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Santi I, Vellekoop H, M Versteegh M, A Huygens S, Dinjens WNM, Mölken MRV. Estimating the Prognostic Value of the NTRK Fusion Biomarker for Comparative Effectiveness Research in The Netherlands. Mol Diagn Ther 2024; 28:319-328. [PMID: 38616205 PMCID: PMC11068666 DOI: 10.1007/s40291-024-00704-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2024] [Indexed: 04/16/2024]
Abstract
OBJECTIVES We evaluated the prognostic value of the neurotrophic tyrosine receptor kinase (NTRK) gene fusions by comparing the survival of patients with NTRK+ tumours with patients without NTRK+ tumours. METHODS We used genomic and clinical registry data from the Center for Personalized Cancer Treatment (CPCT-02) study containing a cohort of cancer patients who were treated in Dutch clinical practice between 2012 and 2020. We performed a propensity score matching analysis, where NTRK+ patients were matched to NTRK- patients in a 1:4 ratio. We subsequently analysed the survival of the matched sample of NTRK+ and NTRK- patients using the Kaplan-Meier method and Cox regression, and performed an analysis of credibility to evaluate the plausibility of our result. RESULTS Among 3556 patients from the CPCT-02 study with known tumour location, 24 NTRK+ patients were identified. NTRK+ patients were distributed across nine different tumour types: bone/soft tissue, breast, colorectal, head and neck, lung, pancreas, prostate, skin and urinary tract. NTRK fusions involving the NTRK3 gene (46%) and NTRK1 gene (33%) were most common. The survival analysis rendered a hazard ratio (HR) of 1.44 (95% CI 0.81-2.55) for NTRK+ patients. Using the point estimates of three prior studies on the prognostic value of NTRK fusions, our finding that the HR is > 1 was deemed plausible. CONCLUSIONS NTRK+ patients may have an increased risk of death compared with NTRK- patients. When using historic control data to assess the comparative effectiveness of TRK inhibitors, the prognostic value of the NTRK fusion biomarker should therefore be accounted for.
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Affiliation(s)
- Irene Santi
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, Burgemeester Oudlaan 50, 3062 PA, Rotterdam, The Netherlands.
| | - Heleen Vellekoop
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, Burgemeester Oudlaan 50, 3062 PA, Rotterdam, The Netherlands
| | - Matthijs M Versteegh
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, Burgemeester Oudlaan 50, 3062 PA, Rotterdam, The Netherlands
| | - Simone A Huygens
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, Burgemeester Oudlaan 50, 3062 PA, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Maureen Rutten-van Mölken
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, Burgemeester Oudlaan 50, 3062 PA, Rotterdam, The Netherlands
- School of Health Policy and Management, Erasmus University Rotterdam, Rotterdam, The Netherlands
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2
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Apellaniz-Ruiz M, Sabbaghian N, Chong AL, de Kock L, Cetinkaya S, Bayramoğlu E, Dinjens WNM, McCluggage WG, Wagner A, Yilmaz AA, Foulkes WD. Reclassification of two germline DICER1 splicing variants leads to DICER1 syndrome diagnosis. Fam Cancer 2023; 22:487-493. [PMID: 37248399 PMCID: PMC10541835 DOI: 10.1007/s10689-023-00336-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023]
Abstract
DICER1 syndrome is an inherited condition associated with an increased risk of developing hamartomatous and neoplastic lesions in diverse organs, mainly at early ages. Germline pathogenic variants in DICER1 cause this condition. Detecting a variant of uncertain significance in DICER1 or finding uncommon phenotypes complicate the diagnosis and can negatively impact patient care. We present two unrelated patients suspected to have DICER1 syndrome. Both females (aged 13 and 15 years) presented with multinodular goiter (thyroid follicular nodular disease) and ovarian tumours. One was diagnosed with an ovarian Sertoli-Leydig cell tumour (SLCT) and the other, with an ovarian juvenile granulosa cell tumour, later reclassified as a retiform variant of SLCT. Genetic screening showed no germline pathogenic variants in DICER1. However, two potentially splicing variants were found, DICER1 c.5365-4A>G and c.5527+3A>G. Also, typical somatic DICER1 RNase IIIb hotspot mutations were detected in the thyroid and ovarian tissues. In silico splicing algorithms predicted altered splicing for both germline variants and skipping of exon 25 was confirmed by RNA assays for both variants. The reclassification of the ovarian tumour, leading to recognition of the association with DICER1 syndrome and the characterization of the germline intronic variants were all applied to recently described DICER1 variant classification rules. This ultimately resulted in confirmation of DICER1 syndrome in the two teenage girls.
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Affiliation(s)
- Maria Apellaniz-Ruiz
- Genomics Medicine Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Calle Irunlarrea 3, 31008, Pamplona, Navarra, Spain.
| | - Nelly Sabbaghian
- Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Anne-Laure Chong
- Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Leanne de Kock
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Semra Cetinkaya
- Department of Pediatric Endocrinology, Health Science University, Dr Sami Ulus Obstetrics and Gynecology, Children's Health and Disease Training and Research Hospital, Ankara, Turkey
| | - Elvan Bayramoğlu
- Department of Pediatric Endocrinology, Health Science University, Dr Sami Ulus Obstetrics and Gynecology, Children's Health and Disease Training and Research Hospital, Ankara, Turkey
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - W Glenn McCluggage
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Aslihan Arasli Yilmaz
- Department of Pediatric Endocrinology, Health Science University, Dr Sami Ulus Obstetrics and Gynecology, Children's Health and Disease Training and Research Hospital, Ankara, Turkey
| | - William D Foulkes
- Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Program in Cancer Genetics, Department of Oncology and Human Genetics, McGill University, Montréal, QC, Canada
- Department of Medical Genetics, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
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3
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Hakuno SK, Janson SGT, Trietsch MD, de Graaf M, de Jonge-Muller E, Crobach S, Harryvan TJ, Boonstra JJ, Dinjens WNM, Slingerland M, Hawinkels LJAC. Endoglin and squamous cell carcinomas. Front Med (Lausanne) 2023; 10:1112573. [PMID: 37396898 PMCID: PMC10313935 DOI: 10.3389/fmed.2023.1112573] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Despite the fact that the role of endoglin on endothelial cells has been extensively described, its expression and biological role on (epithelial) cancer cells is still debatable. Especially its function on squamous cell carcinoma (SCC) cells is largely unknown. Therefore, we investigated SCC endoglin expression and function in three types of SCCs; head and neck (HNSCC), esophageal (ESCC) and vulvar (VSCC) cancers. Endoglin expression was evaluated in tumor specimens and 14 patient-derived cell lines. Next to being expressed on angiogenic endothelial cells, endoglin is selectively expressed by individual SCC cells in tumor nests. Patient derived HNSCC, ESCC and VSCC cell lines express varying levels of endoglin with high interpatient variation. To assess the function of endoglin in signaling of TGF-β ligands, endoglin was overexpressed or knocked out or the signaling was blocked using TRC105, an endoglin neutralizing antibody. The endoglin ligand BMP-9 induced strong phosphorylation of SMAD1 independent of expression of the type-I receptor ALK1. Interestingly, we observed that endoglin overexpression leads to strongly increased soluble endoglin levels, which in turn decreases BMP-9 signaling. On the functional level, endoglin, both in a ligand dependent and independent manner, did not influence proliferation or migration of the SCC cells. In conclusion, these data show endoglin expression on individual cells in the tumor nests in SCCs and a role for (soluble) endoglin in paracrine signaling, without directly affecting proliferation or migration in an autocrine manner.
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Affiliation(s)
- Sarah K. Hakuno
- Department of Gastroenterology-Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Stefanus G. T. Janson
- Department of Gastroenterology-Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Marjolijn D. Trietsch
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
- Department of Gynecology, Leiden University Medical Center, Leiden, Netherlands
| | - Manon de Graaf
- Department of Gastroenterology-Hepatology, Leiden University Medical Center, Leiden, Netherlands
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Eveline de Jonge-Muller
- Department of Gastroenterology-Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Stijn Crobach
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | - Tom J. Harryvan
- Department of Gastroenterology-Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Jurjen J. Boonstra
- Department of Gastroenterology-Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Winand N. M. Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, Netherlands
| | - Marije Slingerland
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Lukas J. A. C. Hawinkels
- Department of Gastroenterology-Hepatology, Leiden University Medical Center, Leiden, Netherlands
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Giang J, Mooyaart AL, Martens-de Kemp SR, Jaspars L, Wakkee M, Eijken E, Voogt W, Dinjens WNM, Damman J. Hedgehog pathway mutations are involved in the pathogenesis of plaque-type "trichoblastoma": A report of two cases. J Cutan Pathol 2023. [PMID: 36607280 DOI: 10.1111/cup.14389] [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: 05/25/2022] [Revised: 11/21/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
We present two cases of plaque-type trichoblastoma with atypical foci. A rare variant of trichoblastoma is the plaque variant, which is characterized by poor circumscription and locally infiltrative growth pattern. These lesions mostly require multiple stages of Mohs micrographic surgery. Debate still exists whether this variant should be considered as a benign entity or as "low-grade" malignant counterpart of trichoblastoma. In this report we describe two cases of plaque-type trichoblastoma with atypical foci, which harbored somatic mutations in the Hedgehog pathway, thus should be acknowledged as intermediate malignancies. In addition, extensive molecular workup of both the trichoblastic and atypical component in sequential lesions in the same patient was performed.
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Affiliation(s)
- Jenny Giang
- Department of Pathology, Maasstad Hospital, Rotterdam, The Netherlands
| | - Antien L Mooyaart
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Lies Jaspars
- Department of Pathology, Vrije Universiteit Medical Center, Amsterdam, The Netherlands
| | - Marlies Wakkee
- Department of Dermatology, Erasmus MC, University Medical Center Cancer Institute, Rotterdam, The Netherlands
| | - Erik Eijken
- Laboratory for Pathology East Netherlands (LabPON), Hengelo, The Netherlands
| | - Walter Voogt
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeffrey Damman
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
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5
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Hermans BCM, Derks JL, Hillen LM, van der Baan I, van den Broek EC, von der Thüsen JH, van Suylen R, Atmodimedjo PN, den Toom TD, Coumans‐Stallinga C, Timens W, Dinjens WNM, Dubbink HJ, Speel EM, Dingemans AC. In-depth molecular analysis of combined and co-primary pulmonary large cell neuroendocrine carcinoma and adenocarcinoma. Int J Cancer 2022; 150:802-815. [PMID: 34674268 PMCID: PMC9298697 DOI: 10.1002/ijc.33853] [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: 03/31/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 01/09/2023]
Abstract
Up to 14% of large cell neuroendocrine carcinomas (LCNECs) are diagnosed in continuity with nonsmall cell lung carcinoma. In addition to these combined lesions, 1% to 7% of lung tumors present as co-primary tumors with multiple synchronous lesions. We evaluated molecular and clinicopathological characteristics of combined and co-primary LCNEC-adenocarcinoma (ADC) tumors. Ten patients with LCNEC-ADC (combined) and five patients with multiple synchronous ipsilateral LCNEC and ADC tumors (co-primary) were included. DNA was isolated from distinct tumor parts, and 65 cancer genes were analyzed by next generation sequencing. Immunohistochemistry was performed including neuroendocrine markers, pRb, Ascl1 and Rest. Pure ADC (N = 37) and LCNEC (N = 17) cases were used for reference. At least 1 shared mutation, indicating tumor clonality, was found in LCNEC- and ADC-parts of 10/10 combined tumors but only in 1/5 co-primary tumors. A range of identical mutations was observed in both parts of combined tumors: 8/10 contained ADC-related (EGFR/KRAS/STK11 and/or KEAP1), 4/10 RB1 and 9/10 TP53 mutations. Loss of pRb IHC was observed in 6/10 LCNEC- and 4/10 ADC-parts. The number and intensity of expression of Ascl1 and neuroendocrine markers increased from pure ADC (low) to combined ADC (intermediate) and combined and pure LCNEC (high). The opposite was true for Rest expression. In conclusion, all combined LCNEC-ADC tumors were clonally related indicating a common origin. A relatively high frequency of pRb inactivation was observed in both LCNEC- and ADC-parts, suggesting an underlying role in LCNEC-ADC development. Furthermore, neuroendocrine differentiation might be modulated by Ascl1(+) and Rest(-) expression.
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Affiliation(s)
- Bregtje C. M. Hermans
- Department of Pulmonary DiseasesMaastricht University Medical Centre+MaastrichtThe Netherlands,GROW—School for Oncology & Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - Jules L. Derks
- Department of Pulmonary DiseasesMaastricht University Medical Centre+MaastrichtThe Netherlands,GROW—School for Oncology & Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - Lisa M. Hillen
- GROW—School for Oncology & Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands,Department of PathologyMaastricht University Medical Centre+MaastrichtThe Netherlands
| | - Irene van der Baan
- GROW—School for Oncology & Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands,Department of PathologyMaastricht University Medical Centre+MaastrichtThe Netherlands
| | | | - Jan H. von der Thüsen
- Department of PathologyErasmus MC Cancer Institute, University Medical Center RotterdamRotterdamThe Netherlands
| | | | - Peggy N. Atmodimedjo
- Department of PathologyErasmus MC Cancer Institute, University Medical Center RotterdamRotterdamThe Netherlands
| | - T. Dorine den Toom
- Department of PathologyErasmus MC Cancer Institute, University Medical Center RotterdamRotterdamThe Netherlands
| | - Cecile Coumans‐Stallinga
- GROW—School for Oncology & Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands,Department of PathologyMaastricht University Medical Centre+MaastrichtThe Netherlands
| | - Wim Timens
- Department of Pathology and Medical BiologyUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Winand N. M. Dinjens
- Department of PathologyErasmus MC Cancer Institute, University Medical Center RotterdamRotterdamThe Netherlands
| | - Hendrikus J. Dubbink
- Department of PathologyErasmus MC Cancer Institute, University Medical Center RotterdamRotterdamThe Netherlands
| | - Ernst‐Jan M. Speel
- GROW—School for Oncology & Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands,Department of PathologyMaastricht University Medical Centre+MaastrichtThe Netherlands
| | - Anne‐Marie C. Dingemans
- Department of Pulmonary DiseasesMaastricht University Medical Centre+MaastrichtThe Netherlands,GROW—School for Oncology & Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands,Department of PulmonologyErasmus MC Cancer Institute, University Medical Center RotterdamRotterdamThe Netherlands
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6
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Spoor J, Eyck BM, Atmodimedjo PN, Jansen MPHM, Helmijr JCA, Martens JWM, van der Wilk BJ, van Lanschot JJB, Dinjens WNM. Liquid biopsy in esophageal cancer: a case report of false-positive circulating tumor DNA detection due to clonal hematopoiesis. Ann Transl Med 2021; 9:1264. [PMID: 34532401 PMCID: PMC8421960 DOI: 10.21037/atm-21-525] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/28/2021] [Indexed: 01/05/2023]
Abstract
Circulating tumor DNA (ctDNA) analysis is a promising non-invasive technique for active surveillance after chemoradiotherapy for locally advanced resectable esophageal carcinoma. In other malignancies false-positive results in ctDNA analysis have been reported due to clonal hematopoiesis. In this case, we present a 66-year-old male who had adenocarcinoma of the gastroesophageal junction for which he received neoadjuvant chemoradiotherapy and underwent a transhiatal esophagectomy. Postoperatively our patient received follow-up with ctDNA analysis using next generation sequencing (NGS) and droplet digital PCR (ddPCR). This case report illustrates a number of the current challenges in ctDNA diagnostics in esophageal carcinoma. Firstly, the TP53 c.524G>A; p.R175H mutation that was found in preoperative tumor biopsies became detectable in ctDNA only after distant metastases had already been confirmed by clinical symptoms and standard imaging- and biopsy techniques. Secondly our patient repeatedly had false-positive outcomes of ctDNA analysis. Genomic analysis of white blood cells revealed that the origin of these discordant mutations lies in clonal hematopoiesis. Failure to detect TP53 c.524G>A; p.R175H in cell-free DNA (cfDNA) is most likely due to the amount of ctDNA in the cfDNA fraction being below the limit of detection for NGS and ddPCR analyses. Clinicians should be aware of the possibility of finding mutations originating from clonal hematopoiesis when using ctDNA analysis during active surveillance for esophageal carcinoma. We recommend correlation of mutations in cfDNA with mutations in tumor biopsies.
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Affiliation(s)
- Jonathan Spoor
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Ben M Eyck
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Maurice P H M Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Jean C A Helmijr
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Berend J van der Wilk
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - J Jan B van Lanschot
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
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7
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Kamp EJCA, Dinjens WNM, Doukas M, Bruno MJ, de Jonge PJF, Peppelenbosch MP, de Vries AC. Optimal tissue sampling during ERCP and emerging molecular techniques for the differentiation of benign and malignant biliary strictures. Therap Adv Gastroenterol 2021; 14:17562848211002023. [PMID: 33948111 PMCID: PMC8053835 DOI: 10.1177/17562848211002023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 02/04/2023] Open
Abstract
Patients with cholangiocarcinoma have poor survival since the majority of patients are diagnosed at a stage precluding surgical resection, due to locally irresectable tumors and/or metastases. Optimization of diagnostic strategies, with a principal role for tissue diagnosis, is essential to detect cancers at an earlier stage amenable to curative treatment. Current barriers for a tissue diagnosis include both insufficient tissue sampling and a difficult cyto- or histopathological assessment. During endoscopic retrograde cholangiopancreatography, optimal brush sampling includes obtaining more than one brush within an individual patient to increase its diagnostic value. Currently, no significant increase of the diagnostic accuracy for the new cytology brush devices aiming to enhance the cellularity of brushings versus standard biliary brush devices has been demonstrated. Peroral cholangioscopy with bile duct biopsies appears to be a valuable tool in the diagnostic work-up of indeterminate biliary strictures, and may overcome current technical difficulties of fluoroscopic-guided biopsies. Over the past years, molecular techniques to detect chromosomal instability, mutations and methylation profiling of tumors have revolutionized, and implementation of these techniques on biliary tissue during diagnostic work-up of biliary strictures may be awaited in the near future. Fluorescence in situ hybridization has already been implemented in routine diagnostic evaluation of biliary strictures in several centers. Next-generation sequencing is promising for standard diagnostic care in biliary strictures, and recent studies have shown adequate detection of prevalent genomic alterations in KRAS, TP53, CDKN2A, SMAD4, PIK3CA, and GNAS on biliary brush material. Detection of DNA methylation of tumor suppressor genes and microRNAs may evolve over the coming years to a valuable diagnostic tool for cholangiocarcinoma. This review summarizes optimal strategies for biliary tissue sampling during endoscopic retrograde cholangiopancreatography and focuses on the evolving molecular techniques on biliary tissue to improve the differentiation of benign and malignant biliary strictures.
