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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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Haarman AE, Klaver CC, Tedja MS, Roosing S, Astuti G, Gilissen C, Hoefsloot LH, van Tienhoven M, Brands T, Magielsen FJ, Eussen BH, de Klein A, Brosens E, Verhoeven VJ. Identification of rare variants involved in high myopia unraveled by whole genome sequencing. Ophthalmology Science 2023; 3:100303. [DOI: 10.1016/j.xops.2023.100303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 03/24/2023] [Accepted: 03/31/2023] [Indexed: 04/09/2023]
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van den Bosch QCC, Nguyen JQN, Brands T, van den Bosch TPP, Verdijk RM, Paridaens D, Naus NC, de Klein A, Kiliç E, Brosens E. FOXD1 Is a Transcription Factor Important for Uveal Melanocyte Development and Associated with High-Risk Uveal Melanoma. Cancers (Basel) 2022; 14:cancers14153668. [PMID: 35954332 PMCID: PMC9367502 DOI: 10.3390/cancers14153668] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/12/2022] [Accepted: 07/22/2022] [Indexed: 11/27/2022] Open
Abstract
Simple Summary Despite successful treatment of primary uveal melanoma (UM), metastases still occur in approximately 50% of the patients. Unfortunately, little is known about the mechanism behind metastasized UM. By reanalyzing publicly available single-cell RNA sequencing data of embryonic zebrafish larvae and validating the results with UM data, we have identified five transcription regulators of interest: ELL2, KDM5B, REXO4, RBFOX2 and FOXD1. The most significant finding is FOXD1, which is nearly exclusively expressed in high-risk UM and is associated with poor survival. FOXD1 is a novel gene which could be involved in the metastatic capability of UM. Elucidating its function and role in metastatic UM could help to understand and develop treatment for UM. Abstract Uveal melanoma (UM) is a deadly ocular malignancy, originating from uveal melanocytes. Although much is known regarding prognostication in UM, the exact mechanism of metastasis is mostly unknown. Metastatic tumor cells are known to express a more stem-like RNA profile which is seen often in cell-specific embryonic development to induce tumor progression. Here, we identified novel transcription regulators by reanalyzing publicly available single cell RNA sequencing experiments. We identified five transcription regulators of interest: ELL2, KDM5B, REXO4, RBFOX2 and FOXD1. Our most significant finding is FOXD1, as this gene is nearly exclusively expressed in high-risk UM and its expression is associated with a poor prognosis. Even within the BAP1-mutated UM, the expression of FOXD1 is correlated with poor survival. FOXD1 is a novel factor which could potentially be involved in the metastatic capacity of high-risk UM. Elucidating the function of FOXD1 in UM could provide insight into the malignant transformation of uveal melanocytes, especially in high-risk UM.
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Affiliation(s)
- Quincy C. C. van den Bosch
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Josephine Q. N. Nguyen
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Tom Brands
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Thierry P. P. van den Bosch
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center Rotterdam, 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 MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (T.P.P.v.d.B.); (R.M.V.)
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Dion Paridaens
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands;
| | - Nicole C. Naus
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Correspondence: (E.K.); (E.B.); Tel.: +31-107030683 (E.B.)
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
- Correspondence: (E.K.); (E.B.); Tel.: +31-107030683 (E.B.)
