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van Poppelen NM, Cassoux N, Turunen JA, Naus NC, Verdijk RM, Vaarwater J, Cohen V, Papastefanou VP, Kiratli H, Saakyan SV, Tsygankov AY, Rospond-Kubiak I, Mudhar HS, Salvi SM, Kiilgaard JF, Heegaard S, Moulin AP, Saornil MA, Garciá-Alvarez C, Fili M, Eide NA, Meyer P, Kivelä TT, de Klein A, Kilic E, Al-Jamal RT. The Pediatric and Young Adult Choroidal and Ciliary Body Melanoma Genetic Study, A Survey by the European Ophthalmic Oncology Group. Invest Ophthalmol Vis Sci 2024; 65:12. [PMID: 38573618 PMCID: PMC10996971 DOI: 10.1167/iovs.65.4.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/28/2023] [Indexed: 04/05/2024] Open
Abstract
Purpose To explore the genetic background of choroidal and ciliary body melanoma among children and young adults, with special focus on BAP1 germline variants in this age group. Methods Patients under the age of 25 and with confirmed choroidal or ciliary body melanoma were included in this retrospective, multicenter observational study. Nuclear BAP1 immunopositivity was used to evaluate the presence of functional BAP1 in the tumor. Next-generation sequencing using Ion Torrent platform was used to determine pathogenic variants of BAP1, EIF1AX, SF3B1, GNAQ and GNA11 and chromosome 3 status in the tumor or in DNA extracted from blood or saliva. Survival was analyzed using Kaplan-Meier estimates. Results The mean age at diagnosis was 17 years (range 5.0-24.8). A germline BAP1 pathogenic variant was identified in an 18-year-old patient, and a somatic variant, based mainly on immunohistochemistry, in 13 (42%) of 31 available specimens. One tumor had a somatic SF3B1 pathogenic variant. Disomy 3 and the absence of a BAP1 pathogenic variant in the tumor predicted the longest metastasis-free survival. Males showed longer metastasis-free survival than females (P = 0.018). Conclusions We did not find a stronger-than-average BAP1 germline predisposition for choroidal and ciliary body melanoma among children and young adults compared to adults. Males had a more favorable survival and disomy 3, and the absence of a BAP1 mutation in the tumor tissue predicted the most favorable metastasis-free survival. A BAP1 germline pathogenic variant was identified in one patient (1%), and a somatic variant based mainly on immunohistochemistry in 13 (42%).
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Affiliation(s)
- Natasha M. van Poppelen
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Nathalie Cassoux
- Department of Ophthalmology, Curie Institute, Université Paris Cité UFR Médecine, Paris, France
| | - Joni A. Turunen
- Ocular Oncology Service, Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Eye Genetics Group, Folkhälsan Research Center, Helsinki, Finland
| | - Nicole C. Naus
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robert M. Verdijk
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Pathology, Leiden Universital Medical Center, Leiden, The Netherlands
| | - Jolanda Vaarwater
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Victoria Cohen
- Ocular Oncology Service, Moorfields Eye Hospital, London, United Kingdom
| | | | - Hayyam Kiratli
- Department of Ophthalmology, Hacettepe University School of Medicine, Ankara, Turkey
| | - Svetlana V. Saakyan
- Department of Ophthalmology, Moscow Helmholtz Research Institute of Eye Diseases, Moscow, Russia
| | - Alexander Y. Tsygankov
- Department of Ophthalmology, Moscow Helmholtz Research Institute of Eye Diseases, Moscow, Russia
| | - Iwona Rospond-Kubiak
- Department of Ophthalmology, Poznan University of Medical Sciences, Poznán, Poland
| | - Hardeep S. Mudhar
- National Specialist Ophthalmic Pathology Service (NSOPS), Department of Histopathology, Royal Hallamshire Hospital, Sheffield, United Kingdom
| | - Sachin M. Salvi
- Sheffield Ocular Oncology Service, Department of Ophthalmology, Royal Hallamshire Hospital, Sheffield, United Kingdom
| | - Jens F. Kiilgaard