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Affiliation(s)
- Eline J. C. A. Kamp
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Winand N. M. Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Michail Doukas
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Marco J. Bruno
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Pieter Jan F. de Jonge
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Maikel P. Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Annemarie C. de Vries
- Department of Gastroenterology & Hepatology, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, Room Na-609, Rotterdam, 3015 GD, The Netherlands
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8
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Radonic T, Geurts-Giele WRR, Samsom KG, Roemen GMJM, von der Thüsen JH, Thunnissen E, Meijssen IC, Sleddens HFBM, Dinjens WNM, Boelens MC, Weijers K, Speel EJM, Finn SP, O'Brien C, van Wezel T, Cohen D, Monkhorst K, Roepman P, Dubbink HJ. RET Fluorescence In Situ Hybridization Analysis Is a Sensitive but Highly Unspecific Screening Method for RET Fusions in Lung Cancer. J Thorac Oncol 2021; 16:798-806. [PMID: 33588111 DOI: 10.1016/j.jtho.2021.01.1619] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 09/12/2020] [Revised: 01/09/2021] [Accepted: 01/19/2021] [Indexed: 12/31/2022]
Abstract
INTRODUCTION RET gene fusions are established oncogenic drivers in 1% of NSCLC. Accurate detection of advanced patients with RET fusions is essential to ensure optimal therapy choice. We investigated the performance of fluorescence in situ hybridization (FISH) as a diagnostic test for detecting functional RET fusions. METHODS Between January 2016 and November 2019, a total of 4873 patients with NSCLC were routinely screened for RET fusions using either FISH (n = 2858) or targeted RNA next-generation sequencing (NGS) (n = 2015). If sufficient material was available, positive cases were analyzed by both methods (n = 39) and multiple FISH assays (n = 17). In an independent cohort of 520 patients with NSCLC, whole-genome sequencing data were investigated for disruptive structural variations and functional fusions in the RET and compared with ALK and ROS1 loci. RESULTS FISH analysis revealed RET rearrangement in 48 of 2858 cases; of 30 rearranged cases double tested with NGS, only nine had a functional RET fusion. RNA NGS yielded RET fusions in 14 of 2015 cases; all nine cases double tested by FISH had RET locus rearrangement. Of these 18 verified RET fusion cases, 16 had a split signal and two a complex rearrangement by FISH. By whole-genome sequencing, the prevalence of functional fusions compared with all disruptive events was lower in the RET (4 of 9, 44%) than the ALK (27 of 34, 79%) and ROS1 (9 of 12, 75%) loci. CONCLUSIONS FISH is a sensitive but unspecific technique for RET screening, always requiring a confirmation using an orthogonal technique, owing to frequently occurring RET rearrangements not resulting in functional fusions in NSCLC.
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Affiliation(s)
- Teodora Radonic
- Department of Pathology, Cancer Center Amsterdam, Vrije University, Amsterdam University Medical Center, Amsterdam, The Netherlands.
| | - W R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Kris G Samsom
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Guido M J M Roemen
- Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jan H von der Thüsen
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Erik Thunnissen
- Department of Pathology, Cancer Center Amsterdam, Vrije University, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Isabelle C Meijssen
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Hein F B M Sleddens
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mirjam C Boelens
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karin Weijers
- Department of Pathology, Cancer Center Amsterdam, Vrije University, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Ernst Jan M Speel
- Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands; School for Oncology and Developmental Biology (GROW), Maastricht, The Netherlands
| | - Stephen P Finn
- Department of Histopathology, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Cancer Molecular Diagnostics, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital and Trinity College Dublin, Dublin, Ireland
| | - Cathal O'Brien
- Department of Histopathology, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Cancer Molecular Diagnostics, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital and Trinity College Dublin, Dublin, Ireland
| | - Tom van Wezel
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Danielle Cohen
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kim Monkhorst
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - H J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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9
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Bos MK, Nasserinejad K, Jansen MPHM, Angus L, Atmodimedjo PN, de Jonge E, Dinjens WNM, van Schaik RHN, Del Re M, Dubbink HJ, Sleijfer S, Martens JWM. Comparison of variant allele frequency and number of mutant molecules as units of measurement for circulating tumor DNA. Mol Oncol 2021; 15:57-66. [PMID: 33070443 PMCID: PMC7782075 DOI: 10.1002/1878-0261.12827] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/10/2020] [Accepted: 10/15/2020] [Indexed: 12/26/2022] Open
Abstract
Quantification of tumor-specific variants (TSVs) in cell-free DNA is rapidly evolving as a prognostic and predictive tool in patients with cancer. Currently, both variant allele frequency (VAF) and number of mutant molecules per mL plasma are used as units of measurement to report those TSVs. However, it is unknown to what extent both units of measurement agree and what are the factors underlying an existing disagreement. To study the agreement between VAF and mutant molecules in current clinical studies, we analyzed 1116 TSVs from 338 patients identified with next-generation sequencing (NGS) or digital droplet PCR (ddPCR). On different study cohorts, a Deming regression analysis was performed and its 95% prediction interval was used as surrogate for the limits of agreement between VAF and number of mutant molecules per mL and to identify outliers. VAF and number of mutant molecules per mL plasma yielded greater agreement when using ddPCR than NGS. In case of discordance between VAF and number of mutant molecules per mL, insufficient molecular coverage in NGS and high cell-free DNA concentration were the main responsible factors. We propose several optimization steps needed to bring monitoring of TSVs in cell-free DNA to its full potential.
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Affiliation(s)
- Manouk K. Bos
- Department of Medical OncologyErasmus MC Cancer Institute, University Medical CenterRotterdamThe Netherlands
| | - Kazem Nasserinejad
- Department of HematologyHOVON Data CenterErasmus MC Cancer Institute, University Medical CenterRotterdamThe Netherlands
| | - Maurice P. H. M. Jansen
- Department of Medical OncologyErasmus MC Cancer Institute, University Medical CenterRotterdamThe Netherlands
| | - Lindsay Angus
- Department of Medical OncologyErasmus MC Cancer Institute, University Medical CenterRotterdamThe Netherlands
| | - Peggy N. Atmodimedjo
- Department of PathologyErasmus MC Cancer Institute, University Medical CenterRotterdamThe Netherlands
| | - Evert de Jonge
- Department of Clinical ChemistryErasmus University Medical CenterRotterdamThe Netherlands
| | - Winand N. M. Dinjens
- Department of PathologyErasmus MC Cancer Institute, University Medical CenterRotterdamThe Netherlands
| | - Ron H. N. van Schaik
- Department of Clinical ChemistryErasmus University Medical CenterRotterdamThe Netherlands
| | - Marzia Del Re
- Department of Clinical ChemistryErasmus University Medical CenterRotterdamThe Netherlands
- Unit of Clinical Pharmacology and PharmacogeneticsDepartment of Clinical and Experimental MedicineUniversity Hospital of PisaItaly
| | - Hendrikus J. Dubbink
- Department of PathologyErasmus MC Cancer Institute, University Medical CenterRotterdamThe Netherlands
| | - Stefan Sleijfer
- Department of Medical OncologyErasmus MC Cancer Institute, University Medical CenterRotterdamThe Netherlands
| | - John W. M. Martens
- Department of Medical OncologyErasmus MC Cancer Institute, University Medical CenterRotterdamThe Netherlands
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10
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Steendam CMJ, Veerman GDM, Pruis MA, Atmodimedjo P, Paats MS, van der Leest C, von der Thüsen JH, Yick DCY, Oomen-de Hoop E, Koolen SLW, Dinjens WNM, van Schaik RHN, Mathijssen RHJ, Aerts JGJV, Dubbink HJ, Dingemans AMC. Plasma Predictive Features in Treating EGFR-Mutated Non-Small Cell Lung Cancer. Cancers (Basel) 2020; 12:E3179. [PMID: 33138052 PMCID: PMC7692448 DOI: 10.3390/cancers12113179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/17/2022] Open
Abstract
Although epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) are the preferred treatment for patients with EGFR-mutated non-small cell lung cancer (NSCLC), not all patients benefit. We therefore explored the impact of the presence of mutations found in cell-free DNA (cfDNA) and TKI plasma concentrations during treatment on progression-free survival (PFS). In the prospective START-TKI study blood samples from 41 patients with EGFR-mutated NSCLC treated with EGFR-TKIs were available. Next generation sequencing (NGS) on cfDNA was performed, and plasma TKI concentrations were measured. Patients without complete plasma conversion of EGFR mutation at week 6 had a significantly shorter PFS (5.5 vs. 17.0 months, p = 0.002) and OS (14.0 vs. 25.5 months, p = 0.003) compared to patients with plasma conversion. In thirteen (second line) osimertinib-treated patients with a (plasma or tissue) concomitant TP53 mutation at baseline, PFS was significantly shorter compared to six wild-type cases; 8.8 vs. 18.8 months, p = 0.017. Erlotinib Cmean decrease of ≥10% in the second tertile of treatment was also associated with a significantly shorter PFS; 8.9 vs. 23.6 months, p = 0.037. We obtained evidence that absence of plasma loss of the primary EGFR mutation, isolated plasma p.T790M loss after six weeks, baseline concomitant TP53 mutations, and erlotinib Cmean decrease during treatment are probably related to worse outcome.
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Affiliation(s)
- Christi M. J. Steendam
- Department of Pulmonology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands; (C.M.J.S.); (M.A.P.); (M.S.P.); (J.G.J.V.A.)
- Department of Pulmonology, Amphia Hospital, 4818 CK Breda, The Netherlands;
| | - G. D. Marijn Veerman
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands; (G.D.M.V.); (E.O.-d.H.); (S.L.W.K.); (R.H.J.M.)
| | - Melinda A. Pruis
- Department of Pulmonology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands; (C.M.J.S.); (M.A.P.); (M.S.P.); (J.G.J.V.A.)
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands; (G.D.M.V.); (E.O.-d.H.); (S.L.W.K.); (R.H.J.M.)
| | - Peggy Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands; (P.A.); (J.H.v.d.T.); (W.N.M.D.)
| | - Marthe S. Paats
- Department of Pulmonology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands; (C.M.J.S.); (M.A.P.); (M.S.P.); (J.G.J.V.A.)
| | - Cor van der Leest
- Department of Pulmonology, Amphia Hospital, 4818 CK Breda, The Netherlands;
| | - Jan H. von der Thüsen
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands; (P.A.); (J.H.v.d.T.); (W.N.M.D.)
| | - David C. Y. Yick
- Department of Pathology, Amphia Hospital, 4818 CK Breda, The Netherlands;
| | - Esther Oomen-de Hoop
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands; (G.D.M.V.); (E.O.-d.H.); (S.L.W.K.); (R.H.J.M.)
| | - Stijn L. W. Koolen
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands; (G.D.M.V.); (E.O.-d.H.); (S.L.W.K.); (R.H.J.M.)
| | - Winand N. M. Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands; (P.A.); (J.H.v.d.T.); (W.N.M.D.)
| | - Ron H. N. van Schaik
- Department of Clinical Chemistry, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands;
| | - Ron H. J. Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands; (G.D.M.V.); (E.O.-d.H.); (S.L.W.K.); (R.H.J.M.)
| | - Joachim G. J. V. Aerts
- Department of Pulmonology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands; (C.M.J.S.); (M.A.P.); (M.S.P.); (J.G.J.V.A.)
| | - Hendrikus Jan Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands; (P.A.); (J.H.v.d.T.); (W.N.M.D.)
| | - Anne-Marie C. Dingemans
- Department of Pulmonology, Erasmus MC Cancer Institute, University Medical Center, 3015 GD Rotterdam, The Netherlands; (C.M.J.S.); (M.A.P.); (M.S.P.); (J.G.J.V.A.)
- Department of Pulmonology, Maastricht UMC+, 6229 HX Maastricht, The Netherlands
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11
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van Doeveren T, Nakauma-Gonzalez JA, Mason AS, van Leenders GJLH, Zuiverloon TCM, Zwarthoff EC, Meijssen IC, van der Made AC, van der Heijden AG, Hendricksen K, van Rhijn BWG, Voskuilen CS, van Riet J, Dinjens WNM, Dubbink HJ, van de Werken HJG, Boormans JL. The clonal relation of primary upper urinary tract urothelial carcinoma and paired urothelial carcinoma of the bladder. Int J Cancer 2020; 148:981-987. [PMID: 33006377 PMCID: PMC7821318 DOI: 10.1002/ijc.33327] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 08/06/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022]
Abstract
The risk of developing urothelial carcinoma of the bladder (UCB) in patients treated by radical nephroureterectomy (RNU) for an upper urinary tract urothelial carcinoma (UTUC) is 22% to 47% in the 2 years after surgery. Subject of debate remains whether UTUC and the subsequent UCB are clonally related or represent separate origins. To investigate the clonal relationship between both entities, we performed targeted DNA sequencing of a panel of 41 genes on matched normal and tumor tissue of 15 primary UTUC patients treated by RNU who later developed 19 UCBs. Based on the detected tumor‐specific DNA aberrations, the paired UTUC and UCB(s) of 11 patients (73.3%) showed a clonal relation, whereas in four patients the molecular results did not indicate a clear clonal relationship. Our results support the hypothesis that UCBs following a primary surgically resected UTUC are predominantly clonally derived recurrences and not separate entities. What's new? Patients treated by radical nephroureterectomy for upper urinary tract cancer have an increased risk of developing bladder carcinoma following surgery. It remains unclear, however, whether the upper urinary tract cancer and subsequent bladder carcinoma are clonally related or have separate origins. This targeted DNA sequencing study shows that almost 75% of patients have tumors that are clonally related, suggesting that seeding of tumor cells is the main mechanism of bladder carcinoma development following radical nephroureterectomy. This result underscores the need to minimalize the risk of seeding during surgery and/or diagnostic ureterorenoscopy plus biopsy, and to apply peri‐operative intravesical instillations with chemotherapy.
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Affiliation(s)
- Thomas van Doeveren
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Jose A Nakauma-Gonzalez
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Andrew S Mason
- Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, The University of York, York, UK.,York Biomedical Research Institute, The University of York, York, UK
| | - Geert J L H van Leenders
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Tahlita C M Zuiverloon
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Ellen C Zwarthoff
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Isabelle C Meijssen
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Angelique C van der Made
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Antoine G van der Heijden
- Department of Urology, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Kees Hendricksen
- Department of Urology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Bas W G van Rhijn
- Department of Urology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.,Department of Urology, Caritas St. Josef Medical Center, University of Regensburg, Regensburg, Germany
| | - Charlotte S Voskuilen
- Department of Urology, Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Job van Riet
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Harmen J G van de Werken
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Joost L Boormans
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
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12
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Clarke M, Mackay A, Ismer B, Pickles JC, Tatevossian RG, Newman S, Bale TA, Stoler I, Izquierdo E, Temelso S, Carvalho DM, Molinari V, Burford A, Howell L, Virasami A, Fairchild AR, Avery A, Chalker J, Kristiansen M, Haupfear K, Dalton JD, Orisme W, Wen J, Hubank M, Kurian KM, Rowe C, Maybury M, Crosier S, Knipstein J, Schüller U, Kordes U, Kram DE, Snuderl M, Bridges L, Martin AJ, Doey LJ, Al-Sarraj S, Chandler C, Zebian B, Cairns C, Natrajan R, Boult JKR, Robinson SP, Sill M, Dunkel IJ, Gilheeney SW, Rosenblum MK, Hughes D, Proszek PZ, Macdonald TJ, Preusser M, Haberler C, Slavc I, Packer R, Ng HK, Caspi S, Popović M, Faganel Kotnik B, Wood MD, Baird L, Davare MA, Solomon DA, Olsen TK, Brandal P, Farrell M, Cryan JB, Capra M, Karremann M, Schittenhelm J, Schuhmann MU, Ebinger M, Dinjens WNM, Kerl K, Hettmer S, Pietsch T, Andreiuolo F, Driever PH, Korshunov A, Hiddingh L, Worst BC, Sturm D, Zuckermann M, Witt O, Bloom T, Mitchell C, Miele E, Colafati GS, Diomedi-Camassei F, Bailey S, Moore AS, Hassall TEG, Lowis SP, Tsoli M, Cowley MJ, Ziegler DS, Karajannis MA, Aquilina K, Hargrave DR, Carceller F, Marshall LV, von Deimling A, Kramm CM, Pfister SM, Sahm F, Baker SJ, Mastronuzzi A, Carai A, Vinci M, Capper D, Popov S, Ellison DW, Jacques TS, Jones DTW, Jones C. Infant High-Grade Gliomas Comprise Multiple Subgroups Characterized by Novel Targetable Gene Fusions and Favorable Outcomes. Cancer Discov 2020; 10:942-963. [PMID: 32238360 PMCID: PMC8313225 DOI: 10.1158/2159-8290.cd-19-1030] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 03/03/2020] [Accepted: 03/20/2020] [Indexed: 11/16/2022]
Abstract
Infant high-grade gliomas appear clinically distinct from their counterparts in older children, indicating that histopathologic grading may not accurately reflect the biology of these tumors. We have collected 241 cases under 4 years of age, and carried out histologic review, methylation profiling, and custom panel, genome, or exome sequencing. After excluding tumors representing other established entities or subgroups, we identified 130 cases to be part of an "intrinsic" spectrum of disease specific to the infant population. These included those with targetable MAPK alterations, and a large proportion of remaining cases harboring gene fusions targeting ALK (n = 31), NTRK1/2/3 (n = 21), ROS1 (n = 9), and MET (n = 4) as their driving alterations, with evidence of efficacy of targeted agents in the clinic. These data strongly support the concept that infant gliomas require a change in diagnostic practice and management. SIGNIFICANCE: Infant high-grade gliomas in the cerebral hemispheres comprise novel subgroups, with a prevalence of ALK, NTRK1/2/3, ROS1, or MET gene fusions. Kinase fusion-positive tumors have better outcome and respond to targeted therapy clinically. Other subgroups have poor outcome, with fusion-negative cases possibly representing an epigenetically driven pluripotent stem cell phenotype.See related commentary by Szulzewsky and Cimino, p. 904.This article is highlighted in the In This Issue feature, p. 890.