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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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ten Kate CA, de Klein A, de Graaf BM, Doukas M, Koivusalo A, Pakarinen MP, van der Helm R, Brands T, IJsselstijn H, van Bever Y, Wijnen RM, Spaander MC, Brosens E. Intrinsic Cellular Susceptibility to Barrett's Esophagus in Adults Born with Esophageal Atresia. Cancers (Basel) 2022; 14:cancers14030513. [PMID: 35158780 PMCID: PMC8833471 DOI: 10.3390/cancers14030513] [Citation(s) in RCA: 2] [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: 12/04/2021] [Revised: 01/01/2022] [Accepted: 01/10/2022] [Indexed: 11/25/2022] Open
Abstract
Simple Summary We investigated the increased prevalence of Barrett’s esophagus in adults with esophageal atresia. A higher polygenic risk score and disturbances in inflammatory, stress response and oncological pathways upon acid exposure suggest a genetic susceptibility and increased induction of inflammatory processes. Although further research is required to explore this hypothesis, this could be a first-step into selecting patients that are more at risk to develop Barrett’s esophagus and/or esophageal carcinoma. Currently, an endoscopic screening and surveillance program is in practice in our institution for patients born with esophageal atresia, to early detect (pre)malignant lesions. Since recurrent endoscopies can be a burden for the patient, selecting patients by for example genetic susceptibility would allow to only include those at risk in future practice. Abstract The prevalence of Barrett’s esophagus (BE) in adults born with esophageal atresia (EA) is four times higher than in the general population and presents at a younger age (34 vs. 60 years). This is (partly) a consequence of chronic gastroesophageal reflux. Given the overlap between genes and pathways involved in foregut and BE development, we hypothesized that EA patients have an intrinsic predisposition to develop BE. Transcriptomes of Esophageal biopsies of EA patients with BE (n = 19, EA/BE); EA patients without BE (n = 44, EA-only) and BE patients without EA (n = 10, BE-only) were compared by RNA expression profiling. Subsequently, we simulated a reflux episode by exposing fibroblasts of 3 EA patients and 3 controls to acidic conditions. Transcriptome responses were compared to the differential expressed transcripts in the biopsies. Predisposing single nucleotide polymorphisms, associated with BE, were slightly increased in EA/BE versus BE-only patients. RNA expression profiling and pathway enrichment analysis revealed differences in retinoic acid metabolism and downstream signaling pathways and inflammatory, stress response and oncological processes. There was a similar effect on retinoic acid signaling and immune response in EA patients upon acid exposure. These results indicate that epithelial tissue homeostasis in EA patients is more prone to acidic disturbances.
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Affiliation(s)
- Chantal A. ten Kate
- Department of Pediatric Surgery and Intensive Care Children, Erasmus MC-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (C.A.t.K.); (H.I.); (R.M.H.W.)
- Department of Gastroenterology and Hepatology, Erasmus MC Cancer Institute, 3000 CA Rotterdam, The Netherlands;
- Department of Clinical Genetics, Erasmus MC Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (B.M.d.G.); (R.v.d.H.); (T.B.); (Y.v.B.)
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (B.M.d.G.); (R.v.d.H.); (T.B.); (Y.v.B.)
| | - Bianca M. de Graaf
- Department of Clinical Genetics, Erasmus MC Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (B.M.d.G.); (R.v.d.H.); (T.B.); (Y.v.B.)
| | - Michail Doukas
- Department of Pathology, Erasmus MC, 3000 CA Rotterdam, The Netherlands;
| | - Antti Koivusalo
- Department of Pediatric Surgery, University of Helsinki, Children’s Hospital, 281, 000290 Helsinki, Finland; (A.K.); (M.P.P.)
| | - Mikko P. Pakarinen
- Department of Pediatric Surgery, University of Helsinki, Children’s Hospital, 281, 000290 Helsinki, Finland; (A.K.); (M.P.P.)
| | - Robert van der Helm
- Department of Clinical Genetics, Erasmus MC Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (B.M.d.G.); (R.v.d.H.); (T.B.); (Y.v.B.)
| | - Tom Brands
- Department of Clinical Genetics, Erasmus MC Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (B.M.d.G.); (R.v.d.H.); (T.B.); (Y.v.B.)
| | - Hanneke IJsselstijn
- Department of Pediatric Surgery and Intensive Care Children, Erasmus MC-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (C.A.t.K.); (H.I.); (R.M.H.W.)
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus MC Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (B.M.d.G.); (R.v.d.H.); (T.B.); (Y.v.B.)
| | - René M.H. Wijnen
- Department of Pediatric Surgery and Intensive Care Children, Erasmus MC-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (C.A.t.K.); (H.I.); (R.M.H.W.)
| | - Manon C.W. Spaander
- Department of Gastroenterology and Hepatology, Erasmus MC Cancer Institute, 3000 CA Rotterdam, The Netherlands;
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (A.d.K.); (B.M.d.G.); (R.v.d.H.); (T.B.); (Y.v.B.)