- Department of Ophthalmology, University of Copenhagen, Copenhagen, Denmark
| | - Steffen Heegaard
- Department of Ophthalmology, University of Copenhagen, Copenhagen, Denmark
- Department of Pathology, University of Copenhagen, Copenhagen, Denmark
| | - Alexandre P. Moulin
- Department of Ophthalmology, Jules-Gonin Eye Hospital, Lausanne University, Lausanne, Switzerland
| | - Maria A. Saornil
- Department of Ophthalmology, Hospital Clinico Universitario de Valladolid, Valladolid, Spain
| | - Ciro Garciá-Alvarez
- Department of Ophthalmology, Hospital Clinico Universitario de Valladolid, Valladolid, Spain
| | - Maria Fili
- Department of Ophthalmology, St. Erik Eye Hospital, Stockholm, Sweden
| | - Nils A. Eide
- Department of Ophthalmology, Oslo University Hospital, Oslo, Norway
| | - Peter Meyer
- Department of Ophthalmology, Basel University Hospital, Basel, Switzerland
| | - Tero T. Kivelä
- Ocular Oncology Service, Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Emine Kilic
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Rana'a T. Al-Jamal
- Ocular Oncology Service, Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Ocular Oncology Service, Moorfields Eye Hospital, London, United Kingdom
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de Bruyn DP, van Poppelen NM, Brands T, van den Boom SC, Eikenboom E, Wagner A, van Veghel-Plandsoen MM, Geeven G, Beverloo B, van Rij CM, Verdijk RM, Naus NC, Bagger MM, Kiilgaard JF, de Klein A, Brosens E, Kiliç E. Evaluation of Circulating Tumor DNA as a Liquid Biomarker in Uveal Melanoma. Invest Ophthalmol Vis Sci 2024; 65:11. [PMID: 38319670 PMCID: PMC10854420 DOI: 10.1167/iovs.65.2.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/14/2023] [Indexed: 02/07/2024] Open
Abstract
Purpose Uveal melanoma (UM) has a high propensity to metastasize. Prognosis is associated with specific driver mutations and copy number variations (CNVs), but limited primary tumor tissue is available for molecular characterization due to eye-sparing irradiation treatment. This study aimed to assess the rise in circulating tumor DNA (ctDNA) levels in UM and evaluate its efficacy for CNV-profiling of patients with UM. Methods In a pilot study, we assessed ctDNA levels in the blood of patients with UM (n = 18) at various time points, including the time of diagnosis (n = 13), during fractionated stereotactic radiotherapy (fSRT) treatment (n = 6), and upon detection of metastatic disease (n = 13). Shallow whole-genome sequencing (sWGS) combined with in silico size-selection was used to identify prognostically relevant CNVs in patients with UM (n = 26) from peripheral blood retrieved at the time of diagnosis (n = 9), during fSRT (n = 5), during post-treatment follow-up (n = 4), metastasis detection (n = 6), and metastasis follow-up (n = 4). Results A total of 34 patients had blood analyzed for ctDNA detection (n = 18) and/or CNV analysis (n = 26) at various time points. At the time of diagnosis, 5 of 13 patients (38%) had detectable ctDNA (median = 0 copies/mL). Upon detection of metastatic disease, ctDNA was detected in 10 of 13 patients (77%) and showed increased ctDNA levels (median = 24 copies/mL, P < 0.01). Among the six patients analyzed during fSRT, three (50%) patients had detectable ctDNA at baseline and three of six (50%) patients had undetectable levels of ctDNA. During the fSRT regimen, ctDNA levels remained unchanged (P > 0.05). The ctDNA fractions were undetectable to low in localized disease, and sWGS did not elucidate chromosome 3 status from blood samples. However, in 7 of 10 (70%) patients with metastases, the detection of chromosome 3 loss corresponded to the high metastatic-risk class. Conclusions The rise in ctDNA levels observed in patients with UM harboring metastases suggests its potential utility for CNV profiling. These findings highlight the potential of using ctDNA for metastasis detection and patient inclusion in therapeutic studies targeting metastatic UM.