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Affiliation(s)
- Matthew Clarke
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Alan Mackay
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Britta Ismer
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Jessica C Pickles
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Ruth G Tatevossian
- Department of Neuropathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Tejus A Bale
- Department of Neuropathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Iris Stoler
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany
| | - Elisa Izquierdo
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Sara Temelso
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Diana M Carvalho
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Valeria Molinari
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Anna Burford
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Louise Howell
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Alex Virasami
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Amy R Fairchild
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Aimee Avery
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Jane Chalker
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Mark Kristiansen
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Kelly Haupfear
- Department of Neuropathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - James D Dalton
- Department of Neuropathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Wilda Orisme
- Department of Neuropathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ji Wen
- Department of Neuropathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael Hubank
- Molecular Diagnostics, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom
| | - Kathreena M Kurian
- Brain Tumour Research Centre, University of Bristol, Bristol, United Kingdom
| | - Catherine Rowe
- Brain Tumour Research Centre, University of Bristol, Bristol, United Kingdom
| | - Mellissa Maybury
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Australia
- Oncology Service, Queensland Children's Hospital, Brisbane, Australia
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
| | - Stephen Crosier
- Newcastle Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - Jeffrey Knipstein
- Division of Pediatric Hematology/Oncology/BMT, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Ulrich Schüller
- Department of Neuropathology, University Hospital Hamburg-Eppendorf, and Research Institute Children's Cancer Center, Hamburg, Germany
- Pediatric Hematology and Oncology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Uwe Kordes
- Pediatric Hematology and Oncology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - David E Kram
- Section of Pediatric Hematology-Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Matija Snuderl
- Department of Neuropathology, NYU Langone Health, New York, New York
| | - Leslie Bridges
- Department of Neuropathology, St George's Hospital NHS Trust, London, United Kingdom
| | - Andrew J Martin
- Department of Neurosurgery, St George's Hospital NHS Trust, London, United Kingdom
| | - Lawrence J Doey
- Department of Clinical Neuropathology, Kings College Hospital NHS Trust, London, United Kingdom
| | - Safa Al-Sarraj
- Department of Clinical Neuropathology, Kings College Hospital NHS Trust, London, United Kingdom
| | - Christopher Chandler
- Department of Neurosurgery, Kings College Hospital NHS Trust, London, United Kingdom
| | - Bassel Zebian
- Department of Neurosurgery, Kings College Hospital NHS Trust, London, United Kingdom
| | - Claire Cairns
- Department of Neurosurgery, Kings College Hospital NHS Trust, London, United Kingdom
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Jessica K R Boult
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
| | - Simon P Robinson
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
| | - Martin Sill
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ira J Dunkel
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Stephen W Gilheeney
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Marc K Rosenblum
- Department of Neuropathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Debbie Hughes
- Molecular Diagnostics, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom
| | - Paula Z Proszek
- Molecular Diagnostics, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom
| | - Tobey J Macdonald
- Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Matthias Preusser
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christine Haberler
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Roger Packer
- Center for Neuroscience and Behavioural Medicine, Children's National Medical Center, Washington, DC
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, China
| | - Shani Caspi
- Cancer Research Center, Sheba Medical Center, Tel Aviv, Israel
| | - Mara Popović
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Barbara Faganel Kotnik
- Department of Hematology and Oncology, University Children's Hospital, Ljubljana, Slovenia
| | - Matthew D Wood
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Lissa Baird
- Department of Neurosurgery, Oregon Health & Science University, Portland, Oregon
| | - Monika Ashok Davare
- Department of Pediatrics, Oregon Health & Science University, Portland, Oregon
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, California
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, California
| | - Thale Kristin Olsen
- Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden
| | - Petter Brandal
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Michael Farrell
- Department of Histopathology, Beaumont Hospital, Dublin, Ireland
| | - Jane B Cryan
- Department of Histopathology, Beaumont Hospital, Dublin, Ireland
| | - Michael Capra
- Paediatric Oncology, Our Lady's Children's Hospital, Dublin, Ireland
| | - Michael Karremann
- Department of Pediatrics, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jens Schittenhelm
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Germany
| | | | - Martin Ebinger
- Department of Pediatric Hematology and Oncology, University Hospital Tübingen, Germany
| | - Winand N M Dinjens
- Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Hospital Muenster, Germany
| | - Simone Hettmer
- Department of Pediatric Hematology and Oncology, University Hospital Freiburg, Germany
| | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn Medical Center, Bonn, Germany
| | - Felipe Andreiuolo
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn Medical Center, Bonn, Germany
| | - Pablo Hernáiz Driever
- Department of Paediatric Haematology/Oncology Charité Universitätsmedizin, Berlin, Germany
| | - Andrey Korshunov
- Department of Neuropathology, University Hospital Heidelberg, Germany
| | - Lotte Hiddingh
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara C Worst
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Dominik Sturm
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marc Zuckermann
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Olaf Witt
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Tabitha Bloom
- BRAIN UK, University of Southampton, Southampton, United Kingdom
| | - Clare Mitchell
- BRAIN UK, University of Southampton, Southampton, United Kingdom
| | - Evelina Miele
- Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Giovanna Stefania Colafati
- Oncological Neuroradiology Unit, Department of Diagnostic Imaging, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | | | - Simon Bailey
- Newcastle Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - Andrew S Moore
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Australia
- Oncology Service, Queensland Children's Hospital, Brisbane, Australia
- Child Health Research Centre, The University of Queensland, South Brisbane, Australia
| | - Timothy E G Hassall
- Oncology Service, Queensland Children's Hospital, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Stephen P Lowis
- Brain Tumour Research Centre, University of Bristol, Bristol, United Kingdom
| | - Maria Tsoli
- Children's Cancer Institute, University of New South Wales, Sydney, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia
| | - Mark J Cowley
- Children's Cancer Institute, University of New South Wales, Sydney, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia
| | - David S Ziegler
- Children's Cancer Institute, University of New South Wales, Sydney, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, Australia
| | - Matthias A Karajannis
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Kristian Aquilina
- Department of Neurosurgery, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Darren R Hargrave
- Department of Paediatric Oncology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Fernando Carceller
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children & Young People's Unit, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom
| | - Lynley V Marshall
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children & Young People's Unit, Royal Marsden Hospital NHS Trust, Sutton, United Kingdom
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christof M Kramm
- Division of Pediatric Hematology and Oncology, University Medical Centre Göttingen, Germany
| | - Stefan M Pfister
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Department of Paediatric Haematology/Oncology Charité Universitätsmedizin, Berlin, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Suzanne J Baker
- Department of Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Angela Mastronuzzi
- Neuro-oncology Unit, Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Andrea Carai
- Oncological Neurosurgery Unit, Department of Neuroscience and Neurorehabilitation, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Maria Vinci
- Department of Onco-haematology, Cell and Gene Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - David Capper
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sergey Popov
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
- Department of Pathology, University of Wales Hospital NHS Trust, Cardiff, United Kingdom
| | - David W Ellison
- Department of Neuropathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Thomas S Jacques
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom.
| | - David T W Jones
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Chris Jones
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom.
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13
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den Bakker MA, den Toom DT, Damen THC, Sleddens HFBM, Meijssen IC, Deloose S, Kliffen M, Dinjens WNM. Anisometric Cell and Dysplastic Lipomas in a Retinoblastoma Patient. Int J Surg Pathol 2020; 28:793-798. [PMID: 32362169 DOI: 10.1177/1066896920917220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Anisometric cell lipoma (ACL) and dysplastic lipoma (DL) are underrecognized subtypes of benign lipomatous tumors, with wide variation in cell size, microscopic fat necrosis, and no or mild nuclear changes (DL). ACL/DL appear more commonly in retinoblastoma patients, in whom an increased incidence of lipomas has been established. The occurrence of ACL/DL in retinoblastoma patients suggests that RB1 aberrations play a role in its pathogenesis, similar to spindle cell/pleomorphic lipoma. In this article, we present a patient with a history of retinoblastoma with multiple lipomas histologically consistent with ACL/DL. Analysis of the lipomas supports involvement of RB1 in the development of ACL/DL. Dysplastic changes were only seen in a single lipoma, which harbored an additional TP53 mutation. While providing further support for the occurrence of ACL/DL in retinoblastoma patients, we also suggest that DL is an ACL with TP53 mutation.
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Affiliation(s)
- Michael A den Bakker
- Maasstad Hospital, Rotterdam, Netherlands.,Erasmus MC Cancer Institute, Rotterdam, Netherlands
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14
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Goverde A, Eikenboom EL, Viskil EL, Bruno MJ, Doukas M, Dinjens WNM, Dubbink EJ, van den Ouweland AMW, Hofstra RMW, Wagner A, Spaander MCW. Yield of Lynch Syndrome Surveillance for Patients With Pathogenic Variants in DNA Mismatch Repair Genes. Clin Gastroenterol Hepatol 2020; 18:1112-1120.e1. [PMID: 31470178 DOI: 10.1016/j.cgh.2019.08.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/19/2019] [Accepted: 08/02/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Patients with Lynch syndrome are offered the same colorectal cancer (CRC) surveillance programs (colonoscopy every 2 years), regardless of the pathogenic DNA mismatch repair gene variant the patient carries. We aimed to assess the yield of surveillance for patients with these variants in MLH1, MSH2, MSH6, and PMS2. METHODS We analyzed data on colonoscopy surveillance, including histopathology analysis, from all patients diagnosed with Lynch syndrome (n = 264) at a single center. We compared the development of (advanced) adenomas and CRC among patients with pathogenic variants in the DNA mismatch repair genes MLH1 (n = 55), MSH2 (n = 44), MSH6 (n = 143), or PMS2 (n = 22) over 1836 years of follow-up (median follow-up of 6 years per patient). RESULTS At first colonoscopy, CRC was found in 8 patients. During 916 follow-up colonoscopies, CRC was found in 9 patients. No CRC was found in patients with variants in MSH6 or PMS2 over the entire follow-up period. There were no significant differences in the number of colonoscopies with adenomas or advanced adenomas among the groups. The median time of adenoma development was 3 years (IQR, 2-6 years). There were no significant differences in time to development of adenoma. However, patients with variants in MSH6 had a significant longer time to development of advanced neoplasia (advanced adenoma or CRC) than patients in the other groups. Six carriers died during follow up (5 from cancer, of which 3 from pancreatic cancer). CONCLUSIONS No CRC was found during follow-up of patients with Lynch syndrome carrying pathogenic variants in MSH6; advanced neoplasia developed over shorter follow-up time periods in patients with pathogenic variants in MLH1 or MSH2. The colonoscopy interval for patients with pathogenic variants in MSH6 might be increased to 3 years from the regular 2-year interval.
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Affiliation(s)
- Anne Goverde
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ellis L Eikenboom
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ellemieke L Viskil
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marco J Bruno
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Michael Doukas
- Department of Pathology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Erik Jan Dubbink
- Department of Pathology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ans M W van den Ouweland
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Robert M W Hofstra
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Manon C W Spaander
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands.
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15
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Agahozo MC, Timmermans MAM, Sleddens HFBM, Foekens R, Trapman-Jansen AMAC, Schröder CP, van Leeuwen-Stok E, Martens JWM, N. M. Dinjens W, van Deurzen CHM. Loss of Y-Chromosome during Male Breast Carcinogenesis. Cancers (Basel) 2020; 12:cancers12030631. [PMID: 32182822 PMCID: PMC7139680 DOI: 10.3390/cancers12030631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 01/16/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 01/18/2023] Open
Abstract
Loss of Y-chromosome (LOY) is associated with increased cancer mortality in males. The prevalence of LOY in male breast cancer (BC) is unknown. The aim of this study is to assess the presence and prognostic effect of LOY during male BC progression. We included male BC patients diagnosed between 1989 and 2009 (n = 796). A tissue microarray (TMA) was constructed to perform immunohistochemistry and fluorescent in situ hybridization (FISH), using an X and Y probe. We also performed this FISH on a selected number of patients using whole tissue slides to study LOY during progression from ductal carcinoma in situ (DCIS) to invasive BC. In total, LOY was present in 12.7% (n = 92) of cases, whereby LOY was associated with ER and PR negative tumors (p = 0.017 and p = 0.01). LOY was not associated with the outcome. Using whole slides including invasive BC and adjacent DCIS (n = 22), we detected a concordant LOY status between both components in 17 patients. In conclusion, LOY is an early event in male breast carcinogenesis, which generally starts at the DCIS stage and is associated with ER and PR negative tumors.
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Affiliation(s)
- Marie Colombe Agahozo
- Department of Pathology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.C.A.); (H.F.B.M.S.); (W.N.M.D.)
| | - Mieke A. M. Timmermans
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015GD Rotterdam, The Netherlands; (M.A.M.T.); (R.F.); (A.M.A.C.T.-J.); (J.W.M.M.)
| | - Hein F. B. M. Sleddens
- Department of Pathology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.C.A.); (H.F.B.M.S.); (W.N.M.D.)
| | - Renée Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015GD Rotterdam, The Netherlands; (M.A.M.T.); (R.F.); (A.M.A.C.T.-J.); (J.W.M.M.)
| | - Anita M. A. C. Trapman-Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015GD Rotterdam, The Netherlands; (M.A.M.T.); (R.F.); (A.M.A.C.T.-J.); (J.W.M.M.)
| | - Carolien P. Schröder
- Department of Medical Oncology, University Medical Center Groningen, 9700AB Groningen, The Netherlands
| | - Elise van Leeuwen-Stok
- Dutch Breast Cancer Research Group, BOOG Study Center, 1006 AE Amsterdam, The Netherlands;
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015GD Rotterdam, The Netherlands; (M.A.M.T.); (R.F.); (A.M.A.C.T.-J.); (J.W.M.M.)
| | - Winand N. M. Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.C.A.); (H.F.B.M.S.); (W.N.M.D.)
| | - Carolien H. M. van Deurzen
- Department of Pathology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.C.A.); (H.F.B.M.S.); (W.N.M.D.)
- Correspondence: ; Tel.: +31-107043901
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16
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Vitale SR, Groenendijk FH, van Marion R, Beaufort CM, Helmijr JC, Jan Dubbink H, N. M. Dinjens W, Ewing-Graham PC, Smolders R, van Doorn HC, Boere IA, Berns EMJJ, Helleman J, Jansen MPHM. TP53 Mutations in Serum Circulating Cell-Free Tumor DNA As Longitudinal Biomarker for High-Grade Serous Ovarian Cancer. Biomolecules 2020; 10:biom10030415. [PMID: 32156073 PMCID: PMC7175353 DOI: 10.3390/biom10030415] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/06/2020] [Accepted: 03/05/2020] [Indexed: 12/30/2022] Open
Abstract
The aim of this study was to determine an optimal workflow to detect TP53 mutations in baseline and longitudinal serum cell free DNA (cfDNA) from high-grade serous ovarian carcinomas (HGSOC) patients and to define whether TP53 mutations are suitable as biomarker for disease. TP53 was investigated in tissue and archived serum from 20 HGSOC patients by a next-generation sequencing (NGS) workflow alone or combined with digital PCR (dPCR). AmpliSeq™-focused NGS panels and customized dPCR assays were used for tissue DNA and longitudinal cfDNAs, and Oncomine NGS panel with molecular barcoding was used for baseline cfDNAs. TP53 missense mutations were observed in 17 tissue specimens and in baseline cfDNA for 4/8 patients by AmpliSeq, 6/9 patients by Oncomine, and 4/6 patients by dPCR. Mutations in cfDNA were detected in 4/6 patients with residual disease and 3/4 patients with disease progression within six months, compared to 5/11 patients with no residual disease and 6/13 patients with progression after six months. Finally, mutations were detected at progression in 5/6 patients, but not during chemotherapy. NGS with molecular barcoding and dPCR were most optimal workflows to detect TP53 mutations in baseline and longitudinal serum cfDNA, respectively. TP53 mutations were undetectable in cfDNA during treatment but re-appeared at disease progression, illustrating its promise as a biomarker for disease monitoring.
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Affiliation(s)
- Silvia R. Vitale
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico-Vittorio Emanuele, 95123 Catania, Italy
- Correspondence: ; Tel.: +39-095-3781946
| | - Floris H. Groenendijk
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Corine M. Beaufort
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Jean C. Helmijr
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Hendrikus Jan Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Winand N. M. Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Patricia C. Ewing-Graham
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (F.H.G.); (R.v.M.); (H.J.D.); (W.N.M.D.); (P.C.E.-G.)
| | - Ramon Smolders
- Department of Gynaecology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (R.S.); (H.C.v.D.)
| | - Helena C. van Doorn
- Department of Gynaecology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (R.S.); (H.C.v.D.)
| | - Ingrid A. Boere
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Els M. J. J. Berns
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Jozien Helleman
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
| | - Maurice P. H. M. Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands; (C.M.B.); (J.C.H.); (I.A.B.); (E.M.J.J.B.); (J.H.); (M.P.H.M.J.)