- Correspondence: ; Tel.: +31-10-70-37643
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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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7
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Ten Kate CA, Brouwer RWW, van Bever Y, Martens VK, Brands T, van Beelen NWG, Brooks AS, Huigh D, van der Helm RM, Eussen BHFMM, van IJcken WFJ, IJsselstijn H, Tibboel D, Wijnen RMH, de Klein A, Hofstra RMW, Brosens E. Infantile hypertrophic pyloric stenosis in patients with esophageal atresia. Birth Defects Res 2020; 112:670-687. [PMID: 32298054 DOI: 10.1002/bdr2.1683] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/25/2020] [Accepted: 04/02/2020] [Indexed: 11/07/2022]
Abstract
BACKGROUND Patients born with esophageal atresia (EA) have a higher incidence of infantile hypertrophic pyloric stenosis (IHPS), suggestive of a relationship. A shared etiology makes sense from a developmental perspective as both affected structures are foregut derived. A genetic component has been described for both conditions as single entities and EA and IHPS are variable components in several monogenetic syndromes. We hypothesized that defects disturbing foregut morphogenesis are responsible for this combination of malformations. METHODS We investigated the genetic variation of 15 patients with both EA and IHPS with unaffected parents using exome sequencing and SNP array-based genotyping, and compared the results to mouse transcriptome data of the developing foregut. RESULTS We did not identify putatively deleterious de novo mutations or recessive variants. However, we detected rare inherited variants in EA or IHPS disease genes or in genes important in foregut morphogenesis, expressed at the proper developmental time-points. Two pathways were significantly enriched (p < 1 × 10-5 ): proliferation and differentiation of smooth muscle cells and self-renewal of satellite cells. CONCLUSIONS None of our findings could fully explain the combination of abnormalities on its own, which makes complex inheritance the most plausible genetic explanation, most likely in combination with mechanical and/or environmental factors. As we did not find one defining monogenetic cause for the EA/IHPS phenotype, the impact of the corrective surgery could should be further investigated.
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Affiliation(s)
- Chantal A Ten Kate
- Department of Pediatric Surgery and Intensive Care Children, Erasmus University Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Rutger W W Brouwer
- Center for Biomics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Vera K Martens
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tom Brands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nicole W G van Beelen
- Department of Pediatric Surgery and Intensive Care Children, Erasmus University Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Daphne Huigh
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert M van der Helm
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bert H F M M Eussen
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Hanneke IJsselstijn
- Department of Pediatric Surgery and Intensive Care Children, Erasmus University Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Dick Tibboel
- Department of Pediatric Surgery and Intensive Care Children, Erasmus University Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Rene M H Wijnen
- Department of Pediatric Surgery and Intensive Care Children, Erasmus University Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert M W Hofstra
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
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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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van der Graaf LM, Gardiner SL, Tok M, Brands T, Boogaard MW, Pepers BA, Eussen B, de Klein A, Aziz NA, Freund C, Buijsen RA, van Roon-Mom WM. Generation of 5 induced pluripotent stem cell lines, LUMCi007-A and B and LUMCi008-A, B and C, from 2 patients with Huntington disease. Stem Cell Res 2019; 39:101498. [DOI: 10.1016/j.scr.2019.101498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/25/2019] [Accepted: 07/09/2019] [Indexed: 11/15/2022] Open
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10
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Smit KN, Chang J, Derks K, Vaarwater J, Brands T, Verdijk RM, Wiemer EAC, Mensink HW, Pothof J, de Klein A, Kilic E. Aberrant MicroRNA Expression and Its Implications for Uveal Melanoma Metastasis. Cancers (Basel) 2019; 11:cancers11060815. [PMID: 31212861 PMCID: PMC6628189 DOI: 10.3390/cancers11060815] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 05/14/2019] [Revised: 06/03/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Uveal melanoma (UM) is the most frequently found primary intra-ocular tumor in adults. It is a highly aggressive cancer that causes metastasis-related mortality in up to half of the patients. Many independent studies have reported somatic genetic changes associated with high metastatic risk, such as monosomy of chromosome 3 and mutations in BAP1. Still, the mechanisms that drive metastatic spread are largely unknown. This study aimed to elucidate the potential role of microRNAs in the metastasis of UM. Using a next-generation sequencing approach in 26 UM samples we identified thirteen differentially expressed microRNAs between high-risk UM and low/intermediate-risk UM, including the known oncomirs microRNA-17-5p, microRNA-21-5p, and miR-151a-3p. Integration of the differentially expressed microRNAs with expression data of predicted target genes revealed 106 genes likely to be affected by aberrant microRNA expression. These genes were involved in pathways such as cell cycle regulation, EGF signaling and EIF2 signaling. Our findings demonstrate that aberrant microRNA expression in UM may affect the expression of genes in a variety of cancer-related pathways. This implies that some microRNAs can be responsible for UM metastasis and are promising potential targets for future treatment.