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Affiliation(s)
- Daniel P. de Bruyn
- Department of Ophthalmology, Erasmus MC, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Natasha M. van Poppelen
- Department of Ophthalmology, Erasmus MC, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Tom Brands
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Ellis Eikenboom
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Geert Geeven
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Berna Beverloo
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Caroline M. van Rij
- Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus MC, Rotterdam, The Netherlands
| | - Robert M. Verdijk
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC, Rotterdam, The Netherlands
- Department of Pathology, LUMC, Leiden, The Netherlands
| | - Nicole C. Naus
- Department of Ophthalmology, Erasmus MC, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Mette M. Bagger
- Department of Ophthalmology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Jens F. Kiilgaard
- Department of Ophthalmology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus MC, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
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de Bruyn DP, Beasley AB, Verdijk RM, van Poppelen NM, Paridaens D, de Keizer ROB, Naus NC, Gray ES, de Klein A, Brosens E, Kiliç E. Is Tissue Still the Issue? The Promise of Liquid Biopsy in Uveal Melanoma. Biomedicines 2022; 10:biomedicines10020506. [PMID: 35203714 PMCID: PMC8962331 DOI: 10.3390/biomedicines10020506] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/18/2022] Open
Abstract
Uveal melanoma (UM) is the second most frequent type of melanoma. Therapeutic options for UM favor minimally invasive techniques such as irradiation for vision preservation. As a consequence, no tumor material is obtained. Without available tissue, molecular analyses for gene expression, mutation or copy number analysis cannot be performed. Thus, proper patient stratification is impossible and patients’ uncertainty about their prognosis rises. Minimally invasive techniques have been studied for prognostication in UM. Blood-based biomarker analysis has become more common in recent years; however, no clinically standardized protocol exists. This review summarizes insights in biomarker analysis, addressing new insights in circulating tumor cells, circulating tumor DNA, extracellular vesicles, proteomics, and metabolomics. Additionally, medical imaging can play a significant role in staging, surveillance, and prognostication of UM and is addressed in this review. We propose that combining multiple minimally invasive modalities using tumor biomarkers should be the way forward and warrant more attention in the coming years.
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Affiliation(s)
- Daniël P. de Bruyn
- Department of Ophthalmology, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (D.P.d.B.); (N.M.v.P.); (D.P.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (E.B.)
- Erasmus MC Cancer Institute, 3000 CA Rotterdam, The Netherlands
| | - Aaron B. Beasley
- Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA 6027, Australia; (A.B.B.); (E.S.G.)
| | - Robert M. Verdijk
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands; (R.M.V.); (R.O.B.d.K.)
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Natasha M. van Poppelen
- Department of Ophthalmology, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (D.P.d.B.); (N.M.v.P.); (D.P.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (E.B.)
- Erasmus MC Cancer Institute, 3000 CA Rotterdam, The Netherlands
| | - Dion Paridaens
- Department of Ophthalmology, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (D.P.d.B.); (N.M.v.P.); (D.P.); (N.C.N.)
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands; (R.M.V.); (R.O.B.d.K.)
| | | | - Nicole C. Naus
- Department of Ophthalmology, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (D.P.d.B.); (N.M.v.P.); (D.P.); (N.C.N.)
- Erasmus MC Cancer Institute, 3000 CA Rotterdam, The Netherlands
| | - Elin S. Gray
- Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA 6027, Australia; (A.B.B.); (E.S.G.)
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (E.B.)
- Erasmus MC Cancer Institute, 3000 CA Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (E.B.)
- Erasmus MC Cancer Institute, 3000 CA Rotterdam, The Netherlands
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands; (D.P.d.B.); (N.M.v.P.); (D.P.); (N.C.N.)
- Erasmus MC Cancer Institute, 3000 CA Rotterdam, The Netherlands
- Correspondence: ; Tel.: +31-107030683
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4
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Drabarek W, van Riet J, Nguyen JQN, Smit KN, van Poppelen NM, Jansen R, Medico-Salsench E, Vaarwater J, Magielsen FJ, Brands T, Eussen B, van den Bosch TPP, Verdijk RM, Naus NC, Paridaens D, de Klein A, Brosens E, van de Werken HJG, Kilic E. Identification of Early-Onset Metastasis in SF3B1 Mutated Uveal Melanoma. Cancers (Basel) 2022; 14:cancers14030846. [PMID: 35159112 PMCID: PMC8834136 DOI: 10.3390/cancers14030846] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/31/2022] Open
Abstract