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17
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Van Bockstal MR, Agahozo MC, van Marion R, Atmodimedjo PN, Sleddens HFBM, Dinjens WNM, Visser LL, Lips EH, Wesseling J, van Deurzen CHM. Somatic mutations and copy number variations in breast cancers with heterogeneous HER2 amplification. Mol Oncol 2020; 14:671-685. [PMID: 32058674 PMCID: PMC7138394 DOI: 10.1002/1878-0261.12650] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 12/08/2019] [Revised: 01/13/2020] [Accepted: 02/13/2020] [Indexed: 12/14/2022] Open
Abstract
Intratumour heterogeneity fuels carcinogenesis and allows circumventing specific targeted therapies. HER2 gene amplification is associated with poor outcome in invasive breast cancer. Heterogeneous HER2 amplification has been described in 5–41% of breast cancers. Here, we investigated the genetic differences between HER2‐positive and HER2‐negative admixed breast cancer components. We performed an in‐depth analysis to explore the potential heterogeneity in the somatic mutational landscape of each individual tumour component. Formalin‐fixed, paraffin‐embedded breast cancer tissue of ten patients with at least one HER2‐negative and at least one HER2‐positive component was microdissected. Targeted next‐generation sequencing was performed using a customized 53‐gene panel. Somatic mutations and copy number variations were analysed. Overall, the tumours showed a heterogeneous distribution of 12 deletions, 9 insertions, 32 missense variants and 7 nonsense variants in 26 different genes, which are (likely) pathogenic. Three splice site alterations were identified. One patient had an EGFR copy number gain restricted to a HER2‐negative in situ component, resulting in EGFR protein overexpression. Two patients had FGFR1 copy number gains in at least one tumour component. Two patients had an 8q24 gain in at least one tumour component, resulting in a copy number increase in MYC and PVT1. One patient had a CCND1 copy number gain restricted to a HER2‐negative tumour component. No common alternative drivers were identified in the HER2‐negative tumour components. This series of 10 breast cancers with heterogeneous HER2 gene amplification illustrates that HER2 positivity is not an unconditional prerequisite for the maintenance of tumour growth. Many other molecular aberrations are likely to act as alternative or collaborative drivers. This study demonstrates that breast carcinogenesis is a dynamically evolving process characterized by a versatile somatic mutational profile, of which some genetic aberrations will be crucial for cancer progression, and others will be mere ‘passenger’ molecular anomalies.
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Affiliation(s)
| | | | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute Rotterdam, The Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute Rotterdam, The Netherlands
| | - Hein F B M Sleddens
- Department of Pathology, Erasmus MC Cancer Institute Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute Rotterdam, The Netherlands
| | - Lindy L Visser
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Esther H Lips
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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18
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Liebrechts-Akkerman G, Liu F, van Marion R, Dinjens WNM, Kayser M. Explaining sudden infant death with cardiac arrhythmias: Complete exon sequencing of nine cardiac arrhythmia genes in Dutch SIDS cases highlights new and known DNA variants. Forensic Sci Int Genet 2020; 46:102266. [PMID: 32145446 DOI: 10.1016/j.fsigen.2020.102266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 07/13/2019] [Revised: 01/23/2020] [Accepted: 02/26/2020] [Indexed: 01/11/2023]
Abstract
Previous studies suggested that Sudden Infant Death Syndrome (SIDS) can partially be genetically explained by cardiac arrhythmias; however, the number of individuals and populations investigated remain limited. We report the first SIDS study on cardiac arrhythmias genes from the Netherlands, a country with the lowest SIDS incidence likely due to parent education on awareness of environmental risk factors. By using targeted massively parallel sequencing (MPS) in 142 Dutch SIDS cases, we performed a complete exon screening of all 173 exons from 9 cardiac arrhythmias genes SCN5A, KCNQ1, KCNH2, KCNE1, KCNE2, CACNA1C, CAV3, ANK2 and KCNJ2 (∼34,000 base pairs), that were selected to harbour previously established SIDS-associated DNA variants. Motivated by the poor DNA quality from the paraffin embedded material used, the application of a conservative sequencing quality control protocol resulted in 102 SIDS cases surviving quality control. Amongst the 102 SIDS cases, we identified a total of 40 DNA variants in 8 cardiac arrhythmia genes found in 60 (58.8 %) cases. Statistical analyses using ancestry-adjusted reference population data and multiple test correction revealed that 13 (32.5 %) of the identified DNA variants in 6 cardiac arrhythmia genes were significantly associated with SIDS, which were observed in 15 (14.7 %) SIDS cases. These 13, and another three, DNA variants were classified as likely pathogenic for cardiac arrhythmias using the American College of Medical Genetics guidelines for interpretation of sequence variants. The 16 likely pathogenic DNA variants were found in 16 (15.7 %) SIDS cases, including i) 3 novel DNA variants not recorded in public databases ii) 7 known DNA variants for which significant SIDS association established here was previously unknown, and iii) 6 known DNA variants for which LQTS association was reported previously. By having replicated previously reported SIDS-associated DNA variants located in cardiac arrhythmia genes and by having highlighting novel SIDS-associated DNA variants in such genes, our findings provide additional empirical evidence for the partial genetic explanation of SIDS by cardiac arrhythmias. On a wider note, our study outcome stresses the need for routine post-mortem genetic screening of assumed SIDS cases, particularly for cardiac arrhythmia genes. When put in practise, it will allow preventing further sudden deaths (not only in infants) in the affected families, thereby allowing forensic molecular autopsy not only to provide answers on the cause of death, but moreover to save lives.
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Affiliation(s)
- Germaine Liebrechts-Akkerman
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Pathology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ronald van Marion
- Department of Pathology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands.
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19
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Mankor JM, Paats MS, Groenendijk FH, Roepman P, Dinjens WNM, Dubbink HJ, Sleijfer S, Cuppen E, Lolkema MPJK. Impact of panel design and cut-off on tumour mutational burden assessment in metastatic solid tumour samples. Br J Cancer 2020; 122:953-956. [PMID: 32094484 PMCID: PMC7109082 DOI: 10.1038/s41416-020-0762-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 07/19/2019] [Revised: 01/10/2020] [Accepted: 02/04/2020] [Indexed: 01/07/2023] Open
Abstract
Tumour mutational burden (TMB) has emerged as a promising biomarker to predict immune checkpoint inhibitors (ICIs) response in advanced solid cancers. However, harmonisation of TMB reporting by targeted gene panels is lacking, especially in metastatic tumour samples. To address this issue, we used data of 2841 whole-genome sequenced metastatic cancer biopsies to perform an in silico analysis of TMB determined by seven gene panels (FD1CDx, MSK-IMPACT™, Caris Molecular Intelligence, Tempus xT, Oncomine Tumour Mutation Load, NeoTYPE Discovery Profile and CANCERPLEX) compared to exome-based TMB as a golden standard. Misclassification rates declined from up to 30% to <1% when the cut-point for high TMB was increased. Receiver operating characteristic analysis demonstrated that, for correct classification, the cut-point for each gene panel may vary more than 20%. In conclusion, we here demonstrate that a major limitation for the use of gene panels is inter-assay variation and the need for dynamic thresholds to compare TMB outcomes.
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Affiliation(s)
- Joanne M Mankor
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Marthe S Paats
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands.
| | | | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | | | | | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands.,Center for Personalized Cancer Treatment, Amsterdam, The Netherlands
| | | | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, The Netherlands.,Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, The Netherlands
| | - Martijn P J K Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands.,Center for Personalized Cancer Treatment, Amsterdam, The Netherlands
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20
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van den Broek D, Hiltermann TJN, Biesma B, Dinjens WNM, 't Hart NA, Hinrichs JWJ, Leers MPG, Monkhorst K, van Oosterhout M, Scharnhorst V, Schuuring E, Speel EJM, van den Heuvel MM, van Schaik RHN, von der Thüsen J, Willems SM, de Visser L, Ligtenberg MJL. Implementation of Novel Molecular Biomarkers for Non-small Cell Lung Cancer in the Netherlands: How to Deal With Increasing Complexity. Front Oncol 2020; 9:1521. [PMID: 32039011 PMCID: PMC6987414 DOI: 10.3389/fonc.2019.01521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/17/2019] [Indexed: 12/30/2022] Open
Abstract
The diagnostic landscape of non-small cell lung cancer (NSCLC) is changing rapidly with the availability of novel treatments. Despite high-level healthcare in the Netherlands, not all patients with NSCLC are tested with the currently relevant predictive tumor markers that are necessary for optimal decision-making for today's available targeted or immunotherapy. An expert workshop on the molecular diagnosis of NSCLC involving pulmonary oncologists, clinical chemists, pathologists, and clinical scientists in molecular pathology was held in the Netherlands on December 10, 2018. The aims of the workshop were to facilitate cross-disciplinary discussions regarding standards of practice, and address recent developments and associated challenges that impact future practice. This paper presents a summary of the discussions and consensus opinions of the workshop participants on the initial challenges of harmonization of the detection and clinical use of predictive markers of NSCLC. A key theme identified was the need for broader and active participation of all stakeholders involved in molecular diagnostic services for NSCLC, including healthcare professionals across all disciplines, the hospitals and clinics involved in service delivery, healthcare insurers, and industry groups involved in diagnostic and treatment innovations. Such collaboration is essential to integrate different technologies into molecular diagnostics practice, to increase nationwide patient access to novel technologies, and to ensure consensus-preferred biomarkers are tested.
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Affiliation(s)
- Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - T. Jeroen N. Hiltermann
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Bonne Biesma
- Department of Pulmonary Diseases, Jeroen Bosch Hospital, 's-Hertogenbosch, Netherlands
| | - Winand N. M. Dinjens
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Nils A. 't Hart
- Department of Pathology, Isala Klinieken, Zwolle, Netherlands
| | - John W. J. Hinrichs
- Symbiant Pathology Expert Centre, Alkmaar, Netherlands
- Department of Pathology, University Medical Center, Utrecht, Netherlands
| | - Mathie P. G. Leers
- Department of Clinical Chemistry, Zuyderland Medical Center, Sittard-Geleen, Netherlands
| | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Ernst-Jan M. Speel
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | | | - Ron H. N. van Schaik
- Department of Clinical Chemistry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jan von der Thüsen
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Stefan M. Willems
- Department of Pathology, University Medical Center, Utrecht, Netherlands
| | | | - Marjolijn J. L. Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
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21
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van der Wilk BJ, Noordman BJ, Atmodimedjo PN, Dinjens WNM, Laheij RJF, Wagner A, Wijnhoven BPL, van Lanschot JJB. Development of esophageal squamous cell cancer in patients with FAMMM syndrome: Two clinical reports. Eur J Med Genet 2020; 63:103840. [PMID: 31923587 DOI: 10.1016/j.ejmg.2020.103840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 09/26/2019] [Revised: 12/10/2019] [Accepted: 01/05/2020] [Indexed: 12/20/2022]
Abstract
Familial atypical multiple mole melanoma (FAMMM) syndrome is a hereditary syndrome characterized by multiple dysplastic nevi and melanoma. Patients with FAMMM may have a heterozygous, inactivating, pathogenic germline variant in the CDKN2A gene, especially the NM_000077.4: c.225_243del19 (p.p75fs) variant, also known as p16-Leiden variant. Patients with this variant are at high risk for developing melanomas and pancreatic cancer due to somatic inactivation of the wild-type CDKN2A allele. The combination of an inactivating germline CDKN2A mutation and somatic inactivation of the wild-type CDKN2A allele in the same cell results in tumor formation. It has been suggested that carriers of a germline CDKN2A mutation are also at increased risk for several other cancer types, including esophageal cancer. Here, we describe two unrelated patients with the p16-Leiden variant who developed esophageal squamous cell cancer. Evidence of loss of the wild-type CDKN2A allele was obtained in the tumor tissue of both patients indicating biallelic inactivation of p16 in the tumor cells. These results suggest that these patients developed esophageal squamous cell cancer in the context of FAMMM syndrome.
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Affiliation(s)
- Berend J van der Wilk
- Department of Surgery, Erasmus MC - University Medical Center, Rotterdam, the Netherlands.
| | - Bo J Noordman
- Department of Surgery, Erasmus MC - University Medical Center, Rotterdam, the Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute - Erasmus University Medical Center Rotterdam, the Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute - Erasmus University Medical Center Rotterdam, the Netherlands
| | - Robert J F Laheij
- Department of Gastroenterology and Hepatology, Elisabeth - Tweesteden Hospital, Tilburg, the Netherlands
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus MC Cancer Institute - Erasmus University Medical Center Rotterdam, the Netherlands
| | - Bas P L Wijnhoven
- Department of Surgery, Erasmus MC - University Medical Center, Rotterdam, the Netherlands
| | - J Jan B van Lanschot
- Department of Surgery, Erasmus MC - University Medical Center, Rotterdam, the Netherlands
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22
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Meijer TG, Verkaik NS, van Deurzen CHM, Dubbink HJ, den Toom TD, Sleddens HFBM, De Hoop EO, Dinjens WNM, Kanaar R, van Gent DC, Jager A. Direct Ex Vivo Observation of Homologous Recombination Defect Reversal After DNA-Damaging Chemotherapy in Patients With Metastatic Breast Cancer. JCO Precis Oncol 2019; 3:1-12. [PMID: 35100677 DOI: 10.1200/po.18.00268] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Biomarkers that predict response to poly (ADP-ribose) polymerase inhibitors (PARPis) are required to detect PARPi sensitivity beyond germline BRCA-mutated (gBRCAm) cancers and PARPi resistance among reverted gBRCAm cancers. Therefore, we previously developed the Repair Capacity (RECAP) test, a functional homologous recombination (HR) assay that exploits the formation of RAD51 foci in proliferating cells after ex vivo irradiation of fresh primary breast cancer tissue. The aim of the current study was to validate the feasibility of this test on histologic biopsy specimens from metastatic breast cancer and to explore the utility of the RECAP test as a predictive tool for treatment with DNA-damaging agents, such as PARPis. METHODS Fresh tissue biopsies from easily accessible metastatic lesions from patients with locally advanced or metastatic breast cancer were irradiated with 5 Gy and cultured for 2 hours followed by detection of RAD51 foci presence (HR proficient) or absence (HR deficient [HRD]). HRD biopsy specimens as well as platinum/PARP-resistant specimens were subjected to BRCA1/2 sequencing. RESULTS RECAP had a success rate of 93% on biopsy specimens from metastatic breast cancer lesions (n = 44). Although HRD was detected in 13 (32%) of 41 specimens, only five showed a gBRCAm. In three patients with gBRCAm, post-treatment RECAP tests showed HR phenotype reversion after in vivo progressive disease on platinum and PARPi treatment, which was explained in one patient by a secondary BRCA1 mutation. CONCLUSION The RECAP test, which reflects real-time HR status regardless of BRCA mutations, is feasible in metastatic breast cancer biopsy specimens. Compared with gBRCA analysis, it may identify twice as many candidates for PARPi treatment.
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Affiliation(s)
- Titia G Meijer
- Erasmus MC-University Medical Center, Rotterdam, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Nicole S Verkaik
- Erasmus MC-University Medical Center, Rotterdam, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | | | | | | | | | | | | | - Roland Kanaar
- Erasmus MC-University Medical Center, Rotterdam, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Dik C van Gent
- Erasmus MC-University Medical Center, Rotterdam, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Agnes Jager
- Erasmus MC Cancer Institute, Rotterdam, the Netherlands
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23
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Pruis M, Geurts WRR, Thüsen JHVD, Meijssen IC, Dinjens WNM, Aerts JGJV, Lolkema MP, Dubbink HJ, Paats MS. Abstract B136: Highly accurate DNA-based detection of MET exon 14 skipping mutations in non-small cell lung cancer and clinical response upon targeted treatment. Mol Cancer Ther 2019. [DOI: 10.1158/1535-7163.targ-19-b136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Approximately 1.6%-5.7% of non-small cell lung cancers (NSCLC) are described to be driven by oncogenic MET exon 14 skipping mutations (METex14del). Although currently no therapy is registered specifically against METex14del, Phase I/II clinical trials and named patient based programs with cMET inhibitors show promising results. RNA-based analysis seems most optimal for METex14del detection, because theoretically, it would capture all MET exon 13-exon 15 fusions, regardless of the underlying DNA changes. However, acquiring sufficient RNA is often problematic. An alternative is DNA-based analysis, but commercially available DNA-based panels only detect up to 63% of known METex14del alterations. The goal of this study is to describe an optimized DNA-based diagnostic test for METex14del, and to report the histologic and clinical features of a real world METex14del non-squamous NSCLC patient cohort, including follow-up of patients treated with cMET-targeted therapy and consequent resistance mechanisms to cMET inhibition. Methods: Routine diagnostic pathology NSCLC FFPE specimens were investigated by a custom-made DNA-based targeted amplicon-based next generation sequencing (NGS) panel which includes 4 amplicons for METex14del detection. Retrospectively, histopathological characteristics and clinical follow up were investigated for advanced NSCLC with METex14del. We only present data of patients receiving crizotinib in a named patient based program (Pfizer Oncology). Results: In silico analysis showed that our custom-made NGS panel can detect 96% of reported METex14 alterations. From Jan 2016 - May 2018, METex14del was found in 2% of patients with NSCLC tested for therapeutic purposes (31/1496). Outside above mentioned timeframe and tested for other purposes, an additional 15 patients were detected, making a total of 46 NSCLC patients with METex14del, since introduction of our panel in May 2015. Adenocarcinoma was the most common histological type (31/46, 68.9%), followed by sarcomatoid carcinoma (8/46, 17.8%). Thirty-six patients had advanced NSCLC, they were predominantly male (69% vs 31%) and mostly (ex) smokers (64% vs 31%), with a median age of 76.5 years at disease onset [range 53-90]. Eleven patients were treated with targeted therapy, either with crizotinib in named patient based program or in clinical trials. With crizotinib, disease control was achieved for 4 out of 5 patients (3 PR [PFS 4 -12 mo], 1 SD [14 mo]). Biopsy at progression revealed a resistance mechanism (MET c.3682G>A; p.D1228N) to crizotinib in two patients, respectively, 6 and 12 months after start of crizotinib treatment. Conclusions: In this study, we show that we can detect 96% of the known MET exon 14 skipping mutations using our custom-made DNA based NGS approach for DNA isolated from FFPE tissue. In this large consecutive series, METex14del was found in 2% of NSCLC, mostly elderly patients, in a good condition and with a smoking history. Although a small cohort, patients responded well to targeted treatment, underlining the need for routine testing of METex14del in advanced non-squamous NSCLC to guarantee optimal personalized treatment.
