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Gelmi MC, de Ru AH, van Veelen PA, Tjokrodirijo RTN, Stern MH, Houy A, Verdijk RM, Vu THK, Ksander BR, Vaarwater J, Kilic E, Brosens E, Jager MJ. Protein and mRNA Expression in Uveal Melanoma Cell Lines Are Related to GNA and BAP1 Mutation Status. Invest Ophthalmol Vis Sci 2024; 65:37. [PMID: 39042403 PMCID: PMC11268447 DOI: 10.1167/iovs.65.8.37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024] Open
Abstract
Purpose Cell lines are being used in preclinical uveal melanoma (UM) research. Because not all cell lines harbor typical GNAQ or GNA11 hotspot mutations, we aimed at better classifying them and determining whether we could find genetic causes to explain the protein and mRNA expression profiles of the cell lines. Methods We studied protein and mRNA expression of 14 UM cell lines and determined the presence of single nucleotide variants and small insertions and deletions with next-generation sequencing and copy number alterations with a single nucleotide polymorphism array. The lists of differentially expressed proteins and genes were merged, and shared lists were created, keeping only terms with concordant mRNA and protein expression. Enrichment analyses were performed on the shared lists. Results Cell lines Mel285 and Mel290 are separate from GNA-mutated cell lines and show downregulation of melanosome-related markers. Both lack typical UM mutations but each harbors four putatively deleterious variants in CTNNB1, PPP1R10, LIMCH1, and APC in Mel285 and ARID1A, PPP1R10, SPG11, and RNF43 in Mel290. The upregulated terms in Mel285 and Mel290 did not point to a convincing alternative origin. Mel285 shows loss of chromosomes 1p, 3p, partial 3q, 6, and partial 8p, whereas Mel290 shows loss of 1p and 6. Expression in the other 12 cell lines was related to BAP1 expression. Conclusions Although Mel285 and Mel290 have copy number alterations that fit UM, multi-omics analyses show that they belong to a separate group compared to the other analyzed UM cell lines. Therefore, they may not be representative models to test potential therapeutic targets for UM.
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Affiliation(s)
- Maria Chiara Gelmi
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Marc-Henri Stern
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Institut Curie, PSL Research University, Paris, France
| | - Alexandre Houy
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Institut Curie, PSL Research University, Paris, France
| | - Robert M. Verdijk
- Department of Pathology, Ophthalmic Pathology Section, Erasmus MC, Rotterdam, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - T. H. Khanh Vu
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Bruce R. Ksander
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States
| | - Jolanda Vaarwater
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Department of Ophthalmology, Erasmus MC, Rotterdam, The Netherlands
| | - Emine Kilic
- Department of Ophthalmology, Erasmus MC, Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Martine J. Jager
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
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2
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Tura A, Zhu Y, Vardanyan S, Prasuhn M, Kakkassery V, Lüke J, Merz H, Paulsen F, Rades D, Cremers F, Bartz-Schmidt KU, Grisanti S. Radiation-Induced DNA Damage in Uveal Melanoma Is Influenced by Dose Delivery and Chromosome 3 Status. Invest Ophthalmol Vis Sci 2024; 65:7. [PMID: 38833258 PMCID: PMC11156202 DOI: 10.1167/iovs.65.6.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 03/15/2024] [Indexed: 06/06/2024] Open
Abstract
Purpose The purpose of this study was to analyze the extent of DNA breaks in primary uveal melanoma (UM) with regard to radiotherapy dose delivery (single-dose versus fractionated) and monosomy 3 status. Methods A total of 54 patients with UM were included. Stereotactic radiotherapy (SRT) was performed in 23 patients, with 8 undergoing single-dose SRT (sdSRT) treatment and 15 receiving fractionated SRT (fSRT). DNA breaks in the enucleated or endoresected tumors were visualized by a TUNEL assay and quantified by measuring the TUNEL-positive area. Protein expression was analyzed by immunohistochemistry. Co-detection of chromosome 3 with proteins was performed by immuno-fluorescent in situ hybridization. Results The amount of DNA breaks in the total irradiated group was increased by 2.7-fold (P < 0.001) compared to non-irradiated tissue. Tumors treated with fSRT were affected more severely, showing 2.1-fold more DNA damage (P = 0.007) compared to the cases after single (high) dose irradiation (sdSRT). Monosomy 3 tumors showed less DNA breaks compared to disomy 3 samples (P = 0.004). The presence of metastases after radiotherapy correlated with monosomy 3 and less DNA breaks compared to patients with non-metastatic cancer in the combined group with fSRT and sdSRT (P < 0.05). Conclusions Fractionated irradiation led to more DNA damage than single-dose treatment in primary UM. As tumors with monosomy 3 showed less DNA breaks than those with disomy 3, this may indicate that they are less radiosensitive, which may influence the efficacy of irradiation.