Simple Summary This study describes clinical and genetic characteristics of the largest aggregated cohort of Splicing Factor 3 Subunit B1 (SF3B1)-mutated Uveal Melanoma (UM) in the literature (n = 146). Missense mutations in the spliceosome gene SF3B1 result in an altered splice site recognition and aberrant mRNA transcripts. The SF3B1-mutated UM show early- and late-onset of metastatic disease for which, currently, no distinguishing biomarkers exist. Using a cutoff of 60 months for stratification, we found that a largest basal tumor diameter was more prevalent in the early-onset metastatic disease group. Furthermore, using differential gene expression and the detection of aberrant transcripts, we found that the expression of alpha/beta-Hydrolase domain containing 6 (ABHD6) is associated with early-onset metastatic SF3B1 and aberrant transcripts that are associated with early-onset SF3B1-mutated UM. Our results provide more accurate prognostication and targets for future functional studies in an effort to elucidate pathogenesis of SF3B1-mutated UM. Abstract Approximately 25% of all uveal melanoma (UM) contain driver mutations in the gene encoding the spliceosome factor SF3B1, and whilst patients with such SF3B1 mutations generally have an intermediate risk on developing metastatic disease, a third of these patients develop early metastasis within 5 years after diagnosis. We therefore investigated whether clinical and/or genetic variables could be indicative of short progression-free survival (PFS < 60 months) or long PFS (PFS ≥ 60 months) for SF3B1-mutated (SF3B1mut) UM patients. We collected 146 SF3B1mut UM from our Rotterdam Ocular Melanoma Studygroup (ROMS) database and external published datasets. After stratification of all SF3B1mut UM using short PFS vs. long PFS, only largest tumor diameter (LTD) was significantly larger (mean: 17.7 mm (±2.8 SD) in the short PFS SF3B1mut group vs. the long PFS group (mean: 14.7 (±3.7 SD, p = 0.001). Combined ROMS and The Cancer Genome Atlas (TCGA) transcriptomic data were evaluated, and we identified SF3B1mut-specific canonical transcripts (e.g., a low expression of ABHD6 indicative for early-onset metastatic disease) or distinct expression of SF3B1mut UM aberrant transcripts, indicative of early- or late-onset or no metastatic SF3B1mut UM.
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Affiliation(s)
- Wojtek Drabarek
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Job van Riet
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands;
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, 3000 CA, Rotterdam, The Netherlands;
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Josephine Q. N. Nguyen
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Kyra N. Smit
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Natasha M. van Poppelen
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Rick Jansen
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, 3000 CA, Rotterdam, The Netherlands;
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Eva Medico-Salsench
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Jolanda Vaarwater
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
| | - Frank J. Magielsen
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Tom Brands
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Bert Eussen
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Thierry. P. P. van den Bosch
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (T.P.P.v.d.B.); (R.M.V.)
| | - Robert M. Verdijk
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (T.P.P.v.d.B.); (R.M.V.)
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands
| | - Nicole C. Naus
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
| | - Dion Paridaens
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.M.-S.); (F.J.M.); (B.E.); (A.d.K.); (E.B.)
| | - Harmen J. G. van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, 3000 CA, Rotterdam, The Netherlands;
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands
- Department of Immunology, Erasmus MC Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands
- Correspondence: (H.J.G.v.d.W.); (E.K.); Tel.: +31-107044467 (H.J.G.v.d.W.); +31-107044272 (E.K.)
| | - Emine Kilic
- Department of Ophthalmology, Erasmus MC Cancer Institute, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (W.D.); (J.Q.N.N.); (K.N.S.); (N.M.v.P.); (J.V.); (T.B.); (N.C.N.); (D.P.)
- Correspondence: (H.J.G.v.d.W.); (E.K.); Tel.: +31-107044467 (H.J.G.v.d.W.); +31-107044272 (E.K.)
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5
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van Poppelen NM, van Ipenburg JA, van den Bosch Q, Vaarwater J, Brands T, Eussen B, Magielsen F, Dubbink HJ, Paridaens D, Brosens E, Naus N, de Klein A, Kiliç E, Verdijk RM. Molecular Genetics of Conjunctival Melanoma and Prognostic Value of TERT Promoter Mutation Analysis. Int J Mol Sci 2021; 22:ijms22115784. [PMID: 34071371 PMCID: PMC8198138 DOI: 10.3390/ijms22115784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 12/16/2022] Open
Abstract
The aim of this study was exploration of the genetic background of conjunctival melanoma (CM) and correlation with recurrent and metastatic disease. Twenty-eight CM from the Rotterdam Ocular Melanoma Study group were collected and DNA was isolated from the formalin-fixed paraffin embedded tissue. Targeted next-generation sequencing was performed using a panel covering GNAQ, GNA11, EIF1AX, BAP1, BRAF, NRAS, c-KIT, PTEN, SF3B1, and TERT genes. Recurrences and metastasis were present in eight (29%) and nine (32%) CM cases, respectively. TERT promoter mutations were most common (54%), but BRAF (46%), NRAS (21%), BAP1 (18%), PTEN (14%), c-KIT (7%), and SF3B1 (4%) mutations were also observed. No mutations in GNAQ, GNA11, and EIF1AX were found. None of the mutations was significantly associated with recurrent disease. Presence of a TERT promoter mutation was associated with metastatic disease (p-value = 0.008). Based on our molecular findings, CM comprises a separate entity within melanoma, although there are overlapping molecular features with uveal melanoma, such as the presence of BAP1 and SF3B1 mutations. This warrants careful interpretation of molecular data, in the light of clinical findings. About three quarter of CM contain drug-targetable mutations, and TERT promoter mutations are correlated to metastatic disease in CM.