Citation Format: Melinda Pruis, WRR Geurts, JH von der Thüsen, IC Meijssen, WNM Dinjens, JGJV Aerts, MP Lolkema, HJ Dubbink, MS Paats. Highly accurate DNA-based detection of MET exon 14 skipping mutations in non-small cell lung cancer and clinical response upon targeted treatment [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B136. doi:10.1158/1535-7163.TARG-19-B136
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24
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Pruis MA, Geurts-Giele WRR, von der TJH, Meijssen IC, Dinjens WNM, Aerts JGJV, Dingemans AMC, Lolkema MP, Paats MS, Dubbink HJ. Highly accurate DNA-based detection and treatment results of MET exon 14 skipping mutations in lung cancer. Lung Cancer 2019; 140:46-54. [PMID: 31862577 DOI: 10.1016/j.lungcan.2019.11.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [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: 08/20/2019] [Revised: 11/01/2019] [Accepted: 11/14/2019] [Indexed: 12/15/2022]
Abstract
OBJECTIVES The oncogenic MET exon 14 skipping mutation (METex14del) is described to drive 1.3 %-5.7 % of non-small-cell lung cancer (NSCLC) and multiple studies with cMET inhibitors show promising clinical responses. RNA-based analysis seems most optimal for METex14del detection, however, acquiring sufficient RNA material is often problematic. An alternative is DNA-based analysis, but commercially available DNA-based panels only detect up to 63 % of known METex14del alterations. The goal of this study is to describe an optimized DNA-based diagnostic test for METex14del in NSCLC, including clinical features and follow-up of patients treated with cMET-targeted therapy and consequent resistance mechanisms. MATERIAL AND METHODS Routinely processed diagnostic pathology non-squamous NSCLC specimens were investigated by a custom-made DNA-based targeted amplicon-based next generation sequencing (NGS) panel, which includes 4 amplicons for METex14del detection. Retrospectively, histopathological characteristics and clinical follow up were investigated for advanced non-squamous NSCLC with METex14del. RESULTS In silico analysis showed that our NGS panel is able to detect 96 % of reported METex14 alterations. METex14del was found in 2 % of patients with non-squamous NSCLC tested for therapeutic purposes. In total, from May 2015 - Sep 2018, METex14del was found in 46 patients. Thirty-six of these patients had advanced non-squamous NSCLC, they were predominantly elderly (76.5 years [53-90]), male (25/36) and (ex)-smokers (23/36). Five patients received treatment with crizotinib (Pfizer Oncology), in a named patient based program, disease control was achieved for 4/5 patients (3 partial responses, 1 stable disease) and one patient had a mixed response. Two patients developed a MET D1228N mutation during crizotinib treatment, inducing a resistance mechanism to crizotinib. CONCLUSIONS This study shows that METex14del can be reliably detected by routine DNA NGS analysis. Although a small cohort, patients responded well to targeted treatment, underlining the need for routine testing of METex14del in advanced non-squamous NSCLC to guarantee optimal personalized treatment.
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Affiliation(s)
- M A Pruis
- Department of Pulmonary Diseases, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - W R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Thüsen J H von der
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - I C Meijssen
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - W N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - J G J V Aerts
- Department of Pulmonary Diseases, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - A M C Dingemans
- Department of Pulmonary Diseases, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Department of Pulmonary Diseases, Maastricht UMC +, Maastricht, the Netherlands
| | - M P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - M S Paats
- Department of Pulmonary Diseases, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - H J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
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25
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Dasgupta S, Ewing-Graham PC, Groenendijk FH, Stam O, Biermann KE, Doukas M, Dubbink HJ, van Velthuysen MF, Dinjens WNM, Van Bockstal MR. Granular dot-like staining with MLH1 immunohistochemistry is a clone-dependent artefact. Pathol Res Pract 2019; 216:152581. [PMID: 31402167 DOI: 10.1016/j.prp.2019.152581] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/25/2019] [Accepted: 08/03/2019] [Indexed: 11/15/2022]
Abstract
Immunohistochemistry (IHC) for DNA mismatch repair proteins MLH1, PMS2, MSH2, and MSH6 is used for microsatellite instability (MSI) screening in colorectal carcinoma (CRC) and endometrial carcinoma (EC). Loss of PMS2, with retained MLH1 staining occurs in germline mutations of PMS2 gene, and is an indication for genetic testing. We report a pitfall of immunohistochemical interpretation in an EC, initially regarded as MLH1-positive and PMS2-negative. Review of the MLH1-IHC (M1-clone) revealed a granular, dot-like, nuclear staining. On repeating the MLH1-IHC with a different clone (ES05-clone), complete negativity was noted, and on molecular testing, MLH1 promotor methylation was detected. The dot-like pattern was therefore adjudged a clone-dependent artefact. On reviewing the archived MLH1-IHC slides, we observed the same dot-like pattern in two CRCs; in both cases the M1-clone had been used. Awareness of this artefact may prevent reporting errors, and unnecessary referrals for germline mutation testing.
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Affiliation(s)
- S Dasgupta
- Department of Pathology, Erasmus MC, University Medical Centre Rotterdam, the Netherlands.
| | - P C Ewing-Graham
- Department of Pathology, Erasmus MC, University Medical Centre Rotterdam, the Netherlands.
| | - F H Groenendijk
- Department of Pathology, Erasmus MC, University Medical Centre Rotterdam, the Netherlands.
| | - O Stam
- Department of Pathology, Pathan BV, Sint Franciscus Gasthuis, Rotterdam, the Netherlands.
| | - K E Biermann
- Department of Pathology, Erasmus MC, University Medical Centre Rotterdam, the Netherlands.
| | - M Doukas
- Department of Pathology, Erasmus MC, University Medical Centre Rotterdam, the Netherlands.
| | - H J Dubbink
- Department of Pathology, Erasmus MC, University Medical Centre Rotterdam, the Netherlands.
| | - M F van Velthuysen
- Department of Pathology, Erasmus MC, University Medical Centre Rotterdam, the Netherlands.
| | - W N M Dinjens
- Department of Pathology, Erasmus MC, University Medical Centre Rotterdam, the Netherlands.
| | - M R Van Bockstal
- Department of Pathology, Erasmus MC, University Medical Centre Rotterdam, the Netherlands; Department of Pathology, University Clinics Saint-Luc, Brussels, Belgium.
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26
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Wijnenga MMJ, van der Voort SR, French PJ, Klein S, Dubbink HJ, Dinjens WNM, Atmodimedjo PN, de Groot M, Kros JM, Schouten JW, Dirven CMF, Vincent AJPE, Smits M, van den Bent MJ. Differences in spatial distribution between WHO 2016 low-grade glioma molecular subgroups. Neurooncol Adv 2019; 1:vdz001. [PMID: 33889844 PMCID: PMC8051437 DOI: 10.1093/noajnl/vdz001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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] [Indexed: 01/01/2023] Open
Abstract
Background Several studies reported a correlation between anatomic location and genetic background of low-grade gliomas (LGGs). As such, tumor location may contribute to presurgical clinical decision-making. Our purpose was to visualize and compare the spatial distribution of different WHO 2016 gliomas, frequently aberrated single genes and DNA copy number alterations within subgroups, and groups of postoperative tumor volume. Methods Adult grade II glioma patients (WHO 2016 classified) diagnosed between 2003 and 2016 were included. Tumor volume and location were assessed with semi-automatic software. All volumes of interest were mapped to a standard reference brain. Location heatmaps were created for each WHO 2016 glioma subgroup, frequently aberrated single genes and copy numbers (CNVs), as well as heatmaps according to groups of postoperative tumor volume. Differences between subgroups were determined using voxelwise permutation testing. Results A total of 110 IDH mutated astrocytoma patients, 92 IDH mutated and 1p19q co-deleted oligodendroglioma patients, and 22 IDH wild-type astrocytoma patients were included. We identified small regions in which specific molecular subtypes occurred more frequently. IDH-mutated LGGs were more frequently located in the frontal lobes and IDH wild-type tumors more frequently in the basal ganglia of the right hemisphere. We found no localizations of significant difference for single genes/CNVs in subgroups, except for loss of 9p in oligodendrogliomas with a predilection for the left parietal lobes. More extensive resections in LGG were associated with frontal locations. Conclusions WHO low-grade glioma subgroups show differences in spatial distribution. Our data may contribute to presurgical clinical decision-making in LGG patients.
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Affiliation(s)
- Maarten M J Wijnenga
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Sebastian R van der Voort
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands.,Department of Medical Informatics, Erasmus MC, Rotterdam, The Netherlands
| | - Pim J French
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Stefan Klein
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands.,Department of Medical Informatics, Erasmus MC, Rotterdam, The Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Marius de Groot
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands.,Department of Medical Informatics, Erasmus MC, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Johan M Kros
- Department of Pathology, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Joost W Schouten
- Department of Neurosurgery, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Clemens M F Dirven
- Department of Neurosurgery, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Arnaud J P E Vincent
- Department of Neurosurgery, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Marion Smits
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Martin J van den Bent
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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27
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Agahozo MC, Sieuwerts AM, Doebar SC, Verhoef EI, Beaufort CM, Ruigrok-Ritstier K, de Weerd V, Sleddens HFBM, Dinjens WNM, Martens JWM, van Deurzen CHM. PIK3CA mutations in ductal carcinoma in situ and adjacent invasive breast cancer. Endocr Relat Cancer 2019; 26:471-482. [PMID: 30844755 DOI: 10.1530/erc-19-0019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 12/20/2022]
Abstract
PIK3CA is one of the most frequently mutated genes in invasive breast cancer (IBC). These mutations are generally associated with hyper-activation of the phosphatidylinositol 3-kinase signaling pathway, which involves increased phosphorylation of AKT (p-AKT). This pathway is negatively regulated by the tumor suppressor PTEN. Data are limited regarding the variant allele frequency (VAF) of PIK3CA, PTEN and p-AKT expression during various stages of breast carcinogenesis. Therefore, the aim of this study was to gain insight into PIK3CA VAF and associated PTEN and p-AKT expression during the progression from ductal carcinoma in situ (DCIS) to IBC. We isolated DNA from DCIS tissue, synchronous IBC and metastasis when present. These samples were pre-screened for PIK3CA hotspot mutations using the SNaPshot assay and, if positive, validated and quantified by digital PCR. PTEN and p-AKT expression was evaluated by immunohistochemistry using the Histo-score (H-score). Differences in PIK3CA VAF, PTEN and p-AKT H-scores between DCIS and IBC were analyzed. PIK3CA mutations were detected in 17 out of 73 DCIS samples, 16 out of 73 IBC samples and 3 out of 23 lymph node metastasis. We detected a significantly higher VAF of PIK3CA in the DCIS component compared to the adjacent IBC component (P = 0.007). The expression of PTEN was significantly higher in DCIS compared to the IBC component in cases with a wild-type (WT) PIK3CA status (P = 0.007), while it remained similar in both components when PIK3CA was mutated. There was no difference in p-AKT expression between DCIS and the IBC component. In conclusion, our data suggest that PIK3CA mutations could be essential specifically in early stages of breast carcinogenesis. In addition, these mutations do not co-occur with PTEN expression during DCIS progression to IBC in the majority of patients. These results may contribute to further unraveling the process of breast carcinogenesis, and this could aid in the development of patient-specific treatment.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Class I Phosphatidylinositol 3-Kinases/genetics
- Disease Progression
- Female
- Follow-Up Studies
- Gene Expression Regulation, Neoplastic
- Humans
- Inflammatory Breast Neoplasms/genetics
- Inflammatory Breast Neoplasms/pathology
- Middle Aged
- Mutation
- Neoplasm Invasiveness
- Neoplasm Metastasis
- Prognosis
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Affiliation(s)
| | - Anieta M Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - S Charlane Doebar
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Esther I Verhoef
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Corine M Beaufort
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Hein F B M Sleddens
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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28
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Meijer TG, Verkaik NS, Sieuwerts AM, van Riet J, Naipal KAT, van Deurzen CHM, den Bakker MA, Sleddens HFBM, Dubbink HJ, den Toom TD, Dinjens WNM, Lips E, Nederlof PM, Smid M, van de Werken HJG, Kanaar R, Martens JWM, Jager A, van Gent DC. Correction: Functional Ex Vivo Assay Reveals Homologous Recombination Deficiency in Breast Cancer Beyond BRCA Gene Defects. Clin Cancer Res 2019; 25:2935. [PMID: 31043383 DOI: 10.1158/1078-0432.ccr-19-0936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Eijkelenboom A, Tops BBJ, van den Berg A, van den Brule AJC, Dinjens WNM, Dubbink HJ, Ter Elst A, Geurts-Giele WRR, Groenen PJTA, Groenendijk FH, Heideman DAM, Huibers MMH, Huijsmans CJJ, Jeuken JWM, van Kempen LC, Korpershoek E, Kroeze LI, de Leng WWJ, van Noesel CJM, Speel EJM, Vogel MJ, van Wezel T, Nederlof PM, Schuuring E, Ligtenberg MJL. Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics. Virchows Arch 2019; 474:673-680. [PMID: 30888490 PMCID: PMC6581937 DOI: 10.1007/s00428-019-02555-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 12/04/2018] [Revised: 02/14/2019] [Accepted: 03/03/2019] [Indexed: 01/09/2023]
Abstract
Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity.
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Affiliation(s)
- Astrid Eijkelenboom
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Anke van den Berg
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Arja Ter Elst
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Willemina R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Floris H Groenendijk
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Daniëlle A M Heideman
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Manon M H Huibers
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | - Léon C van Kempen
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Esther Korpershoek
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Carel J M van Noesel
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ernst-Jan M Speel
- Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Maartje J Vogel
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Petra M Nederlof
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands. .,Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.
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30
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Koelsche C, Stichel D, Griewank KG, Schrimpf D, Reuss DE, Bewerunge-Hudler M, Vokuhl C, Dinjens WNM, Petersen I, Mittelbronn M, Cuevas-Bourdier A, Buslei R, Pfister SM, Flucke U, Mechtersheimer G, Mentzel T, von Deimling A. Genome-wide methylation profiling and copy number analysis in atypical fibroxanthomas and pleomorphic dermal sarcomas indicate a similar molecular phenotype. Clin Sarcoma Res 2019; 9:2. [PMID: 30809375 PMCID: PMC6375211 DOI: 10.1186/s13569-019-0113-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [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: 11/27/2018] [Accepted: 02/05/2019] [Indexed: 12/14/2022] Open
Abstract
Background Atypical fibroxanthomas (AFX) and pleomorphic dermal sarcomas (PDS) are lesions of the skin with overlapping histologic features and unspecific molecular traits. PDS behaves aggressive compared to AFX. Thus, a precise delineation, although challenging in some instances, is relevant. Methods We examined the value of DNA-methylation profiling and copy number analysis for separating these tumors. DNA-methylation data were generated from 17 AFX and 15 PDS using the Illumina EPIC array. These were compared with DNA-methylation data generated from 196 tumors encompassing potential histologic mimics like cutaneous squamous carcinomas (cSCC; n = 19), basal cell carcinomas (n = 10), melanoma metastases originating from the skin (n = 11), leiomyosarcomas (n = 11), angiosarcomas of the skin and soft tissue (n = 11), malignant peripheral nerve sheath tumors (n = 19), dermatofibrosarcomas protuberans (n = 13), extraskeletal myxoid chondrosarcomas (n = 9), myxoid liposarcomas (n = 14), schwannomas (n = 10), neurofibromas (n = 21), alveolar (n = 19) and embryonal (n = 17) rhabdomyosarcomas as well as undifferentiated pleomorphic sarcomas (n = 12). Results DNA-methylation profiling did not separate AFX from PDS. The DNA-methylation profiles of the other cases, however, were distinct from AFX/PDS. They reliably assigned to subtype-specific DNA-methylation clusters, although overlap occurred between some AFX/PDS and cSCC. Copy number profiling revealed alterations in a similar frequency and distribution between AFX and PDS. They involved losses of 9p (22/32) and 13q (25/32). Gains frequently involved 8q (8/32). Notably, a homozygous deletion of CDKN2A was more frequent in PDS (6/15) than in AFX (2/17), whereas amplifications were non-recurrent and overall rare (5/32). Conclusions Our findings support the concept that AFX and PDS belong to a common tumor spectrum. We could demonstrate the diagnostic value of DNA-methylation profiling to delineating AFX/PDS from potential mimics. However, the assessment of certain histologic features remains crucial for separating PDS from AFX.
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Affiliation(s)
- Christian Koelsche
- 1Department of General Pathology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Baden-Württemberg Germany
| | - Damian Stichel
- 2Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Baden-Württemberg Germany.,3Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg Germany.,4German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Baden-Württemberg Germany
| | - Klaus G Griewank
- 5Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen and the German Cancer Consortium (DKTK), Essen, North Rhine-Westphalia Germany.,Dermatopathologie bei Mainz, Nieder-Olm, Rhineland-Palatinate Germany
| | - Daniel Schrimpf
- 2Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Baden-Württemberg Germany.,3Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg Germany.,4German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Baden-Württemberg Germany
| | - David E Reuss
- 2Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Baden-Württemberg Germany.,3Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg Germany.,4German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Baden-Württemberg Germany
| | - Melanie Bewerunge-Hudler
- 4German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Baden-Württemberg Germany.,7Genomics and Proteomics Core Facility, Microarray Unit, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg Germany
| | - Christian Vokuhl
- 8Department of Pediatric Pathology, University Hospital of Schleswig-Holstein, Kiel, Schleswig-Holstein Germany
| | - Winand N M Dinjens
- 9Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Iver Petersen
- Institute of Pathology, SRH Poliklinik Gera GmbH, Gera, Germany
| | - Michel Mittelbronn
- Luxembourg Centre of Neuropathology (LCNP), Luxembourg City, Luxembourg.,12Laboratoire National de Santé (LNS), Dudelange, Luxembourg.,13Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg City, Luxembourg.,14NORLUX Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg City, Luxembourg
| | | | - Rolf Buslei
- 15Institute of Pathology, Sozialstiftung Bamberg, Bamberg, Germany
| | - Stefan M Pfister
- 4German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Baden-Württemberg Germany.,16Hopp Childrens Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany.,17Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg Germany.,18Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Baden-Württemberg Germany
| | - Uta Flucke
- 19Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gunhild Mechtersheimer
- 1Department of General Pathology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Baden-Württemberg Germany
| | - Thomas Mentzel
- Dermatopathology Bodensee, Friedrichshafen, Baden-Württemberg Germany
| | - Andreas von Deimling
- 2Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Baden-Württemberg Germany.,3Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg Germany.,4German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Baden-Württemberg Germany
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31
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Wijnenga MMJ, French PJ, Dubbink HJ, Dinjens WNM, Atmodimedjo PN, Kros JM, Smits M, Gahrmann R, Rutten GJ, Verheul JB, Fleischeuer R, Dirven CMF, Vincent AJPE, van den Bent MJ. The impact of surgery in molecularly defined low-grade glioma: an integrated clinical, radiological, and molecular analysis. Neuro Oncol 2019; 20:103-112. [PMID: 29016833 DOI: 10.1093/neuonc/nox176] [Citation(s) in RCA: 193] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Extensive resections in low-grade glioma (LGG) are associated with improved overall survival (OS). However, World Health Organization (WHO) classification of gliomas has been completely revised and is now predominantly based on molecular criteria. This requires reevaluation of the impact of surgery in molecularly defined LGG subtypes. Methods We included 228 adults who underwent surgery since 2003 for a supratentorial LGG. Pre- and postoperative tumor volumes were assessed with semiautomatic software on T2-weighted images. Targeted next-generation sequencing was used to classify samples according to current WHO classification. Impact of postoperative volume on OS, corrected for molecular profile, was assessed using a Cox proportional hazards model. Results Median follow-up was 5.79 years. In 39 (17.1%) histopathologically classified gliomas, the subtype was revised after molecular analysis. Complete resection was achieved in 35 patients (15.4%), and in 54 patients (23.7%) only small residue (0.1-5.0 cm3) remained. In multivariable analysis, postoperative volume was associated with OS, with a hazard ratio of 1.01 (95% CI: 1.002-1.02; P = 0.016) per cm3 increase in volume. The impact of postoperative volume was particularly strong in isocitrate dehydrogenase (IDH) mutated astrocytoma patients, where even very small postoperative volumes (0.1-5.0 cm) already negatively affected OS. Conclusion Our data provide the necessary reevaluation of the impact of surgery in molecularly defined LGG and support maximal resection as first-line treatment for molecularly defined LGG. Importantly, in IDH mutated astrocytoma, even small postoperative volumes have negative impact on OS, which argues for a second-look operation in this subtype to remove minor residues if safely possible.
