously reported recurrent mutations, occurring at 38.98% (23/59) of all cases. Of interest were three cases of mosaic RB1 mutations detected in the blood from patients with unilateral retinoblastoma. Additionally, two germline mutations previously reported to be associated with low-penetrance phenotypes: missense-c.1981C>T and splice variant-c.607+1G>T, were observed in a bilateral and a unilateral proband, respectively. These findings have implications for genetic counselling and risk prediction for the affected families. This is the first published report on the spectrum of mutations in RB patients from Singapore and shows that further improved mutation screening strategies are required in order to provide a definitive molecular diagnosis for every case of RB. Our findings also underscore the importance of genetic testing in supporting individualized disease management plans for patients and asymptomatic family members carrying low-penetrance, germline mosaicism or heritable unilateral mutational phenotypes.
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Affiliation(s)
- Swati Tomar
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Raman Sethi
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Gangadhara Sundar
- Department of Ophthalmology, National University Hospital, Singapore, Singapore
| | - Thuan Chong Quah
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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50
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Gupta A, Tsuchiya Y, Ohta M, Shiratsuchi G, Kitagawa D. NEK7 is required for G1 progression and procentriole formation. Mol Biol Cell 2017; 28:2123-2134. [PMID: 28539406 PMCID: PMC5509424 DOI: 10.1091/mbc.e16-09-0643] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 04/27/2017] [Accepted: 05/18/2017] [Indexed: 12/11/2022] Open
Abstract
As cells exit mitosis, the decision to commit to the next cell cycle is made during G1. Not only DNA replication, but also centriole duplication is initiated as cells enter the S-phase. The kinase NEK7 is required for the timely regulation of G1 progression, S-phase entry, and procentriole formation. The decision to commit to the cell cycle is made during G1 through the concerted action of various cyclin–CDK complexes. Not only DNA replication, but also centriole duplication is initiated as cells enter the S-phase. The NIMA-related kinase NEK7 is one of many factors required for proper centriole duplication, as well as for timely cell cycle progression. However, its specific roles in these events are poorly understood. In this study, we find that depletion of NEK7 inhibits progression through the G1 phase in human U2OS cells via down-regulation of various cyclins and CDKs and also inhibits the earliest stages of procentriole formation. Depletion of NEK7 also induces formation of primary cilia in human RPE1 cells, suggesting that NEK7 acts at least before the restriction point during G1. G1-arrested cells in the absence of NEK7 exhibit abnormal accumulation of the APC/C cofactor Cdh1 at the vicinity of centrioles. Furthermore, the ubiquitin ligase APC/CCdh1 continuously degrades the centriolar protein STIL in these cells, thus inhibiting centriole assembly. Collectively our results demonstrate that NEK7 is involved in the timely regulation of G1 progression, S-phase entry, and procentriole formation.
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Affiliation(s)
- Akshari Gupta
- Division of Centrosome Biology, Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan
| | - Yuki Tsuchiya
- Division of Centrosome Biology, Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan
| | - Midori Ohta
- Division of Centrosome Biology, Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Gen Shiratsuchi
- Division of Centrosome Biology, Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Daiju Kitagawa
- Division of Centrosome Biology, Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan .,Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan
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