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Affiliation(s)
- Natasha M. van Poppelen
- Department of Ophthalmology, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (J.V.); (T.B.); (B.E.); (D.P.); (N.N.); (E.K.)
- Department of Clinical Genetics, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (F.M.); (E.B.); (A.d.K.)
| | - Jolique A. van Ipenburg
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (J.A.v.I.); (Q.v.d.B.); (H.J.D.)
- Department of Pathology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Quincy van den Bosch
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (J.A.v.I.); (Q.v.d.B.); (H.J.D.)
| | - Jolanda Vaarwater
- Department of Ophthalmology, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (J.V.); (T.B.); (B.E.); (D.P.); (N.N.); (E.K.)
- Department of Clinical Genetics, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (F.M.); (E.B.); (A.d.K.)
| | - Tom Brands
- Department of Ophthalmology, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (J.V.); (T.B.); (B.E.); (D.P.); (N.N.); (E.K.)
- Department of Clinical Genetics, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (F.M.); (E.B.); (A.d.K.)
| | - Bert Eussen
- Department of Ophthalmology, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (J.V.); (T.B.); (B.E.); (D.P.); (N.N.); (E.K.)
- Department of Clinical Genetics, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (F.M.); (E.B.); (A.d.K.)
| | - Frank Magielsen
- Department of Clinical Genetics, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (F.M.); (E.B.); (A.d.K.)
| | - Hendrikus J. Dubbink
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (J.A.v.I.); (Q.v.d.B.); (H.J.D.)
| | - Dion Paridaens
- Department of Ophthalmology, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (J.V.); (T.B.); (B.E.); (D.P.); (N.N.); (E.K.)
- Department of Ocular Oncology, The Rotterdam Eye Hospital, Schiedamse Vest 180, 3011 BH Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (F.M.); (E.B.); (A.d.K.)
| | - Nicole Naus
- Department of Ophthalmology, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (J.V.); (T.B.); (B.E.); (D.P.); (N.N.); (E.K.)
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (F.M.); (E.B.); (A.d.K.)
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (J.V.); (T.B.); (B.E.); (D.P.); (N.N.); (E.K.)
| | - Robert M. Verdijk
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (J.A.v.I.); (Q.v.d.B.); (H.J.D.)
- Department of Ocular Oncology, The Rotterdam Eye Hospital, Schiedamse Vest 180, 3011 BH Rotterdam, The Netherlands
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
- Correspondence:
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6
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van Poppelen NM, de Bruyn DP, Bicer T, Verdijk R, Naus N, Mensink H, Paridaens D, de Klein A, Brosens E, Kiliҫ E. Genetics of Ocular Melanoma: Insights into Genetics, Inheritance and Testing. Int J Mol Sci 2020; 22:E336. [PMID: 33396957 PMCID: PMC7795687 DOI: 10.3390/ijms22010336] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/04/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022] Open
Abstract
Ocular melanoma consists of posterior uveal melanoma, iris melanoma and conjunctival melanoma. These malignancies derive from melanocytes in the uveal tract or conjunctiva. The genetic profiles of these different entities differ from each other. In uveal melanoma, GNAQ and GNA11 gene mutations are frequently found and prognosis is based on mutation status of BAP1, SF3B1 and EIF1AX genes. Iris melanoma, also originating from the uvea, has similarities to the genetic makeups of both posterior uveal melanoma (UM) and conjunctival melanoma since mutations in GNAQ and GNA11 are less common and genes involved in conjunctival melanoma such as BRAF have been described. The genetic spectrum of conjunctival melanoma, however, includes frequent mutations in the BRAF, NRAS and TERT promoter genes, which are found in cutaneous melanoma as well. The BRAF status of the tumor is not correlated to prognosis, whereas the TERT promoter gene mutations are. Clinical presentation, histopathological characteristics and copy number alterations are associated with survival in ocular melanoma. Tissue material is needed to classify ocular melanoma in the different subgroups, which creates a need for the use of noninvasive techniques to prognosticate patients who underwent eye preserving treatment.