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Affiliation(s)
- Maarten M J Wijnenga
- Department of Neurology, Erasmus University Medical Center (Erasmus MC) Cancer Institute, Rotterdam, the Netherlands
| | - Pim J French
- Department of Neurology, Erasmus University Medical Center (Erasmus MC) Cancer Institute, Rotterdam, the Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Johan M Kros
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Marion Smits
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Renske Gahrmann
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Geert-Jan Rutten
- Department of Neurosurgery, St Elisabeth Hospital, Tilburg, the Netherlands
| | - Jeroen B Verheul
- Department of Neurosurgery, St Elisabeth Hospital, Tilburg, the Netherlands
| | - Ruth Fleischeuer
- Department of Pathology, St Elisabeth Hospital, Tilburg, the Netherlands
| | - Clemens M F Dirven
- Department of Neurosurgery, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Arnaud J P E Vincent
- Department of Neurosurgery, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Martin J van den Bent
- Department of Neurology, Erasmus University Medical Center (Erasmus MC) Cancer Institute, Rotterdam, the Netherlands
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32
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Synhaeve NE, van den Bent MJ, French PJ, Dinjens WNM, Atmodimedjo PN, Kros JM, Verdijk R, Dirven CMF, Dubbink HJ. Clinical evaluation of a dedicated next generation sequencing panel for routine glioma diagnostics. Acta Neuropathol Commun 2018; 6:126. [PMID: 30470264 PMCID: PMC6251173 DOI: 10.1186/s40478-018-0633-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/11/2018] [Indexed: 12/15/2022] Open
Abstract
Since 2013 next-generation sequencing (NGS) targeting genes mutated in diffuse gliomas is part of routine diagnostics in our institute. In the present report, we evaluate the use of this custom tailored NGS platform on 434 samples. The NGS panel assesses mutations in ATRX, CIC, EGFR, FUBP1, NOTCH1, PTEN; H3F3A, IDH1/2, PIK3CA, and BRAF, amplifications in EGFR or MDM2 and copy number alterations (CNA) of chromosome 1p, 7, 10 and 19q. TERT promoter mutations were assessed separately when indicated. Of the 433 samples of individual tumors with NGS data available, 176 cases were diagnosed as grade 2 or 3 glioma (40.6) and in 201 patients a glioblastoma (46.4%). Of the remaining 56 patients, 22 had inconclusive histology. In 378 cases (87.1%) a diagnosis solely based on glioma-targeted NGS could be established and resulted in a different diagnosis in ~ 1/4 of the cases. In 17 out of 22 cases without a conclusive histological diagnosis NGS resulted in a molecular diagnosis. The current study on a large cohort of patients confirms the diagnostic strength of the platform we developed, with a clear separation of glioma subgroups with different outcomes. It demonstrates the diagnostic value and the efficiency of glioma-targeted NGS for routine glioma diagnostics allowing with a single assay a glioma diagnosis in the large majority of cases. It allows in one run the molecular assessments required for the WHO classification of diffuse gliomas, including the recent recommendations to assess copy number alterations of chromosome 7 and 10, and of the TERT promoter region in IDHwt lower grade glioma.
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33
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Goverde A, Wagner A, Bruno MJ, Hofstra RMW, Doukas M, van der Weiden MM, Dubbink HJ, Dinjens WNM, Spaander MCW. Routine Molecular Analysis for Lynch Syndrome Among Adenomas or Colorectal Cancer Within a National Screening Program. Gastroenterology 2018; 155:1410-1415. [PMID: 30063919 DOI: 10.1053/j.gastro.2018.07.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 07/19/2018] [Accepted: 07/26/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS It is important to identify individuals with Lynch syndrome because surveillance programs can reduce their morbidity and mortality from colorectal cancer (CRC). We assessed the diagnostic yield of immunohistochemistry to detect Lynch syndrome in patients with advanced and multiple adenomas within our national CRC screening program. METHODS We performed a prospective study of all participants (n = 1101; 55% male; median age, 66 years; interquartile range, 61-70 years) referred to the Erasmus MC in The Netherlands after a positive result from a fecal immunohistochemical test, from December 2013 to December 2016. Colon tissues were collected from patients with advanced adenomas, ≥4 nonadvanced adenomas, or CRC, and analyzed by immunohistochemistry to identify patients with loss of mismatch repair (MMR) proteins (MLH1, MSH2, MSH6, or PMS2): a marker of Lynch syndrome. Specimens from patients with loss of MLH1 were analyzed for MLH1 promoter hypermethylation. Patients with an MMR-deficient tumor or adenoma without MLH1 promoter hypermethylation were referred for genetic analysis. RESULTS At colonoscopy, 456 patients (41%) (65% male; mean age, 67 years; interquartile range, 63-71 years) were found to have CRC and/or an adenoma eligible for analysis by immunohistochemistry. Of 56 CRCs, 7 (13%) had lost an MMR protein and 5 had hypermethylation of the MLH1 promoter. Analyses of tumor DNA revealed that 2 patients without MLH1 promoter hypermethylation had developed sporadic tumors. In total, 400 patients with adenomas were analyzed. Of the examined adenomas, 208 (52%) had a villous component and/or high-grade dysplasia: 186 (47%) had a villous component and 41 (10%) had high-grade dysplasia. Only 1 adenoma had lost an MMR protein. This adenoma was found to have 2 somatic mutations in MSH6. CONCLUSIONS In a CRC screening program in The Netherlands for individuals aged 55 to 75 years, routine screening for Lynch syndrome by immunohistochemistry analysis of colon tissues from patients with advanced and multiple adenomas identified no individuals with this genetic disorder.
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Affiliation(s)
- Anne Goverde
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, the Netherlands; Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, the Netherlands
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, the Netherlands
| | - Marco J Bruno
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, the Netherlands
| | - Robert M W Hofstra
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam, the Netherlands
| | - Michael Doukas
- Department of Pathology, Erasmus MC University Medical Center Rotterdam, the Netherlands
| | | | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC University Medical Center Rotterdam, the Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC University Medical Center Rotterdam, the Netherlands
| | - Manon C W Spaander
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, the Netherlands.
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34
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van der Leest C, Wagner A, Pedrosa RM, Aerts JG, Dinjens WNM, Dubbink HJ. Novel EGFR V834L Germline Mutation Associated With Familial Lung Adenocarcinoma. JCO Precis Oncol 2018; 2:1700266. [PMID: 32913987 PMCID: PMC7446426 DOI: 10.1200/po.17.00266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Cor van der Leest
- and Amphia Ziekenhuis, Breda; and and Erasmus University Medical Center, Rotterdam, Netherlands
| | - Anja Wagner
- and Amphia Ziekenhuis, Breda; and and Erasmus University Medical Center, Rotterdam, Netherlands
| | - Rute M Pedrosa
- and Amphia Ziekenhuis, Breda; and and Erasmus University Medical Center, Rotterdam, Netherlands
| | - Joachim G Aerts
- and Amphia Ziekenhuis, Breda; and and Erasmus University Medical Center, Rotterdam, Netherlands
| | - Winand N M Dinjens
- and Amphia Ziekenhuis, Breda; and and Erasmus University Medical Center, Rotterdam, Netherlands
| | - Hendrikus J Dubbink
- and Amphia Ziekenhuis, Breda; and and Erasmus University Medical Center, Rotterdam, Netherlands
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Dubbink HJ, Hollink IHIM, Avenca Valente C, Wang W, Liu P, Doukas M, van Noesel MM, Dinjens WNM, Wagner A, Smits R. A novel tissue-based ß-catenin gene and immunohistochemical analysis to exclude familial adenomatous polyposis among children with hepatoblastoma tumors. Pediatr Blood Cancer 2018; 65:e26991. [PMID: 29446530 DOI: 10.1002/pbc.26991] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/28/2017] [Accepted: 01/02/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND The Wnt/β-catenin pathway plays a central role in the pathogenesis of most hepatoblastomas (HBs), that is, up to 60-80% carry activating CTNNB1 mutations. HBs can however also be the first manifestation of familial adenomatous polyposis (FAP). As this is a severe disease, it is important for the patient and related family members to firmly exclude FAP at an early stage. Current diagnosis largely depends on APC germline mutation detection on genomic DNA, which is associated with 10-20% false-negative results. Here, we establish and validate a tissue-based β-catenin gene and immunohistochemical analysis, which complements germline mutation screening to exclude the diagnosis of FAP among HB patients. METHODS Tumor tissues of 18 HB patients, including three FAP cases were subjected to CTNNB1 exon 3 mutational analysis and immunohistochemistry comparing staining patterns for total and exon 3 specific β-catenin antibodies. RESULTS Our novel tissue-based method reliably identified all three FAP patients. Their tumors were characterized by a wild-type exon 3 sequence and a comparable nuclear staining for both antibodies. In contrast, the non-FAP tumors carried missense CTNNB1 mutations combined with a clearly reduced staining for the exon 3 antibody, or complete loss of staining in case of lesions with exon 3 deletions. CONCLUSION We have successfully established and validated a novel ß-catenin gene and immunohistochemical diagnostic method, which, when combined with routine germline DNA testing, allows the exclusion of the diagnosis of FAP among HB patients.
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Affiliation(s)
- Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Iris H I M Hollink
- Clinical Genetics, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Carolina Avenca Valente
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Wenhui Wang
- Gastroenterology and Hepatology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Pengyu Liu
- Gastroenterology and Hepatology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Michail Doukas
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Max M van Noesel
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Anja Wagner
- Clinical Genetics, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Ron Smits
- Gastroenterology and Hepatology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
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Riegman PHJ, Bosch AL, Riegman PHJ, Dinjens WNM, Oomen MHA, Spatz A, Ratcliffe C, Knox K, Mager R, Kerr D, Pezzella F, van Damme B, van de Vijver M, van Boven H, Morente MM, Alonso S, Kerjaschki D, Pammer J, Lopez-Guerrero JA, Bosch AL, Carbone A, Gloghini A, Teodorovic I, Isabelle M, Jaminé D, Passioukov A, Lejeune S, Therasse P, van Veen EB, Lam KH, Oosterhuis JW. OECI TuBaFrost Tumor Biobanking. Tumori 2018; 94:160-3. [DOI: 10.1177/030089160809400205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OECI TuBaFrost harbors a complete infrastructure for the exchange of frozen tumor samples between European countries. OECI TuBaFrost consists of: • A code of conduct on how to exchange human residual samples in Europe • A central database application accessible over the Internet ( www.tubafrost.org ) where data can be uploaded and searched from samples that can be selected and ordered • Access rules with incentives for collectors • Standardization needed to enable the analysis of high quality samples derived from different centers • Virtual Microscopy to support sample selection with difficult pathology The entire infrastructure was, after completion, which was entirely financed by the European Commission, implemented in the OECI. But so far it has not been used to its capacity. A recent survey held amongst the OECI members shed light on the causes. The main conclusion is that all responders see OECI TuBaFrost as a good platform for exchange of samples, however, the biggest bottleneck found was that potential users are too unfamiliar with the communication between their own biobank tracking system and the TuBaFrost central database application. Therefore, new future plans are drawn. In addition, new infrastructure plans have been developed and the first preparatory steps have been set. For biobanks the BBMRI project has started aiming for Pan-European Biobanking and Biomolecular Resources Research Infrastructure.
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Affiliation(s)
- Peter HJ Riegman
- Department of Pathology, Josephine Nefkens Institute, Erasmus Medical Center Rotterdam, The Netherlands
| | | | | | | | - MHA Oomen
- Erasmus MC, Rotterdam, The Netherlands
| | - A Spatz
- Institut Gustave Roussy, Villejuif, France
| | - C Ratcliffe
- National Translational Cancer Research Network, University of Oxford, Radcliffe Infirmary, Oxford, United Kingdom
| | - K Knox
- National Translational Cancer Research Network, University of Oxford, Radcliffe Infirmary, Oxford, United Kingdom
| | - R Mager
- National Translational Cancer Research Network, University of Oxford, Radcliffe Infirmary, Oxford, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - D Kerr
- National Translational Cancer Research Network, University of Oxford, Radcliffe Infirmary, Oxford, United Kingdom
| | - F. Pezzella
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | | | | | - H van Boven
- Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - MM Morente
- Centro Nacional de Investigaciones Oncologicas, Madrid, Spain
| | - S Alonso
- Centro Nacional de Investigaciones Oncologicas, Madrid, Spain
| | - D Kerjaschki
- Allgemeines Krankenhaus, University of Vienna, Austria
| | - J Pammer
- Allgemeines Krankenhaus, University of Vienna, Austria
| | | | | | - A Carbone
- Centro di Riferimento Oncologico, Aviano (PN), Italy
| | - A Gloghini
- Centro di Riferimento Oncologico, Aviano (PN), Italy
| | | | | | - D Jaminé
- EORTC Data Center, Brussels, Belgium
| | | | - S Lejeune
- EORTC Data Center, Brussels, Belgium
| | | | | | - KH Lam
- Erasmus MC, Rotterdam, The Netherlands
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van Riet J, Krol NMG, Atmodimedjo PN, Brosens E, van IJcken WFJ, Jansen MPHM, Martens JWM, Looijenga LH, Jenster G, Dubbink HJ, Dinjens WNM, van de Werken HJG. SNPitty: An Intuitive Web Application for Interactive B-Allele Frequency and Copy Number Visualization of Next-Generation Sequencing Data. J Mol Diagn 2018; 20:166-176. [PMID: 29305224 DOI: 10.1016/j.jmoldx.2017.11.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 11/16/2017] [Accepted: 11/27/2017] [Indexed: 01/19/2023] Open
Abstract
Exploration and visualization of next-generation sequencing data are crucial for clinical diagnostics. Software allowing simultaneous visualization of multiple regions of interest coupled with dynamic heuristic filtering of genetic aberrations is, however, lacking. Therefore, the authors developed the web application SNPitty that allows interactive visualization and interrogation of variant call format files by using B-allele frequencies of single-nucleotide polymorphisms and single-nucleotide variants, coverage metrics, and copy numbers analysis results. SNPitty displays variant alleles and allelic imbalances with a focus on loss of heterozygosity and copy number variation using genome-wide heterozygous markers and somatic mutations. In addition, SNPitty is capable of generating predefined reports that summarize and highlight disease-specific targets of interest. SNPitty was validated for diagnostic interpretation of somatic events by showcasing a serial dilution series of glioma tissue. Additionally, SNPitty is demonstrated in four cancer-related scenarios encountered in daily clinical practice and on whole-exome sequencing data of peripheral blood from a Down syndrome patient. SNPitty allows detection of loss of heterozygosity, chromosomal and gene amplifications, homozygous or heterozygous deletions, somatic mutations, or any combination thereof in regions or genes of interest. Furthermore, SNPitty can be used to distinguish molecular relationships between multiple tumors from a single patient. On the basis of these data, the authors demonstrate that SNPitty is robust and user friendly in a wide range of diagnostic scenarios.
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Affiliation(s)
- Job van Riet
- Cancer Computational Biology Center, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; Department of Urology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Niels M G Krol
- Cancer Computational Biology Center, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | | | - Maurice P H M Jansen
- Department of Medical Oncology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Leendert H Looijenga
- Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; Department of Urology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.
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38
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Evenepoel L, van Nederveen FH, Oudijk L, Papathomas TG, Restuccia DF, Belt EJT, de Herder WW, Feelders RA, Franssen GJH, Hamoir M, Maiter D, Ghayee HK, Shay JW, Perren A, Timmers HJLM, van Eeden S, Vroonen L, Aydin S, Robledo M, Vikkula M, de Krijger RR, Dinjens WNM, Persu A, Korpershoek E. Expression of Contactin 4 Is Associated With Malignant Behavior in Pheochromocytomas and Paragangliomas. J Clin Endocrinol Metab 2018; 103:46-55. [PMID: 28938490 DOI: 10.1210/jc.2017-01314] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/14/2017] [Indexed: 02/06/2023]
Abstract
CONTEXT Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine, usually benign, tumors. Currently, the only reliable criterion of malignancy is the presence of metastases. OBJECTIVE The aim of this study was to identify genes associated with malignancy in PPGLs. DESIGN Transcriptomic profiling was performed on 40 benign and 11 malignant PPGLs. Genes showing a significantly different expression between benign and malignant PPGLs with a ratio ≥4 were confirmed and tested in an independent series by quantitative real-time polymerase chain reaction (qRT-PCR). Immunohistochemistry was performed for the validated genes on 109 benign and 32 malignant PPGLs. Functional assays were performed with hPheo1 cells. SETTING This study was conducted at the Department of Pathology of the Erasmus MC University Medical Center Rotterdam Human Molecular Genetics laboratory of the de Duve Institute, University of Louvain. PATIENTS PPGL samples from 179 patients, diagnosed between 1972 and 2015, were included. MAIN OUTCOME MEASURES Associations between gene expression and malignancy were tested using supervised clustering approaches. RESULTS Ten differentially expressed genes were selected based on messenger RNA (mRNA) expression array data. Contactin 4 (CNTN4) was overexpressed in malignant vs benign tumors [4.62-fold; false discovery rate (FDR), 0.001]. Overexpression at the mRNA level was confirmed using qRT-PCR (2.90-fold, P = 0.02; validation set: 4.26-fold, P = 0.005). Consistent findings were obtained in The Cancer Genome Atlas cohort (2.7-fold; FDR, 0.02). CNTN4 protein was more frequently expressed in malignant than in benign PPGLs by immunohistochemistry (58% vs 17%; P = 0.002). Survival after 7 days of culture under starvation conditions was significantly enhanced in hPheo1 cells transfected with CNTN4 complementary DNA. CONCLUSION CNTN4 expression is consistently associated with malignant behavior in PPGLs.