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Affiliation(s)
- Kyra N Smit
- Department of Ophthalmology, Erasmus University MC, 3015 GD Rotterdam, The Netherlands.
- Department of Clinical Genetics, Erasmus University MC, 3015 GD Rotterdam, The Netherlands.
| | - Jiang Chang
- Department of Molecular Genetics, Erasmus University MC, 3015 GD Rotterdam, The Netherlands.
| | - Kasper Derks
- Department of Molecular Genetics, Erasmus University MC, 3015 GD Rotterdam, The Netherlands.
| | - Jolanda Vaarwater
- Department of Ophthalmology, Erasmus University MC, 3015 GD Rotterdam, The Netherlands.
- Department of Clinical Genetics, Erasmus University MC, 3015 GD Rotterdam, The Netherlands.
| | - Tom Brands
- Department of Clinical Genetics, Erasmus University MC, 3015 GD Rotterdam, The Netherlands.
| | - Rob M Verdijk
- Department of Pathology, Section Ophthalmic Pathology, Erasmus University MC, 3015 GD Rotterdam, The Netherlands.
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands.
| | - Erik A C Wiemer
- Department of Medical Oncology, Erasmus University MC, 3015 GD Rotterdam, The Netherlands.
| | | | - Joris Pothof
- Department of Molecular Genetics, Erasmus University MC, 3015 GD Rotterdam, The Netherlands.
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University MC, 3015 GD Rotterdam, The Netherlands.
| | - Emine Kilic
- Department of Ophthalmology, Erasmus University MC, 3015 GD Rotterdam, The Netherlands.
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11
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Daoutsali E, Buijsen RA, van de Pas S, Jong A', Mikkers H, Brands T, Eussen B, de Klein A, van der Graaf LM, Pepers BA, Freund C, Terwindt GM, Orlova VV, van Roon-Mom WM. Generation of 3 human induced pluripotent stem cell lines LUMCi005-A, B and C from a Hereditary Cerebral Hemorrhage with Amyloidosis-Dutch type patient. Stem Cell Res 2019; 34:101359. [DOI: 10.1016/j.scr.2018.101359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 10/27/2022] Open
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12
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Flake C, Brands T, Koß HJ, Dinger R, Bardow A. Nicht-invasive Inline-Analyse von Bioprozessen mit Raman-Spektroskopie und Indirect Hard Modeling (IHM). CHEM-ING-TECH 2018. [DOI: 10.1002/cite.201855314] [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] [Indexed: 11/07/2022]
Affiliation(s)
- C. Flake
- RWTH Aachen; Lehrstuhl für Technische Thermodynamik; Schinkelstraße 8 52062 Aachen Deutschland
| | - T. Brands
- RWTH Aachen; Lehrstuhl für Technische Thermodynamik; Schinkelstraße 8 52062 Aachen Deutschland
| | - H.-J. Koß
- RWTH Aachen; Lehrstuhl für Technische Thermodynamik; Schinkelstraße 8 52062 Aachen Deutschland
| | - R. Dinger
- RWTH Aachen; Aachener Verfahrenstechnik - Bioverfahrenstechnik; Forckenbeckstraße 51 52074 Aachen Deutschland
| | - A. Bardow
- RWTH Aachen; Lehrstuhl für Technische Thermodynamik; Schinkelstraße 8 52062 Aachen Deutschland
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13
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Thien J, Reinpold L, Flake C, Brands T, Koß HJ, Bardow A. Eine Mikrofluidik-Plattform für die automatisierte Bestimmung von Flüssig/flüssig-Gleichgewichten mittels Raman-Spektroskopie. CHEM-ING-TECH 2018. [DOI: 10.1002/cite.201855411] [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] [Indexed: 11/11/2022]
Affiliation(s)
- J. Thien
- RWTH Aachen University; Lehrstuhl für Technische Thermodynamik; Schinkelstraße 8 52062 Aachen Deutschland
| | - L. Reinpold
- RWTH Aachen University; Lehrstuhl für Technische Thermodynamik; Schinkelstraße 8 52062 Aachen Deutschland
| | - C. Flake
- RWTH Aachen University; Lehrstuhl für Technische Thermodynamik; Schinkelstraße 8 52062 Aachen Deutschland
| | - T. Brands
- RWTH Aachen University; Lehrstuhl für Technische Thermodynamik; Schinkelstraße 8 52062 Aachen Deutschland
| | - H.-J. Koß
- RWTH Aachen University; Lehrstuhl für Technische Thermodynamik; Schinkelstraße 8 52062 Aachen Deutschland
| | - A. Bardow
- RWTH Aachen University; Lehrstuhl für Technische Thermodynamik; Schinkelstraße 8 52062 Aachen Deutschland
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14
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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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15
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Yavuzyigitoglu S, Drabarek W, Smit KN, van Poppelen N, Koopmans AE, Vaarwater J, Brands T, Eussen B, Dubbink HJ, van Riet J, van de Werken HJ, Beverloo B, Verdijk RM, Naus N, Paridaens D, Kilic E, de Klein A. Correlation of Gene Mutation Status with Copy Number Profile in Uveal Melanoma. Ophthalmology 2017; 124:573-575. [DOI: 10.1016/j.ophtha.2016.10.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 10/31/2016] [Accepted: 10/31/2016] [Indexed: 02/02/2023] Open
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16