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Affiliation(s)
- Natasha M. van Poppelen
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (A.d.K.); (E.B.)
| | - Daniël P. de Bruyn
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (A.d.K.); (E.B.)
| | - Tolga Bicer
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
- Department of Ophthalmology, University of Health Sciences Diskapi Training and Research Hospital, Ankara 06330, Turkey
| | - Rob Verdijk
- Department of Pathology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands;
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Nicole Naus
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
| | - Hanneke Mensink
- Department of Ophthalmic Oncology, The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands;
| | - Dion Paridaens
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
- Department of Ophthalmic Oncology, The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands;
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (A.d.K.); (E.B.)
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (A.d.K.); (E.B.)
| | - Emine Kiliҫ
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands; (N.M.v.P.); (D.P.d.B.); (T.B.); (N.N.); (D.P.)
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7
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Szalai E, Jiang Y, van Poppelen NM, Jager MJ, de Klein A, Kilic E, Grossniklaus HE. Association of Uveal Melanoma Metastatic Rate With Stochastic Mutation Rate and Type of Mutation. JAMA Ophthalmol 2019; 136:1115-1120. [PMID: 30073324 DOI: 10.1001/jamaophthalmol.2018.2986] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Importance It is necessary to understand the mechanisms of metastasis of uveal melanoma to advise patients and develop treatments for this tumor. Objective To examine the stochastic properties of primary uveal melanoma including the mutation rate as a function of tumor size and metastatic rate relative to the type of mutation. Design, Setting, and Participants We computed the mutation rate in different sized uveal melanomas using previously published large data sets. Tumor volume was estimated using the spherical cap method. We also calculated the metastatic rate using an updated data set of patients with uveal melanoma with known mutations in BAP1, SF3B1, and EIF1AX provided by the Rotterdam Ocular Melanoma Study Group. Data were analyzed from 2 studies, one taking place from August 25, 1970, to August 27, 2008, and the other taking place between 1993 and 2013. Data were analyzed between 2016 and 2017. Main Outcomes and Measures Mutation rates and metastic rates. Results Based on the 5-year metastatic rates, mutation rates ranged from 1.09 × 10-8 to 7.86 × 10-7 per cell division, using our calculation algorithm. A higher mutation rate was found for tumors with smaller thicknesses. EIF1AX mutations were not exclusive of other mutations because 2 cases with EIF1AX mutations and metastasis also had BAP1 mutations. None of the tumors with only an EIF1AX mutation metastasized. After plotting the yearly metastatic rate vs time after treatment, we observed a small peak at 1 year and a large peak at 3.5 years after treatment for BAP1 mutations, with peaks between 2 and 3 years and at 7 years for SF3B1 mutations. Conclusions and Relevance We observed a higher mutation rate for smaller tumors, which may be explained by a greater number of cell divisions occurring during the expansion phase of smaller uveal melanomas. Regarding time to clinically detected metastases, the first 2 peaks appear to be associated with BAP1-mutated tumors and the late peak to SF3B1-mutated tumors.