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Affiliation(s)
- Aysegül Tura
- Department of Ophthalmology, University Clinic Schleswig-Holstein (UKSH), University of Lübeck, Lübeck, Germany
| | - Yingda Zhu
- Department of Ophthalmology, University Clinic Schleswig-Holstein (UKSH), University of Lübeck, Lübeck, Germany
- Department of Ophthalmology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Siranush Vardanyan
- Department of Ophthalmology, University Clinic Schleswig-Holstein (UKSH), University of Lübeck, Lübeck, Germany
| | - Michelle Prasuhn
- Department of Ophthalmology, University Clinic Schleswig-Holstein (UKSH), University of Lübeck, Lübeck, Germany
| | - Vinodh Kakkassery
- Department of Ophthalmology, University Clinic Schleswig-Holstein (UKSH), University of Lübeck, Lübeck, Germany
| | - Julia Lüke
- Department of Ophthalmology, University Clinic Schleswig-Holstein (UKSH), University of Lübeck, Lübeck, Germany
| | - Hartmut Merz
- Reference Center for Lymph Node Pathology and Hematopathology, Lübeck, Germany
| | - Frank Paulsen
- Department of Radiation Oncology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Dirk Rades
- Department of Radiation Oncology, University Clinic Schleswig-Holstein (UKSH), University of Lübeck, Lübeck, Germany
| | - Florian Cremers
- Department of Radiation Oncology, University Clinic Schleswig-Holstein (UKSH), University of Lübeck, Lübeck, Germany
| | | | - Salvatore Grisanti
- Department of Ophthalmology, University Clinic Schleswig-Holstein (UKSH), University of Lübeck, Lübeck, Germany
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3
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Sato H, Ito T, Hayashi T, Kitano S, Erdjument-Bromage H, Bott MJ, Toyooka S, Zauderer M, Ladanyi M. The BAP1 nuclear deubiquitinase is involved in the nonhomologous end-joining pathway of double-strand DNA repair through interaction with DNA-PK. Oncogene 2024; 43:1087-1097. [PMID: 38383726 PMCID: PMC11449502 DOI: 10.1038/s41388-024-02966-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: 05/22/2021] [Revised: 01/16/2024] [Accepted: 02/02/2024] [Indexed: 02/23/2024]
Abstract
BRCA1-associated protein 1 (BAP1) has emerged as a major tumor suppressor gene in diverse cancer types, notably in malignant pleural mesothelioma (DPM), and has also been identified as a germline cancer predisposition gene for DPM and other select cancers. However, its role in the response to DNA damage has remained unclear. Here, we show that BAP1 inactivation is associated with increased DNA damage both in Met-5A human mesothelial cells and human DPM cell lines. Through proteomic analyses, we identified PRKDC as an interaction partner of BAP1 protein complexes in DPM cells and 293 T human embryonic kidney cells. PRKDC encodes the catalytic subunit of DNA protein kinase (DNA-PKcs) which functions in the nonhomologous end-joining (NHEJ) pathway of DNA repair. Double-stranded DNA damage resulted in prominent nuclear expression of BAP1 in DPM cells and phosphorylation of BAP1 at serine 395. A plasmid-based NHEJ assay confirmed a significant effect of BAP1 knockdown on cellular NHEJ activity. Combination treatment with X-ray irradiation and gemcitabine (as a radiosensitizer) strongly suppressed the growth of BAP1-deficient cells. Our results suggest reciprocal positive interactions between BAP1 and DNA-PKcs, based on phosphorylation of BAP1 by the latter and deubiquitination of DNA-PKcs by BAP1. Thus, functional interaction of BAP1 with DNA-PKcs supports a role for BAP1 in NHEJ DNA repair and may provide the basis for new therapeutic strategies and new insights into its role as a tumor suppressor.