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Kilic E, Yavuzyigitoglu S, Drabarek W, Obulkasim A, Brands T, Eussen B, de Klein A. Chromosomal aberration predict uveal melanoma mutation status. Acta Ophthalmol 2016. [DOI: 10.1111/j.1755-3768.2016.0662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Brands T, Hoegen P. [Röentgen diagnosis and clinical picture of esophagocardial carcinoma]. ZFA (Stuttgart) 1976; 52:1820-6. [PMID: 1014807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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18
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Brands T. [Diagnosis of salivary gland diseases]. Med Klin 1976; 71:1744-7. [PMID: 790132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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19
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Brands T. [Clinical and histological aspects of mucoepidermoid tumors of the salivary glands]. Hippokrates 1975; 46:409-11. [PMID: 1223061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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20
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Brands T, Timm K, Friedrich J. [Diseases of the trachea and bronchi by special consideration of x-ray diagnostic (author's transl)]. Laryngol Rhinol Otol (Stuttg) 1975; 54:34-8. [PMID: 129612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Important aspects for the diagnosis and therapy of diseases of the trachea and bronchi are the surgical anatomy, physiology and histopathology. For the evaluation of these diseases x-ray studies can make a major contribution.
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21
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Brands T, Friedrich J, Stratkötter R. [Clinical aspects and therapy of exulcerated breast carcinoma, cancer en cuirasse and recurrent tumors]. Z Allgemeinmed 1975; 51:29-35. [PMID: 1216879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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22
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Brands T, Wittig G. [Clinical and radiotherapy of hemangiomas and lymphangiomas. Pathology and histology]. Med Welt 1974; 25:1697-704. [PMID: 4431309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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23
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Brands T, Frössler H. [Radiation in the region of the eye (author's transl)]. Klin Monbl Augenheilkd 1974; 164:340-5. [PMID: 4849561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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24
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Brands T, Frössler H. [Diagnostic errors in radiology of the ear, nose and throat (author's transl)]. Laryngol Rhinol Otol (Stuttg) 1974; 53:155-64. [PMID: 4836314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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25
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Brands T, Löbbel H. [Pathogenesis, clinical picture and diagnosis of traumatic diaphragmatic ruptures]. Med Welt 1973; 24:1639-43. [PMID: 4764057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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26
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Brands T, Fröbbler H. [Radiological diagnosis of the oesophagus]. Z Laryngol Rhinol Otol 1973; 52:398-405. [PMID: 4200341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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27
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Brands T, Dinkloh H. [Tomography of the facial skeleton]. Zahnarztl Prax 1973; 24:177-80. [PMID: 4514463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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28
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Brands T, Dinkloh H. [Acute injuries of the oesophagus]. HNO 1973; 21:123-4. [PMID: 4710036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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29
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Brands T, Wannemacher M. [Clinical aspects and therapy of hemangiopericytoma]. Z Allgemeinmed 1973; 49:319-24. [PMID: 4782780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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30
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Brands T, Benz H. [Value and significance of salivary gland scintigraphy using technetium 99m for the diagnosis of salivary gland diseases]. Z Allgemeinmed 1973; 49:145-50. [PMID: 4739811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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31
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Meyer HJ, Brands T. [Unusual tumor of the macula (lymphomatous hyperplasia of the uvea)]. Klin Monbl Augenheilkd 1972; 161:684-7. [PMID: 4655897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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32
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Brands T. [Diagnosis of salivary gland diseases]. Z Laryngol Rhinol Otol 1972; 51:639-59. [PMID: 5081034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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33