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Affiliation(s)
- Lucie Evenepoel
- Pole of Cardiovascular Research, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, Netherlands
- Human Molecular Genetics, de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | | | - Lindsey Oudijk
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, Netherlands
| | - Thomas G Papathomas
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, Netherlands
- Department of Histopathology, King's College Hospital, London, United Kingdom
| | - David F Restuccia
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, Netherlands
| | - Eric J T Belt
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, Netherlands
| | - Wouter W de Herder
- Internal Medicine, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, Netherlands
| | - Richard A Feelders
- Internal Medicine, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, Netherlands
| | - Gaston J H Franssen
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, Netherlands
| | - Marc Hamoir
- Otolaryngology Department, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Dominique Maiter
- Endocrinology Department, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Hans K Ghayee
- Department of Internal Medicine, Division of Endocrinology, University of Florida, Gainesville, Florida
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Aurel Perren
- Clinical Pathology Division, University of Bern, Bern, Switzerland
| | - Henri J L M Timmers
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Susanne van Eeden
- Department of Pathology, Academic Medical Center, Amsterdam, Netherlands
| | - Laurent Vroonen
- Department of Endocrinology, Centre Hospitalier Universitaire de Liège, University of Liège, Domaine Universitaire du Sart-Tilman, Liège, Belgium
| | - Selda Aydin
- Department of Pathology, Cliniques universitaires Saint Luc, Université catholique de Louvain, Brussels, Belgium
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases, Madrid, Spain
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Ronald R de Krijger
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, Netherlands
- Department of Pathology, Reinier de Graaf Hospital, Delft, Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, Netherlands
| | - Alexandre Persu
- Pole of Cardiovascular Research, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
- Division of Cardiology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Esther Korpershoek
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, Netherlands
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Wijnenga MMJ, Dubbink HJ, French PJ, Synhaeve NE, Dinjens WNM, Atmodimedjo PN, Kros JM, Dirven CMF, Vincent AJPE, van den Bent MJ. Molecular and clinical heterogeneity of adult diffuse low-grade IDH wild-type gliomas: assessment of TERT promoter mutation and chromosome 7 and 10 copy number status allows superior prognostic stratification. Acta Neuropathol 2017; 134:957-959. [PMID: 29052002 DOI: 10.1007/s00401-017-1781-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 10/16/2017] [Accepted: 10/16/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Maarten M J Wijnenga
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Institute, PO Box 5201, 3008AE, Rotterdam, The Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Pim J French
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Institute, PO Box 5201, 3008AE, Rotterdam, The Netherlands
| | - Nathalie E Synhaeve
- Department of Neurology, Elisabeth Tweesteden Hospital, Tilburg, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Johan M Kros
- Department of Pathology, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Clemens M F Dirven
- Department of Neurosurgery, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Arnaud J P E Vincent
- Department of Neurosurgery, Brain Tumor Center at Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Martin J van den Bent
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Institute, PO Box 5201, 3008AE, Rotterdam, The Netherlands.
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Ten Kate FJC, Suzuki L, Dorssers LCJ, Dinjens WNM, Jones DTW, Nieboer D, Doukas M, Van Lanschot JJB, Wijnhoven BPL, Looijenga LHJ, Biermann K. Pattern of p53 protein expression is predictive for survival in chemoradiotherapy-naive esophageal adenocarcinoma. Oncotarget 2017; 8:104123-104135. [PMID: 29262626 PMCID: PMC5732792 DOI: 10.18632/oncotarget.22021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 07/31/2017] [Accepted: 09/22/2017] [Indexed: 12/14/2022] Open
Abstract
Introduction TP53 mutations are considered to be the driving factor in the initiation of esophageal adenocarcinoma (EAC). However, the impact of this gene and its encoded protein as a prognostic marker has not been definitely established yet. Methods In total, 204 chemoradiotherapy (CRT)-naive patients with EAC were included for p53 protein expression evaluation by immunohistochemistry (IHC) on the resection specimens, categorized as overexpression, heterogeneous or loss of expression, and correlated with disease free survival (DFS) and overall survival (OS) using multivariable Cox regression analysis. In a subset representing all three IHC subgroups mutational status of selected candidate genes (n=33) and high throughput methylation profiling (n=16) was assessed. Results Compared to heterogeneous p53 expression, loss and overexpression were both independently predictive for adverse DFS and OS. TP53 mutational status significantly correlated with the IHC categories (p=0.035). Most of the EAC with loss- or overexpression harbored TP53 mutations (18/20, representing nonsense and missense mutations respectively). In contrast, 6/13 EAC with heterogeneous expression were TP53 wild type, of which two demonstrated MDM4 or MDM2 amplification. Combined genomic hypomethylation and high frequency of intra-chromosomal breaks was found in a selection of EAC without p53 overexpression. Conclusion P53 expression pattern is prognostic for DFS and OS in this historical cohort of CRT-naive EAC. P53 IHC is an informative readout for TP53 mutational status in EAC with either loss- or overexpression, but not in case of a heterogeneous p53 pattern. Different EAC pathogenesis might exist, related to p53 and other candidate gene status, DNA hypomethylation and intrachromosomal breaks.
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Affiliation(s)
- Fiebo J C Ten Kate
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lucia Suzuki
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lambert C J Dorssers
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Daan Nieboer
- Department of Public Health, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Michael Doukas
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - J Jan B Van Lanschot
- Department of Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bas P L Wijnhoven
- Department of Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Katharina Biermann
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
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41
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van den Bent MJ, Baumert B, Erridge SC, Vogelbaum MA, Nowak AK, Sanson M, Brandes AA, Clement PM, Baurain JF, Mason WP, Wheeler H, Chinot OL, Gill S, Griffin M, Brachman DG, Taal W, Rudà R, Weller M, McBain C, Reijneveld J, Enting RH, Weber DC, Lesimple T, Clenton S, Gijtenbeek A, Pascoe S, Herrlinger U, Hau P, Dhermain F, van Heuvel I, Stupp R, Aldape K, Jenkins RB, Dubbink HJ, Dinjens WNM, Wesseling P, Nuyens S, Golfinopoulos V, Gorlia T, Wick W, Kros JM. Interim results from the CATNON trial (EORTC study 26053-22054) of treatment with concurrent and adjuvant temozolomide for 1p/19q non-co-deleted anaplastic glioma: a phase 3, randomised, open-label intergroup study. Lancet 2017; 390:1645-1653. [PMID: 28801186 PMCID: PMC5806535 DOI: 10.1016/s0140-6736(17)31442-3] [Citation(s) in RCA: 232] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 03/26/2017] [Accepted: 03/28/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND The role of temozolomide chemotherapy in newly diagnosed 1p/19q non-co-deleted anaplastic gliomas, which are associated with lower sensitivity to chemotherapy and worse prognosis than 1p/19q co-deleted tumours, is unclear. We assessed the use of radiotherapy with concurrent and adjuvant temozolomide in adults with non-co-deleted anaplastic gliomas. METHODS This was a phase 3, randomised, open-label study with a 2 × 2 factorial design. Eligible patients were aged 18 years or older and had newly diagnosed non-co-deleted anaplastic glioma with WHO performance status scores of 0-2. The randomisation schedule was generated with the electronic EORTC web-based ORTA system. Patients were assigned in equal numbers (1:1:1:1), using the minimisation technique, to receive radiotherapy (59·4 Gy in 33 fractions of 1·8 Gy) alone or with adjuvant temozolomide (12 4-week cycles of 150-200 mg/m2 temozolomide given on days 1-5); or to receive radiotherapy with concurrent temozolomide 75 mg/m2 per day, with or without adjuvant temozolomide. The primary endpoint was overall survival adjusted for performance status score, age, 1p loss of heterozygosity, presence of oligodendroglial elements, and MGMT promoter methylation status, analysed by intention to treat. We did a planned interim analysis after 219 (41%) deaths had occurred to test the null hypothesis of no efficacy (threshold for rejection p<0·0084). This trial is registered with ClinicalTrials.gov, number NCT00626990. FINDINGS At the time of the interim analysis, 745 (99%) of the planned 748 patients had been enrolled. The hazard ratio for overall survival with use of adjuvant temozolomide was 0·65 (99·145% CI 0·45-0·93). Overall survival at 5 years was 55·9% (95% CI 47·2-63·8) with and 44·1% (36·3-51·6) without adjuvant temozolomide. Grade 3-4 adverse events were seen in 8-12% of 549 patients assigned temozolomide, and were mainly haematological and reversible. INTERPRETATION Adjuvant temozolomide chemotherapy was associated with a significant survival benefit in patients with newly diagnosed non-co-deleted anaplastic glioma. Further analysis of the role of concurrent temozolomide treatment and molecular factors is needed. FUNDING Schering Plough and MSD.
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Affiliation(s)
- Martin J van den Bent
- Neuro-Oncology Unit, Brain Tumour Centre at Erasmus MC Cancer Institute, Rotterdam, Netherlands.
| | - Brigitta Baumert
- Department of Radiation-Oncology (MAASTRO), Maastricht University Medical Centre (MUMC), Maastricht, Netherlands; GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre (MUMC), Maastricht, Netherlands; Department of Radiation-Oncology, University of Münster, Münster, Germany; Paracelsus Clinic, Osnabrück, Germany
| | - Sara C Erridge
- Edinburgh Centre for Neuro-Oncology, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Michael A Vogelbaum
- Department of Neurosurgery, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA; Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, OH, USA
| | - Anna K Nowak
- School of Medicine and Pharmacology, University of Western Australia, Crawley, WA, Australia; Co-Operative Group for Neuro-Oncology, University of Sydney, Camperdown, NSW, Australia; Department of Medical Oncology, Sir Charles Gairdner Hospital, Hospital Avenue, Nedlands, WA, Australia
| | - Marc Sanson
- Sorbonne Universités UPMC, University Paris VI, INSERM, CNRS, APHP, Institut du Cerveau et de la Moelle (ICM), Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - Alba Ariela Brandes
- Medical Oncology Department, AUSL-IRCCS Scienze Neurologiche, Bologna, Italy
| | - Paul M Clement
- Department of Oncology, KU Leuven, Leuven, Belgium; Department of General Medical Oncology, UZ Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Jean Francais Baurain
- Medical Oncology Department, King Albert II Cancer Institute, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Warren P Mason
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Helen Wheeler
- Northern Sydney Cancer Centre, North Shore Hospital, St Leonards, NSW, Australia; Department of Medicine, University of Sydney, Sydney, NSW, Australia
| | - Olivier L Chinot
- Neuro-Oncology Division, Aix-Marseille University, AP-HM, Marseille, France
| | - Sanjeev Gill
- Department of Medical Oncology, Alfred Hospital, Melbourne, VIC, Australia
| | - Matthew Griffin
- Department of Clinical Oncology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - David G Brachman
- Department of Radiation Oncology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Walter Taal
- Neuro-Oncology Unit, Brain Tumour Centre at Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Roberta Rudà
- Department of Neuro-Oncology, City of Health and Science Hospital and University of Turin, Turin, Italy
| | - Michael Weller
- Department of Neurology and Brain Tumour Centre, University Hospital and University of Zurich, Zurich, Switzerland
| | - Catherine McBain
- Department of Clinical Oncology, Christie NHS Foundation Trust, Manchester, UK
| | - Jaap Reijneveld
- VUmc Cancer Centre Amsterdam, VU University Medical Centre, Amsterdam, Netherlands; Department of Neurology, VU University Medical Centre, Amsterdam, Netherlands; Department of Neurology, Academic Medical Centre, Amsterdam, Netherlands
| | - Roelien H Enting
- Department of Neurology, UMCG, University of Groningen, Groningen, Netherlands
| | - Damien C Weber
- Department of Radiation Oncology, University Hospital of Geneva, Geneva, Switzerland
| | - Thierry Lesimple
- Department of Clinical Oncology, Comprehensive Cancer Center Eugène Marquis, Rennes, France
| | | | - Anja Gijtenbeek
- Department of Neurology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Sarah Pascoe
- Department of Clinical Oncology, Plymouth Hospitals NHS Trust, Plymouth, UK
| | - Ulrich Herrlinger
- Division of Clinical Neuro-Oncology, Department of Neurology, University of Bonn Medical Centre, Bonn, Germany
| | - Peter Hau
- Wilhelm Sander-Neuro-Oncology Unit and Department of Neurology, University Hospital Regensburg, Regensburg, Germany
| | - Frederic Dhermain
- Radiotherapy Department, Gustave Roussy University Hospital, Villejuif, France
| | - Irene van Heuvel
- Neuro-Oncology Unit, Brain Tumour Centre at Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Roger Stupp
- Department of Medical Oncology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Ken Aldape
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hendrikus Jan Dubbink
- Department of Pathology, Brain Tumour Centre at Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Brain Tumour Centre at Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Pieter Wesseling
- Department of Pathology, VU University Medical Centre, Amsterdam, Netherlands; Department of Pathology, Radboud University Medical Centre, Nijmegen, Netherlands
| | | | | | | | - Wolfgang Wick
- Neurologische Klinik und Nationales Zentrum für Tumorerkrankungen Universitätsklinik, Heidelberg, Germany
| | - Johan M Kros
- Department of Pathology, Brain Tumour Centre at Erasmus MC Cancer Institute, Rotterdam, Netherlands
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Creemers SG, Korpershoek E, Atmodimedjo PN, Dinjens WNM, van Koetsveld PM, Feelders RA, Hofland LJ. Identification of Mutations in Cell-Free Circulating Tumor DNA in Adrenocortical Carcinoma: A Case Series. J Clin Endocrinol Metab 2017; 102:3611-3615. [PMID: 28973495 DOI: 10.1210/jc.2017-00174] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/27/2017] [Indexed: 02/13/2023]
Abstract
CONTEXT The disease course of adrenocortical carcinoma (ACC) patients is heterogeneous. A marker for prognosis and treatment response would facilitate choices for diagnosis and therapy. In other cancer types, circulating cell-free tumor DNA predicted tumor dynamics. CASE DESCRIPTIONS The present pilot study included six patients. Next-generation sequencing (NGS) showed mutations in three ACC cases. From these patients, blood was drawn before (1 to 2 weeks) and after surgery and cell-free circulating DNA (cfDNA) was isolated. Tumor-specific mutations were found in the cfDNA of one of the three patients, with metastasized ACC at diagnosis. NGS of the tumor showed an NRAS mutation (c.182A>G:p.Q61R) in 78%, a TP53 mutation (c.856G>A:p.E286K) in 60%, and a TERT gene mutation (1295250C>T) in 28% of the reads. The preoperative cfDNA showed the same mutations at a frequency of 64%, 32%, and 2%, respectively. The postoperative cfDNA showed the same mutations but at lower frequencies (52%, 16%, and 3%, respectively). The patient was postoperatively treated with mitotane and chemotherapy. No mutations were detected in the corresponding leukocyte DNA or in the cfDNA from the two other patients. CONCLUSIONS To the best of our knowledge, we report for the first time mutations occurring at high levels in cfDNA collected before and after surgery from one of three patients, after previous identification in the tumor. However, in the cfDNA from two patients with known mutations, we were unable to reliably detect mutations in the cfDNA. Our results indicate that mutation detection in cfDNA can vary among ACC patients, and other approaches might be required to detect the tumor response and monitor progressive disease.
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Affiliation(s)
- Sara G Creemers
- Division of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Esther Korpershoek
- Department of Pathology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Peter M van Koetsveld
- Division of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Richard A Feelders
- Division of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Leo J Hofland
- Division of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
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43
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van Nistelrooij AMJ, van Marion R, Koppert LB, Biermann K, Spaander MCW, Tilanus HW, van Lanschot JJB, Wijnhoven BPL, Dinjens WNM. Molecular clonality analysis of esophageal adenocarcinoma by multiregion sequencing of tumor samples. BMC Res Notes 2017; 10:144. [PMID: 28376920 PMCID: PMC5379534 DOI: 10.1186/s13104-017-2456-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 08/17/2016] [Accepted: 03/17/2017] [Indexed: 01/10/2023] Open
Abstract
Background Intratumor heterogeneity has been demonstrated in several cancer types, following a model of branched evolution. It is unknown to which extent intratumor heterogeneity is applicable to esophageal adenocarcinoma. Therefore the aim of this study was to characterise intratumor heterogeneity in esophageal adenocarcinoma. Methods Multiregional targeted sequencing of four commonly altered genes was performed on 19 tumor regions collected from five esophageal adenocarcinomas. Alterations were classified as homogeneous or heterogeneous based on mutational and loss of heterozygosity analysis. Results Identical TP53 mutations and homogeneously loss of heterozygosity of the TP53 locus were identified in all separated tumor regions in each of five adenocarcinomas, and in the corresponding Barrett’s esophagus and tumor positive lymph node of one primary tumor. Loss of heterozygosity of the P16 locus was homogeneous among all tumor regions in four adenocarcinomas, and an identical pattern of loss of heterozygosity was present in the Barrett’s esophagus. Loss of heterozygosity of the SMAD4 and APC loci was observed in a heterogeneous pattern. Conclusions Known driver alterations, such as TP53 and P16 are homogeneously present within each adenocarcinoma, and therefore occur early during carcinogenesis and subsequently clonally expand throughout the entire tumor. However, loss of heterozygosity of the SMAD4 and APC loci shows a heterogeneous pattern, indicating intratumor heterogeneity of esophageal adenocarcinoma.