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Affiliation(s)
- Hiroki Sato
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tatsuo Ito
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Hygiene, Kawasaki Medical University, Okayama, Japan
| | - Takuo Hayashi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shigehisa Kitano
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hediye Erdjument-Bromage
- Kimmel Center for Biology and Medicine at Skirball Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Matthew J Bott
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shinichi Toyooka
- Department of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Marjorie Zauderer
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Reggiani F, El Rashed Z, Petito M, Pfeffer M, Morabito A, Tanda ET, Spagnolo F, Croce M, Pfeffer U, Amaro A. Machine Learning Methods for Gene Selection in Uveal Melanoma. Int J Mol Sci 2024; 25:1796. [PMID: 38339073 PMCID: PMC10855534 DOI: 10.3390/ijms25031796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy with a limited five-year survival for metastatic patients. Limited therapeutic treatments are currently available for metastatic disease, even if the genomics of this tumor has been deeply studied using next-generation sequencing (NGS) and functional experiments. The profound knowledge of the molecular features that characterize this tumor has not led to the development of efficacious therapies, and the survival of metastatic patients has not changed for decades. Several bioinformatics methods have been applied to mine NGS tumor data in order to unveil tumor biology and detect possible molecular targets for new therapies. Each application can be single domain based while others are more focused on data integration from multiple genomics domains (as gene expression and methylation data). Examples of single domain approaches include differentially expressed gene (DEG) analysis on gene expression data with statistical methods such as SAM (significance analysis of microarray) or gene prioritization with complex algorithms such as deep learning. Data fusion or integration methods merge multiple domains of information to define new clusters of patients or to detect relevant genes, according to multiple NGS data. In this work, we compare different strategies to detect relevant genes for metastatic disease prediction in the TCGA uveal melanoma (UVM) dataset. Detected targets are validated with multi-gene score analysis on a larger UM microarray dataset.
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Affiliation(s)
- Francesco Reggiani
- Laboratory of Gene Expression Regulation, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy; (F.R.); (M.P.); (A.M.)
| | - Zeinab El Rashed
- Laboratory of Gene Expression Regulation, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy; (F.R.); (M.P.); (A.M.)
| | - Mariangela Petito
- Laboratory of Gene Expression Regulation, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy; (F.R.); (M.P.); (A.M.)
- Department of Experimental Medicine (DIMES), University of Genova, Via Leon Battista Alberti, 16132 Genova, Italy
| | - Max Pfeffer
- Institute of Numerical and Applied Mathematics, University of Göttingen, 37083 Göttingen, Germany;
| | - Anna Morabito
- Laboratory of Gene Expression Regulation, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy; (F.R.); (M.P.); (A.M.)
| | - Enrica Teresa Tanda
- Skin Cancer Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy; (E.T.T.); (F.S.)
- Department of Internal Medicine and Medical Specialties, University of Genova, Viale Benedetto XV, 16132 Genova, Italy
| | - Francesco Spagnolo
- Skin Cancer Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy; (E.T.T.); (F.S.)
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genova, 16132 Genova, Italy
| | - Michela Croce
- Biotherapies, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy;
| | - Ulrich Pfeffer
- Laboratory of Gene Expression Regulation, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy; (F.R.); (M.P.); (A.M.)
| | - Adriana Amaro
- Laboratory of Gene Expression Regulation, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy; (F.R.); (M.P.); (A.M.)
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In uveal melanoma Gα-protein GNA11 mutations convey a shorter disease-specific survival and are more strongly associated with loss of BAP1 and chromosomal alterations than Gα-protein GNAQ mutations. Eur J Cancer 2022; 170:27-41. [DOI: 10.1016/j.ejca.2022.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/08/2022] [Accepted: 04/04/2022] [Indexed: 12/21/2022]
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6
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Glinkina K, Groenewoud A, Teunisse AFAS, Snaar-Jagalska BE, Jochemsen AG. Novel Treatments of Uveal Melanoma Identified with a Synthetic Lethal CRISPR/Cas9 Screen. Cancers (Basel) 2022; 14:3186. [PMID: 35804957 PMCID: PMC9264875 DOI: 10.3390/cancers14133186] [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] [Received: 05/27/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 01/30/2023] Open
Abstract
Currently, no systemic treatment is approved as the standard of care for metastatic uveal melanoma (UM). mTOR has been evaluated as a drug target in UM. However, one of the main limitations is dose reduction due to adverse effects. The combination of everolimus with another targeted agent would allow the reduction of the dose of a single drug, thus widening the therapeutic window. In our study, we aimed to identify a synergistic combination with everolimus in order to develop a novel treatment option for metastatic UM. We exploited CRISPR-Cas9 synthetic lethality screening technology to search for an efficient combination. IGF1R and PRKDC and several other genes were identified as hits in the screen. We investigated the effect of the combination of everolimus with the inhibitors targeting IGF1R and DNA-PKcs on the survival of UM cell lines. These combinations synergistically slowed down cell growth but did not induce apoptosis in UM cell lines. These combinations were tested on PDX UM in an in vivo model, but we could not detect tumor regression. However, we could find significant activity of the dual DNA-PKcs/mTOR inhibitor CC-115 on PDX UM in the in vivo model.