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Rackwitz K, Brands T. [Routine roentgen diagnostics in urologic injuries]. Radiologe 1972; 12:298-9. [PMID: 4642066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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34
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Brands T, Dinkloh H, Hagemeier B. [Thermographic studies of the parotid gland and submandibular gland]. Rontgenpraxis 1972; 25:203-12. [PMID: 4645795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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35
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Frössler H, Brands T. [Irradiation methods in the region of the eye]. Rontgenpraxis 1972; 25:161-8. [PMID: 4627337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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36
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Brands T, Dinkloh H. [Tomography in otorhinolaryngology]. Z Laryngol Rhinol Otol 1972; 51:344-50. [PMID: 5042768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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37
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von Koppenfels R, Brands T. [Complete fistula of the abdominal wall in sigmoid diverticulosis]. Med Welt 1972; 23:379-81. [PMID: 4261122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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38
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von Koppenfels R, Brands T. [Clinical aspects and diagnosis of fecaliths]. Med Welt 1972; 23:154-7. [PMID: 5018084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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39
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Brands T. [Significance of sialography in salivary gland diagnostics]. Med Welt 1971; 51:2021-3. [PMID: 5159947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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40
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Wesseling B, Brands T. [Broncho-esophageal fistula following lung resection for tuberculosis]. Med Klin 1971; 66:1687-90. [PMID: 5136295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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41
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Schütz J, Brands T, Schachinger P. [60Cobalt-teletherapy of brain neoplasms]. Strahlentherapie 1971; 141:367-74. [PMID: 4326700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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42
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Brands T, Schütz J. [Mixed tumors of the salivary glands. Pleomorphic adenomas]. Med Welt 1970; 5:186-92. [PMID: 4315426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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43
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Brands T, Schnepper E, Wannenmacher M. [Sjogren's syndrome and changes in the salivary glands]. Dtsch Zahn Mund Kieferheilkd Zentralbl Gesamte 1969; 53:226-33. [PMID: 5266064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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44
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Brands T. [Hemangioma of the parotid gland with multiple phleboliths]. Zentralbl Chir 1969; 94:1064-7. [PMID: 5369263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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45
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Brands T. [Actinomycosis of the salivary glands]. Med Welt 1969; 31:1681-5 passim. [PMID: 5800737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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46
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Schnepper E, Brands T, Schulte G. [On the clinical findings and therapy of benign giant cell synovioma (pigmented villonodular synovitis, tenosynovitis and bursitis)]. Strahlentherapie 1969; 138:9-14. [PMID: 4310367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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47
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Brands T, Schnepper E, Hartung W, Backmann L. [Hemangiopericytoma of the right pubic bone with skeletal destruction]. Bruns Beitr Klin Chir (1971) 1969; 217:377-83. [PMID: 5372151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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48
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Brands T, Backmann L. [Extraglandular processes in the area of the large salivary glands]. Med Welt 1969; 20:1162-4. [PMID: 5801893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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49
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Brands T. [New sialography technic]. Zahnarztl Prax 1969; 20:25-8. [PMID: 5255061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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50
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Brands T, Schütz J. [Diapositives of X-ray pictures]. Rontgenpraxis 1968; 21:266-272. [PMID: 5729291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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