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Affiliation(s)
- Anna M J van Nistelrooij
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.,Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Linetta B Koppert
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Katharina Biermann
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Manon C W Spaander
- Department of Gastroenterology & Hepatology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Hugo W Tilanus
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - J Jan B van Lanschot
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Bas P L Wijnhoven
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
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44
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Jansen AML, Crobach S, Geurts-Giele WRR, van den Akker BEWM, Garcia MV, Ruano D, Nielsen M, Tops CMJ, Wijnen JT, Hes FJ, van Wezel T, Dinjens WNM, Morreau H. Distinct Patterns of Somatic Mosaicism in the APC Gene in Neoplasms From Patients With Unexplained Adenomatous Polyposis. Gastroenterology 2017; 152:546-549.e3. [PMID: 27816598 DOI: 10.1053/j.gastro.2016.10.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/21/2016] [Accepted: 10/23/2016] [Indexed: 12/02/2022]
Abstract
We investigated the presence and patterns of mosaicism in the APC gene in patients with colon neoplasms not associated with any other genetic variants; we performed deep sequence analysis of APC in at least 2 adenomas or carcinomas per patient. We identified mosaic variants in APC in adenomas from 9 of the 18 patients with 21 to approximately 100 adenomas. Mosaic variants of APC were variably detected in leukocyte DNA and/or non-neoplastic intestinal mucosa of these patients. In a comprehensive sequence analysis of 1 patient, we found no evidence for mosaicism in APC in non-neoplastic intestinal mucosa. One patient was found to carry a mosaic c.4666dupA APC variant in only 10 of 16 adenomas, indicating the importance of screening 2 or more adenomas for genetic variants.
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Affiliation(s)
- Anne M L Jansen
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands; Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Stijn Crobach
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Willemina R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, The Netherlands
| | | | | | - Dina Ruano
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Carli M J Tops
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Juul T Wijnen
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands; Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands.
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45
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Li Y, Buijs-Gladdines JGCAM, Canté-Barrett K, Stubbs AP, Vroegindeweij EM, Smits WK, van Marion R, Dinjens WNM, Horstmann M, Kuiper RP, Buijsman RC, Zaman GJR, van der Spek PJ, Pieters R, Meijerink JPP. IL-7 Receptor Mutations and Steroid Resistance in Pediatric T cell Acute Lymphoblastic Leukemia: A Genome Sequencing Study. PLoS Med 2016; 13:e1002200. [PMID: 27997540 PMCID: PMC5172551 DOI: 10.1371/journal.pmed.1002200] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/11/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Pediatric acute lymphoblastic leukemia (ALL) is the most common childhood cancer and the leading cause of cancer-related mortality in children. T cell ALL (T-ALL) represents about 15% of pediatric ALL cases and is considered a high-risk disease. T-ALL is often associated with resistance to treatment, including steroids, which are currently the cornerstone for treating ALL; moreover, initial steroid response strongly predicts survival and cure. However, the cellular mechanisms underlying steroid resistance in T-ALL patients are poorly understood. In this study, we combined various genomic datasets in order to identify candidate genetic mechanisms underlying steroid resistance in children undergoing T-ALL treatment. METHODS AND FINDINGS We performed whole genome sequencing on paired pre-treatment (diagnostic) and post-treatment (remission) samples from 13 patients, and targeted exome sequencing of pre-treatment samples from 69 additional T-ALL patients. We then integrated mutation data with copy number data for 151 mutated genes, and this integrated dataset was tested for associations of mutations with clinical outcomes and in vitro drug response. Our analysis revealed that mutations in JAK1 and KRAS, two genes encoding components of the interleukin 7 receptor (IL7R) signaling pathway, were associated with steroid resistance and poor outcome. We then sequenced JAK1, KRAS, and other genes in this pathway, including IL7R, JAK3, NF1, NRAS, and AKT, in these 69 T-ALL patients and a further 77 T-ALL patients. We identified mutations in 32% (47/146) of patients, the majority of whom had a specific T-ALL subtype (early thymic progenitor ALL or TLX). Based on the outcomes of these patients and their prednisolone responsiveness measured in vitro, we then confirmed that these mutations were associated with both steroid resistance and poor outcome. To explore how these mutations in IL7R signaling pathway genes cause steroid resistance and subsequent poor outcome, we expressed wild-type and mutant IL7R signaling molecules in two steroid-sensitive T-ALL cell lines (SUPT1 and P12 Ichikawa cells) using inducible lentiviral expression constructs. We found that expressing mutant IL7R, JAK1, or NRAS, or wild-type NRAS or AKT, specifically induced steroid resistance without affecting sensitivity to vincristine or L-asparaginase. In contrast, wild-type IL7R, JAK1, and JAK3, as well as mutant JAK3 and mutant AKT, had no effect. We then performed a functional study to examine the mechanisms underlying steroid resistance and found that, rather than changing the steroid receptor's ability to activate downstream targets, steroid resistance was associated with strong activation of MEK-ERK and AKT, downstream components of the IL7R signaling pathway, thereby inducing a robust antiapoptotic response by upregulating MCL1 and BCLXL expression. Both the MEK-ERK and AKT pathways also inactivate BIM, an essential molecule for steroid-induced cell death, and inhibit GSK3B, an important regulator of proapoptotic BIM. Importantly, treating our cell lines with IL7R signaling inhibitors restored steroid sensitivity. To address clinical relevance, we treated primary T-ALL cells obtained from 11 patients with steroids either alone or in combination with IL7R signaling inhibitors; we found that including a MEK, AKT, mTOR, or dual PI3K/mTOR inhibitor strongly increased steroid-induced cell death. Therefore, combining these inhibitors with steroid treatment may enhance steroid sensitivity in patients with ALL. The main limitation of our study was the modest cohort size, owing to the very low incidence of T-ALL. CONCLUSIONS Using an unbiased sequencing approach, we found that specific mutations in IL7R signaling molecules underlie steroid resistance in T-ALL. Future prospective clinical studies should test the ability of inhibitors of MEK, AKT, mTOR, or PI3K/mTOR to restore or enhance steroid sensitivity and improve clinical outcome.
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Affiliation(s)
- Yunlei Li
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center/Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Jessica G. C. A. M. Buijs-Gladdines
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center/Sophia Children’s Hospital, Rotterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Kirsten Canté-Barrett
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center/Sophia Children’s Hospital, Rotterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Andrew P. Stubbs
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Eric M. Vroegindeweij
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center/Sophia Children’s Hospital, Rotterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Willem K. Smits
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center/Sophia Children’s Hospital, Rotterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Ronald van Marion
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Martin Horstmann
- Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
- Clinic of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Co-operative Study Group for Childhood Acute Lymphoblastic Leukemia, Hamburg, Germany
| | - Roland P. Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | | | - Rob Pieters
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center/Sophia Children’s Hospital, Rotterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jules P. P. Meijerink
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center/Sophia Children’s Hospital, Rotterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- * E-mail:
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46
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Das AM, Bolkestein M, van der Klok T, Oude Ophuis CMC, Vermeulen CE, Rens JAP, Dinjens WNM, Atmodimedjo PN, Verhoef C, Koljenović S, Smits R, Ten Hagen TLM, Eggermont AMM. Tissue inhibitor of metalloproteinase-3 (TIMP3) expression decreases during melanoma progression and inhibits melanoma cell migration. Eur J Cancer 2016; 66:34-46. [PMID: 27522248 DOI: 10.1016/j.ejca.2016.06.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 04/14/2016] [Revised: 06/11/2016] [Accepted: 06/21/2016] [Indexed: 02/09/2023]
Abstract
AIMS Malignant melanoma is the most aggressive form of skin cancer, and metastatic dissemination to regional and visceral sites is responsible for the majority of melanoma-related mortalities. In a recent study by our group, we observed reduced expression of tissue inhibitor of metalloproteinase-3 (TIMP3) in the majority of stage III melanoma samples studied. TIMP3 has been reported as a tumour suppressor in several human malignancies, with reduced expression correlating with poor clinical outcome. In this study, we investigated the changes in TIMP3 expression during melanoma progression. PATIENTS AND METHODS TIMP3 expression was analysed by immunohistochemistry in sequential archived tumour material from stage I/II, stage III and stage IV samples from melanoma patients (n = 33). Protein expression was investigated for associations with disease-free survival and overall survival. Methylation status of the gene promoter was determined using methylation-specific PCR. In vitro assays were used to investigate the functional consequences of TIMP3 expression on behavioural aspects of melanoma cells. RESULTS We show that TIMP3 expression decreases with melanoma progression although no significant clinical associations were obtained. Analysis of the status of promoter methylation using methylation-specific PCR revealed it to be a low-frequency event in melanoma. Additionally, through gene modulation experiments in melanoma cell lines, we show that TIMP3 negatively regulates cell migration, invasion and anoikis resistance. CONCLUSIONS Collectively, our data suggests that TIMP3 functions as a tumour suppressor in melanoma and negatively regulates several aspects of the metastatic cascade.
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Affiliation(s)
- Asha M Das
- Department of Surgical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Michiel Bolkestein
- Department of Surgical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Thom van der Klok
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Cindy E Vermeulen
- Department of Surgical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Joost A P Rens
- Department of Surgical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Cornelis Verhoef
- Department of Surgical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Senada Koljenović
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ron Smits
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Timo L M Ten Hagen
- Department of Surgical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Alexander M M Eggermont
- Department of Surgical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands; Gustave Roussy Cancer Campus Grand Paris, Villejuif, France.
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47
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Koppert LB, Wijnhoven BPL, Tilanus HW, Stijnen T, Van Dekken H, Dinjens WNM. Neuroendocrine Cells in Barrett’s Mucosa and Adenocarcinomas of the Gastroesophageal Junction. Int J Surg Pathol 2016; 12:117-25. [PMID: 15173916 DOI: 10.1177/106689690401200204] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We estimated the prevalence and prognostic significance of neuroendocrine (NE) cells in a series of 208 resection specimens containing gastroesophageal junction (GEJ) adenocarcinomas, with 56 specimens containing Barrett’s mucosa. Immunohistochemically, chromogranin A (CGA) was positive in 49% (102/208) of GEJ adenocarcinomas and in 68% (38/56) of Barrett’s mucosas. CGA in GEJ tumors correlated with pTNM stage. CGA in Barrett correlated with pTNM stage and tumor grade of the adjacent carcinoma. Patients with CGA in Barrett had better survival than patients without CGA in Barrett, with 5-year survival percentages of 56% and 9%, respectively. In multivariate analysis, CGA in Barrett was an independent prognostic factor for survival after surgery. Therefore CGA in Barrett adjacent to GEJ adenocarcinoma might be helpful in the assessment of patient outcome.
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Affiliation(s)
- Linetta B Koppert
- Department of Surgery, Josephine Nefkens Institute, University Medical Center Rotterdam, The Netherlands
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48
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Dubbink HJ, Atmodimedjo PN, van Marion R, Krol NMG, Riegman PHJ, Kros JM, van den Bent MJ, Dinjens WNM. Diagnostic Detection of Allelic Losses and Imbalances by Next-Generation Sequencing: 1p/19q Co-Deletion Analysis of Gliomas. J Mol Diagn 2016; 18:775-786. [PMID: 27461031 DOI: 10.1016/j.jmoldx.2016.06.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 05/06/2016] [Accepted: 06/01/2016] [Indexed: 02/05/2023] Open
Abstract
Cancer cells are genomically unstable and accumulate tumor type-specific molecular aberrations, which may represent hallmarks for predicting prognosis and targets for therapy. Co-deletion of chromosomes 1p and 19q marks gliomas with an oligodendroglioma component and predicts a better prognosis and response to chemotherapy. In the current study, we present a novel method to detect chromosome 1p/19q co-deletion or loss of heterozygosity (LOH) in a diagnostic setting, based on single-nucleotide polymorphism (SNP) analysis and next-generation sequencing (NGS). We selected highly polymorphic SNPs distributed evenly over both chromosome arms. To experimentally determine the sensitivity and specificity of targeted SNP analysis, we used DNAs extracted from 49 routine formalin-fixed, paraffin-embedded glioma tissues and compared the outcome with diagnostic microsatellite-based LOH analysis and calculated estimates. We show that targeted SNP analysis by NGS allows reliable detection of 1p and/or 19q deletion in a background of 70% of normal cells according to calculated outcomes, is more sensitive than microsatellite-based LOH analysis, and requires much less DNA. This specific and sensitive SNP assay is broadly applicable for simultaneous allelic imbalance analysis of multiple genomic regions and can be incorporated easily into NGS mutation analyses. The combined mutation and chromosomal imbalance analysis in a single NGS assay is suited perfectly for routine glioma diagnostics and other diagnostic molecular pathology applications.
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Affiliation(s)
- Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Niels M G Krol
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter H J Riegman
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan M Kros
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martin J van den Bent
- Department of Neuro-Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
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49
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Korpershoek E, Koffy D, Eussen BH, Oudijk L, Papathomas TG, van Nederveen FH, Belt EJT, Franssen GJH, Restuccia DFJ, Krol NMG, van der Luijt RB, Feelders RA, Oldenburg RA, van Ijcken WFJ, de Klein A, de Herder WW, de Krijger RR, Dinjens WNM. Complex MAX Rearrangement in a Family With Malignant Pheochromocytoma, Renal Oncocytoma, and Erythrocytosis. J Clin Endocrinol Metab 2016; 101:453-60. [PMID: 26670126 DOI: 10.1210/jc.2015-2592] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
CONTEXT Familial pheochromocytoma (PCC) has been associated with germline mutations in 16 genes. Here we investigated three siblings presenting with bilateral pheochromocytomas. In addition, the index patient also exhibited renal oncocytoma and erythrocytosis, whereas the second sibling presented with a lymph node metastasis. DESIGN First, single-nucleotide polymorphism array and exome sequencing were performed on germline and PCC-derived DNA to identify genomic alterations in the index patient. Second, alterations were confirmed and validated by Sanger sequencing, analyzed by (multiplexed) PCR to determine the loss of the wild-type allele, and investigated by immunohistochemistry in the tumors of the three siblings. RESULTS The index patient's germline DNA revealed a large complex genomic alteration encompassing the intragenic and promoter regions of Myc-associated factor X (MAX) and alpha-(1,6)-fucosyltransferase (FUT8). In all three siblings the MAX alteration was confirmed, and the loss of the wild-type MAX and FUT8 alleles was demonstrated in all tumors. Uniparental disomy of chromosome 14q, previously demonstrated as a hallmark for MAX-related PCC, was shown in the index patient's PCC by single-nucleotide polymorphism array. Loss of MAX and FUT8 protein expression was demonstrated by immunohistochemistry in the tumors from the three siblings. CONCLUSIONS Our results indicate that large genomic deletions of MAX should be considered in familial and bilateral PCC with prior negative testing for gene mutations. In addition, our results confirm that MAX is a tumor suppressor gene for renal oncocytomas.
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Affiliation(s)
- Esther Korpershoek
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Djamailys Koffy
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Bert H Eussen
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Lindsey Oudijk
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Thomas G Papathomas
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Francien H van Nederveen
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Eric J T Belt
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Gaston J H Franssen
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - David F J Restuccia
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Niels M G Krol
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Rob B van der Luijt
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Richard A Feelders
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Rogier A Oldenburg
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Wilfred F J van Ijcken
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Annelies de Klein
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Wouter W de Herder
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Ronald R de Krijger
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Winand N M Dinjens
- Departments of Pathology (E.K., D.K., L.O., T.G.P., D.F.J.R., N.M.G.K., R.R.d.K., W.N.M.D.), Internal Medicine (R.A.F., W.W.d.H.), and Biomics (W.F.J.v.I.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 CA Rotterdam, The Netherlands; Departments of Clinical Genetics (B.H.E., R.A.O., A.d.K.), and Surgery (E.J.T.B., G.J.H.F.), Erasmus Medical Center Cancer Institute, University Medical Center, 3000 DR Rotterdam, The Netherlands; Department of Histopathology (T.G.P.), King's College Hospital, London, SE5 9RS, United Kingdom; Laboratory for Pathology (F.H.v.N.), Pathologisch Laboratorium Dordrecht, 3317 DA Dordrecht, The Netherlands; Division of Biomedical Genetics (R.B.v.d.L.), University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; and Department of Pathology (R.R.d.K.), Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
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van Nistelrooij AMJ, van Marion R, Biermann K, Spaander MCW, van Lanschot JJB, Wijnhoven BPL, Dinjens WNM. Early onset esophageal adenocarcinoma: a distinct molecular entity? Oncoscience 2016; 3:42-8. [PMID: 26973859 PMCID: PMC4751915 DOI: 10.18632/oncoscience.290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 12/26/2015] [Accepted: 01/22/2016] [Indexed: 12/18/2022] Open
Abstract
Esophageal adenocarcinoma (EAC) is typically diagnosed in elderly with a median age of 68 years. The incidence of EAC has been rising over the last decades, also among young adults. The aim of the study was to investigate whether early onset EAC is a distinct molecular entity. To identify early onset EACs, the nationwide network and registry of histo- and cytopathology in the Netherlands (PALGA) was searched. Twenty-eight tumors of patients aged ≤40 years were selected and matched with 27 tumors of patients aged ≥68 years. DNA was isolated from surgically resected specimen and sequenced on the Ion Torrent Personal Genome Machine with the Ion AmpliSeq Cancer Panel. No differences in mutational load between early onset and conventional EACs were observed (P=0.196). The most frequently mutated genes were TP53 (73%) and P16 (16%). Additional mutations in early onset EACs occurred exclusively in: APC, CDH1, CTNNB1, FGFR2, and STK11. In the conventional EACs additional mutations were exclusively identified in: ABL1, FBXW7, GNA11, GNAS, KRAS, MET, SMAD4, and VHL. Additional mutations besides TP53 and P16 seem to occur in different genes related to cell fate pathways for early onset EACs, while the additional mutations in conventional EACs are related to survival pathways.
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Affiliation(s)
- Anna M J van Nistelrooij
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands; Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | | | - Katharina Biermann
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Manon C W Spaander
- Department of Gastroenterology and Hepatology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - J Jan B van Lanschot
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Bas P L Wijnhoven
- Department of Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
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