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Affiliation(s)
- Kseniya Glinkina
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (K.G.); (A.F.A.S.T.)
| | - Arwin Groenewoud
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, 2300 RC Leiden, The Netherlands; (A.G.); (B.E.S.-J.)
| | - Amina F. A. S. Teunisse
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (K.G.); (A.F.A.S.T.)
| | - B. Ewa Snaar-Jagalska
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, 2300 RC Leiden, The Netherlands; (A.G.); (B.E.S.-J.)
| | - Aart G. Jochemsen
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (K.G.); (A.F.A.S.T.)
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7
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Ye J, Sheahon KM, LeBoit PE, McCalmont TH, Lang UE. BAP1-inactivated melanocytic tumors show prominent centrosome amplification and associated loss of primary cilia. J Cutan Pathol 2021; 48:1353-1360. [PMID: 34085298 DOI: 10.1111/cup.14073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/14/2021] [Accepted: 05/30/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND BRCA1-associated protein (BAP1) is a tumor suppressor whose loss is associated with various malignancies. The primary cilium is an organelle involved in signal transduction and cell cycle progression. Primary cilia have been shown to be absent in melanoma but retained to some extent in melanocytic nevi, and the severity of dysplasia influences the degree of cilia loss. Additionally, studies have revealed roles for BAP1 in centrosome and mitotic spindle formation. Because the primary cilium is nucleated on the mother centriole, we examined the connection between the presence of primary cilia and the formation of centrosomes in BAP1-inactivated melanocytic tumors (BIMTs). METHODS We evaluated the cilia and centrosomes in 11 BIMTs and five conventional melanocytic nevi using immunofluorescence staining of acetylated alpha-tubulin and gamma-tubulin. RESULTS We found that, compared to nevi, BIMTs show loss of primary cilia and amplification of centrosomes. Occasional nevi also showed increased centrioles; however, these foci of amplification were more likely to be ciliated than those in BIMTs. CONCLUSIONS Although centrosome amplification does not absolutely correlate with loss of primary cilia in melanocytic neoplasms, absence of BAP1 exacerbates the phenotype. Moreover, aberrant centrosome and cilia formation are likely critical in the pathogenesis of other BAP1-inactivated tumors.
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Affiliation(s)
- Julia Ye
- Department of Anatomic Pathology, University of California, San Francisco, California, USA
| | - Kathleen M Sheahon
- Department of Anatomic Pathology, University of California, San Francisco, California, USA
| | - Philip E LeBoit
- Department of Anatomic Pathology, University of California, San Francisco, California, USA.,Department of Dermatology, University of California, San Francisco, California, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, California, USA
| | - Timothy H McCalmont
- Department of Anatomic Pathology, University of California, San Francisco, California, USA.,Department of Dermatology, University of California, San Francisco, California, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, California, USA
| | - Ursula E Lang
- Department of Anatomic Pathology, University of California, San Francisco, California, USA.,Department of Dermatology, University of California, San Francisco, California, USA
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8
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Roelofsen CDM, Wierenga APA, van Duinen S, Verdijk RM, Bleeker J, Marinkovic M, Luyten GPM, Jager MJ. Five Decades of Enucleations for Uveal Melanoma in One Center: More Tumors with High Risk Factors, No Improvement in Survival over Time. Ocul Oncol Pathol 2020; 7:133-141. [PMID: 33981696 DOI: 10.1159/000509918] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/05/2020] [Indexed: 12/18/2022] Open
Abstract
Background In order to improve medical care for uveal melanoma (UM) patients, we need to monitor disease and survival to guide our research efforts. We analyzed the data of UM patients who underwent an enucleation at the Leiden University Medical Center over the last five decades and investigated trends in patient and tumor characteristics and survival. Methods Data were collected from charts and pathology reports from all patients who underwent an enucleation for UM between 1973 and 2019 (n = 1,212), of which 1,066 were primary enucleations; data were analyzed according to five time periods: 1973-1979 (n = 209), 1980-1989 (n = 148), 1990-1999 (n = 174), 2000-2009 (n = 280), and 2010-2019 (n = 401). Results Over time, mean patient age at the time of enucleation for UM increased from 54.9 to 64.7 years (p < 0.001), more tumors showed histopathological involvement of the ciliary body (p < 0.001), and were classified in a high TNM/AJCC class (p < 0.001). Overall, the 5- and 10-year UM-related survival rates were 0.68 and 0.59, respectively. Over time, survival showed no change in patients with tumors in AJCC stages I or III, with recently a slightly worse survival in stage II UM (p = 0.02). Conclusion Between 1973 and 2019, we found similar rates of UM-related survival following enucleation, although we noticed a strong increase in more unfavorable patient and tumor characteristics over time, such as an older age and larger tumor size. The lack of improvement indicates that more research should take place to develop adjuvant treatments to prevent metastases and efficient treatments once metastases develop.