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Affiliation(s)
- Eszter Szalai
- Department of Ophthalmology, Emory University School of Medicine, Atlanta, Georgia.,Department of Ophthalmology, University of Debrecen, Debrecen, Hungary
| | - Yi Jiang
- Department of Mathematics and Statistics, Georgia State University, Atlanta
| | - Natasha M van Poppelen
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Martine J Jager
- Department of Ophthalmology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Emine Kilic
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Hans E Grossniklaus
- Department of Ophthalmology, Emory University School of Medicine, Atlanta, Georgia.,Department of Pathology, Emory University School of Medicine, Atlanta, Georgia
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8
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Drabarek W, Yavuzyigitoglu S, Obulkasim A, van Riet J, Smit KN, van Poppelen NM, Vaarwater J, Brands T, Eussen B, Verdijk RM, Naus NC, Mensink HW, Paridaens D, Boersma E, van de Werken HJG, Kilic E, de Klein A. Multi-Modality Analysis Improves Survival Prediction in Enucleated Uveal Melanoma Patients. ACTA ACUST UNITED AC 2019; 60:3595-3605. [DOI: 10.1167/iovs.18-24818] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Wojtek Drabarek
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Serdar Yavuzyigitoglu
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Askar Obulkasim
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Pediatric Oncology/Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Job van Riet
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kyra N. Smit
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Natasha M. van Poppelen
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jolanda Vaarwater
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tom Brands
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bert Eussen
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert M. Verdijk
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- The Rotterdam Eye Hospital, Rotterdam, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Nicole C. Naus
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Dion Paridaens
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
- The Rotterdam Eye Hospital, Rotterdam, The Netherlands
| | - Eric Boersma
- Department of Cardiology, Thoraxcenter, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Harmen J. G. van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Emine Kilic
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
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9
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Chau C, van Doorn R, van Poppelen NM, van der Stoep N, Mensenkamp AR, Sijmons RH, van Paassen BW, van den Ouweland AMW, Naus NC, van der Hout AH, Potjer TP, Bleeker FE, Wevers MR, van Hest LP, Jongmans MCJ, Marinkovic M, Bleeker JC, Jager MJ, Luyten GPM, Nielsen M. Families with BAP1-Tumor Predisposition Syndrome in The Netherlands: Path to Identification and a Proposal for Genetic Screening Guidelines. Cancers (Basel) 2019; 11:cancers11081114. [PMID: 31382694 PMCID: PMC6721807 DOI: 10.3390/cancers11081114] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/26/2019] [Accepted: 08/01/2019] [Indexed: 12/26/2022] Open
Abstract
Germline pathogenic variants in the BRCA1-associated protein-1 (BAP1) gene cause the BAP1-tumor predisposition syndrome (BAP1-TPDS, OMIM 614327). BAP1-TPDS is associated with an increased risk of developing uveal melanoma (UM), cutaneous melanoma (CM), malignant mesothelioma (MMe), renal cell carcinoma (RCC), meningioma, cholangiocarcinoma, multiple non-melanoma skin cancers, and BAP1-inactivated nevi. Because of this increased risk, it is important to identify patients with BAP1-TPDS. The associated tumors are treated by different medical disciplines, emphasizing the need for generally applicable guidelines for initiating genetic analysis. In this study, we describe the path to identification of BAP1-TPDS in 21 probands found in the Netherlands and the family history at the time of presentation. We report two cases of de novo BAP1 germline mutations (2/21, 9.5%). Findings of this study combined with previously published literature, led to a proposal of guidelines for genetic referral. We recommend genetic analysis in patients with ≥2 BAP1-TPDS-associated tumors in their medical history and/or family history. We also propose to test germline BAP1 in patients diagnosed with UM <40 years, CM <18 years, MMe <50 years, or RCC <46 years. Furthermore, other candidate susceptibility genes for tumor types associated with BAP1-TPDS are discussed, which can be included in gene panels when testing patients.
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Affiliation(s)
- Cindy Chau
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Natasha M van Poppelen
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Nienke van der Stoep
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Arjen R Mensenkamp
- Department of Clinical Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Rolf H Sijmons
- Department of Genetics, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Barbara W van Paassen
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | | | - Nicole C Naus
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | | | - Thomas P Potjer
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Fonnet E Bleeker
- Department of Clinical Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Marijke R Wevers
- Department of Clinical Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Liselotte P van Hest
- Department of Clinical Genetics, Amsterdam University Medical Centers, 1081 HV Amsterdam, The Netherlands
| | - Marjolijn C J Jongmans
- Department of Clinical Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Clinical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Marina Marinkovic
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Jaco C Bleeker
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Martine J Jager
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Gregorius P M Luyten
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.
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10
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van Poppelen NM, Vaarwater J, Mudhar HS, Sisley K, van den Bosch QCC, de Klein A, Kiliç E, Verdijk RM. Reply. Ophthalmology 2018; 125:e79-e80. [PMID: 30318045 DOI: 10.1016/j.ophtha.2018.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 05/18/2018] [Indexed: 11/25/2022] Open
Affiliation(s)
- Natasha M van Poppelen
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jolanda Vaarwater
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hardeep S Mudhar
- National Specialist Ophthalmic Pathology Service, Department of Histopathology, Royal Hallamshire Hospital, Sheffield, United Kingdom
| | - Karen Sisley
- Department of Oncology & Metabolism, The University of Sheffield, Sheffield, United Kingdom
| | | | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Robert M Verdijk
- Ophthalmic Pathology, Erasmus MC University Medical Center, Rotterdam, the Netherlands.
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11
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van Poppelen NM, Yavuzyigitoglu S, Smit KN, Vaarwater J, Eussen B, Brands T, Paridaens D, Kiliç E, de Klein A. Chromosomal rearrangements in uveal melanoma: Chromothripsis. Genes Chromosomes Cancer 2018; 57:452-458. [PMID: 29726589 PMCID: PMC6175119 DOI: 10.1002/gcc.4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/26/2018] [Accepted: 04/28/2018] [Indexed: 12/22/2022] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy in the Western world. Recurrent mutations in GNAQ, GNA11, CYSLTR2, PLCB4, BAP1, EIF1AX, and SF3B1 are described as well as non-random chromosomal aberrations. Chromothripsis is a rare event in which chromosomes are shattered and rearranged and has been reported in a variety of cancers including UM. SNP arrays of 249 UM from patients who underwent enucleation, biopsy or endoresection were reviewed for the presence of chromothripsis. Chromothripsis was defined as ten or more breakpoints per chromosome involved. Genetic analysis of GNAQ, GNA11, BAP1, SF3B1, and EIF1AX was conducted using Sanger and next-generation sequencing. In addition, immunohistochemistry for BAP1 was performed. Chromothripsis was detected in 7 out of 249 tumors and the affected chromosomes were chromosomes 3, 5, 6, 8, 12, and 13. The mean total of fragments per chromosome was 39.8 (range 12-116). In 1 UM, chromothripsis was present in 2 different chromosomes. GNAQ, GNA11 or CYSLTR2 mutations were present in 6 of these tumors and 5 tumors harbored a BAP1 mutation and/or lacked BAP1 protein expression by immunohistochemistry. Four of these tumors metastasized and for the fifth only short follow-up data are available. One of these metastatic tumors harbored an SF3B1 mutation. No EIF1AX mutations were detected in any of the tumors. To conclude, chromothripsis is a rare event in UM, occurring in 2.8% of samples and without significant association with mutations in any of the common UM driver genes.
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Affiliation(s)
- Natasha M van Poppelen
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Serdar Yavuzyigitoglu
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kyra N Smit
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jolanda Vaarwater
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bert Eussen
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tom Brands
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Emine Kiliç
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
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12
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Smit KN, van Poppelen NM, Vaarwater J, Verdijk R, van Marion R, Kalirai H, Coupland SE, Thornton S, Farquhar N, Dubbink HJ, Paridaens D, de Klein A, Kiliç E. Combined mutation and copy-number variation detection by targeted next-generation sequencing in uveal melanoma. Mod Pathol 2018; 31:763-771. [PMID: 29327717 DOI: 10.1038/modpathol.2017.187] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/19/2017] [Accepted: 10/19/2017] [Indexed: 11/09/2022]
Abstract
Uveal melanoma is a highly aggressive cancer of the eye, in which nearly 50% of the patients die from metastasis. It is the most common type of primary eye cancer in adults. Chromosome and mutation status have been shown to correlate with the disease-free survival. Loss of chromosome 3 and inactivating mutations in BAP1, which is located on chromosome 3, are strongly associated with 'high-risk' tumors that metastasize early. Other genes often involved in uveal melanoma are SF3B1 and EIF1AX, which are found to be mutated in intermediate- and low-risk tumors, respectively. To obtain genetic information of all genes in one test, we developed a targeted sequencing method that can detect mutations in uveal melanoma genes and chromosomal anomalies in chromosome 1, 3, and 8. With as little as 10 ng DNA, we obtained enough coverage on all genes to detect mutations, such as substitutions, deletions, and insertions. These results were validated with Sanger sequencing in 28 samples. In >90% of the cases, the BAP1 mutation status corresponded to the BAP1 immunohistochemistry. The results obtained in the Ion Torrent single-nucleotide polymorphism assay were confirmed with several other techniques, such as fluorescence in situ hybridization, multiplex ligation-dependent probe amplification, and Illumina SNP array. By validating our assay in 27 formalin-fixed paraffin-embedded and 43 fresh uveal melanomas, we show that mutations and chromosome status can reliably be obtained using targeted next-generation sequencing. Implementing this technique as a diagnostic pathology application for uveal melanoma will allow prediction of the patients' metastatic risk and potentially assess eligibility for new therapies.
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Affiliation(s)
- Kyra N Smit
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Natasha M van Poppelen
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jolanda Vaarwater
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert Verdijk
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ronald van Marion
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Helen Kalirai
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Sarah E Coupland
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Sophie Thornton
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Neil Farquhar
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Hendrikus-Jan Dubbink
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
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