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Affiliation(s)
- Christine D M Roelofsen
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Emergency Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Annemijn P A Wierenga
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sjoerd van Duinen
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Robert M Verdijk
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Pathology, Section Ophthalmic Pathology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Jaco Bleeker
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marina Marinkovic
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Gregorius P M Luyten
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Martine J Jager
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
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9
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DNA-PK in human malignant disorders: Mechanisms and implications for pharmacological interventions. Pharmacol Ther 2020; 215:107617. [PMID: 32610116 DOI: 10.1016/j.pharmthera.2020.107617] [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] [Received: 03/31/2020] [Accepted: 06/15/2020] [Indexed: 12/12/2022]
Abstract
The DNA-PK holoenzyme is a fundamental element of the DNA damage response machinery (DDR), which is responsible for cellular genomic stability. Consequently, and predictably, over the last decades since its identification and characterization, numerous pre-clinical and clinical studies reported observations correlating aberrant DNA-PK status and activity with cancer onset, progression and responses to therapeutic modalities. Notably, various studies have established in recent years the role of DNA-PK outside the DDR network, corroborating its role as a pleiotropic complex involved in transcriptional programs that operate biologic processes as epithelial to mesenchymal transition (EMT), hypoxia, metabolism, nuclear receptors signaling and inflammatory responses. In particular tumor entities as prostate cancer, immense research efforts assisted mapping and describing the overall signaling networks regulated by DNA-PK that control metastasis and tumor progression. Correspondingly, DNA-PK emerges as an obvious therapeutic target in cancer and data pertaining to various pharmacological approaches have been published, largely in context of combination with DNA-damaging agents (DDAs) that act by inflicting DNA double strand breaks (DSBs). Currently, new generation inhibitors are tested in clinical trials. Several excellent reviews have been published in recent years covering the biology of DNA-PK and its role in cancer. In the current article we are aiming to systematically describe the main findings on DNA-PK signaling in major cancer types, focusing on both preclinical and clinical reports and present a detailed current status of the DNA-PK inhibitors repertoire.
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10
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Hussain RN, Coupland SE, Khzouz J, Kalirai H, Parsons JL. Inhibition of ATM Increases the Radiosensitivity of Uveal Melanoma Cells to Photons and Protons. Cancers (Basel) 2020; 12:cancers12061388. [PMID: 32481544 PMCID: PMC7352388 DOI: 10.3390/cancers12061388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/20/2020] [Accepted: 05/25/2020] [Indexed: 02/06/2023] Open
Abstract
Treatment of uveal melanoma (UM) is generally successful, with local primary tumour control being at 90%-95%. Localized radiotherapy in the form of plaque brachytherapy or proton beam radiotherapy is the most common treatment modality in the UK. However, the basic mechanisms of radiation response, DNA repair and tissue reactions in UM have not been well documented previously. We have investigated the comparative radiosensitivity of four UM cell lines in response to exogenous radiation sources (both X-rays and protons), and correlated this with DNA repair protein expression and repair efficiency. We observed a broad range of radiosensitivity of different UM cell lines to X-rays and protons, with increased radioresistance correlating with elevated protein expression of ataxia telangiectasia mutated (ATM), a protein kinase involved in the signaling and repair of DNA double strand breaks. The use of an ATM inhibitor in UM cell lines enhanced radiosensitivity following both X-ray and proton irradiation, particularly in cells that contained high levels of ATM protein which are otherwise comparatively radioresistant. In proton-irradiated compared with non-irradiated primary enucleated UM patient samples, there was no significant difference in ATM protein expression. Our study therefore suggests that ATM is a potential target for increasing the radiosensitivity of more resistant UM subgroups.
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Affiliation(s)
- Rumana N. Hussain
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, William Henry Duncan Building, University of Liverpool, Liverpool L7 8TX, UK; (R.N.H.); (S.E.C.); (J.K.); (H.K.)
- St Paul’s Eye Clinic, Liverpool University Hospitals Foundation Trust, Prescot Street, Liverpool L7 8XP, UK
| | - Sarah E. Coupland
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, William Henry Duncan Building, University of Liverpool, Liverpool L7 8TX, UK; (R.N.H.); (S.E.C.); (J.K.); (H.K.)
- Liverpool Clinical Laboratories, Duncan Building, Liverpool University Hospitals NHS Foundation Trust, Liverpool L69 3GA, UK
| | - Jakub Khzouz
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, William Henry Duncan Building, University of Liverpool, Liverpool L7 8TX, UK; (R.N.H.); (S.E.C.); (J.K.); (H.K.)
| | - Helen Kalirai
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, William Henry Duncan Building, University of Liverpool, Liverpool L7 8TX, UK; (R.N.H.); (S.E.C.); (J.K.); (H.K.)
| | - Jason L. Parsons
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 200 London Road, Liverpool L3 9TA, UK
- Clatterbridge Cancer Centre NHS Foundation Trust, Clatterbridge Road, Bebington CH63 4JY, UK
- Correspondence: ; Tel.: +44-151-794-8848
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11
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Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. UMs are usually initiated by a mutation in GNAQ or GNA11, unlike cutaneous melanomas, which usually harbour a BRAF or NRAS mutation. The annual incidence in Europe and the USA is ~6 per million population per year. Risk factors include fair skin, light-coloured eyes, congenital ocular melanocytosis, ocular melanocytoma and the BAP1-tumour predisposition syndrome. Ocular treatment aims at preserving the eye and useful vision and, if possible, preventing metastases. Enucleation has largely been superseded by various forms of radiotherapy, phototherapy and local tumour resection, often administered in combination. Ocular outcomes are best with small tumours not extending close to the optic disc and/or fovea. Almost 50% of patients develop metastatic disease, which usually involves the liver, and is usually fatal within 1 year. Although UM metastases are less responsive than cutaneous melanoma to chemotherapy or immune checkpoint inhibitors, encouraging results have been reported with partial hepatectomy for solitary metastases, with percutaneous hepatic perfusion with melphalan or with tebentafusp. Better insight into tumour immunology and metabolism may lead to new treatments.
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Increased Non-Homologous End Joining Makes DNA-PK a Promising Target for Therapeutic Intervention in Uveal Melanoma. Cancers (Basel) 2019; 11:cancers11091278. [PMID: 31480356 PMCID: PMC6769470 DOI: 10.3390/cancers11091278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 02/07/2023] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular tumour in adults, with a mean survival of six months following metastasis. The survival rates have not improved in over 30 years. This study has shown that sister chromatid exchange (SCE) is low in UM which is likely due to a reduced expression of FANCD2. As FANCD2 can function to suppress non-homologous end joining (NHEJ), this study therefore investigated NHEJ in UM. The activation of the catalytic subunit of the NHEJ pathway protein DNA-dependent protein kinase (DNA-PK) was measured by analysing the foci formation and the ligation efficiency by NHEJ determined using a plasmid-based end-joining assay. Using small-interfering RNA (siRNA) knock-down, and chemical inhibitors of DNA-PK, the survival of primary UM cultures and two cell lines were determined. To assess the homologous recombination capacity in response to the inhibition of DNA-PK, a SCE analysis was performed. In addition, to support the findings, the messenger RNA (mRNA) expression of genes associated with NHEJ was analysed using the Cancer Genome Atlas (TCGA)-UM RNAseq data (n = 79). The NHEJ activity and DNA-PKcs activation was upregulated in UM and the inhibition of DNA-PK selectively induced apoptosis and sensitized to ionising radiation and inter-strand cross-linking agents. The inhibition of the NHEJ protein DNA-PK is lethal to UM, indicating a potentially effective therapeutic option, either alone or as a sensitizer for other treatments.
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