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Vallentgoed WR, Niers A, van Garderen K, Bent MVD, van Dijk E, Draaisma K, van Eijk P, de Heer I, Kouwenhoven M, Kros J, de Leng W, Martin I, Robe P, Smits M, Tesileanu M, van Thuijl H, Verhaak R, Westerman B, Wiel MVD, Ylstra B, Wesseling P, French P. Abstract 4020: Methylation analysis of matched primary and recurrent IDH-mutant astrocytoma; an update from the GLASS-NL consortium. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-4020] [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
INTRODUCTION. Diffuse gliomas are the most frequent and devastating primary CNS tumors in adults. Standard treatment has limited efficacy and without exception these gliomas recur. The evolutionary processes that drive progression in glioma of the IDH-mutant astrocytoma subgroup, remain unclear. The GLASS-NL consortium was initiated to gain insight into the molecular mechanisms underlying glioma evolution and to identify markers of progression in IDH-mutant astrocytomas. Such markers can ultimately assist clinical decision making. Here, we present the results of genome wide DNA-methylation profiling of samples included in the GLASS-NL study.
METHODS. 110 adult patients were identified with an IDH-mutant, 1p19q non-codeleted, astrocytoma at first diagnosis. All patients underwent surgical resection of the tumor at least twice, separated by >6 months with a median of 41.9 months (IQR:26.5-65.9). After surgical resection of the initial tumor, 63% and 22% of the patients were treated with radiotherapy or chemotherapy respectively. DNA-methylation profiling was performed on 235 samples from 103 patients, using the Illumina Infinium MethylationEPIC BeadChip array. Copy number alterations (CNAs) were extracted from these data. Methylation subclasses were determined according to Capper et al. (Nature, 2018). Overall survival (OS) was measured from date of initial surgery.
RESULTS. Of all primary tumors, 85 (87%) of the tumor samples were assigned to the A_IDH (‘low grade’) methylation subclass and 10 (10%) to the A_IDH_HG (‘high grade’) subclass. The relative proportion of high grade tumors increased ~three-fold at tumor recurrence (32/101, 32%) and even further in the second recurrence (15/29, 52%). The high grade subclass of the recurrent, but not the initial tumor sample, was negatively associated with OS (p < 0.0001). The overall DNA-methylation levels of recurrent samples were lower than that of initial samples. This difference is explained by the increased number of high grade samples at recurrence, since near identical DNA-methylation levels were observed in samples that remained low grade. Analysis of CNAs revealed several chromosomal arms and bands that were more frequently altered in samples of the high grade methylation subclass compared to low grade. In addition, gains and losses of specific genes, such as homozygous deletion (HD) of CDKN2A/B, were more frequent in high grade samples. Overall DNA-methylation levels of recurrent samples with CDKN2A/B HD were lower than that of samples without this deletion. However, CDKN2A/B HD alone does not fully explain DNA-demethylation at malignant progression and other molecular aberrations are likely to contribute as well.
CONCLUSION. Longitudinal methylation profiling analysis of IDH-mutant astrocytoma reveals a shift towards a higher grade at tumor recurrence coinciding with reduced genome-wide DNA-methylation levels.
Citation Format: Wies Rijan Vallentgoed, Anneke Niers, Karin van Garderen, Martin van den Bent, Erik van Dijk, Kaspar Draaisma, Paul van Eijk, Iris de Heer, Mathilde Kouwenhoven, Johan Kros, Wendy de Leng, Ivonne Martin, Pierre Robe, Marion Smits, Mircea Tesileanu, Hinke van Thuijl, Roel Verhaak, Bart Westerman, Mark van de Wiel, Bauke Ylstra, Pieter Wesseling, Pim French. Methylation analysis of matched primary and recurrent IDH-mutant astrocytoma; an update from the GLASS-NL consortium [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4020.
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Affiliation(s)
| | - Anneke Niers
- 2Amsterdam University Medical Centers/VUmc, Amsterdam, Netherlands
| | | | | | - Erik van Dijk
- 2Amsterdam University Medical Centers/VUmc, Amsterdam, Netherlands
| | | | - Paul van Eijk
- 2Amsterdam University Medical Centers/VUmc, Amsterdam, Netherlands
| | - Iris de Heer
- 1Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Mathilde Kouwenhoven
- 5Brain Tumor Center Amsterdam, Amsterdam University Medical Centers/VUmc, Amsterdam, Netherlands
| | - Johan Kros
- 1Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Wendy de Leng
- 4University Medical Center Utrecht, Utrecht, Netherlands
| | - Ivonne Martin
- 2Amsterdam University Medical Centers/VUmc, Amsterdam, Netherlands
| | - Pierre Robe
- 6University Medical Centre Utrecht, Utrecht, Netherlands
| | | | | | - Hinke van Thuijl
- 2Amsterdam University Medical Centers/VUmc, Amsterdam, Netherlands
| | - Roel Verhaak
- 7The Jackson Laboratory For Genomic Medicine, Farmington, CT
| | - Bart Westerman
- 2Amsterdam University Medical Centers/VUmc, Amsterdam, Netherlands
| | - Mark van de Wiel
- 8Erasmus MC Cancer Institute, Amsterdam University Medical Centers/VUmc, Netherlands
| | - Bauke Ylstra
- 2Amsterdam University Medical Centers/VUmc, Amsterdam, Netherlands
| | - Pieter Wesseling
- 2Amsterdam University Medical Centers/VUmc, Amsterdam, Netherlands
| | - Pim French
- 1Erasmus MC Cancer Institute, Rotterdam, Netherlands
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Hehir-Kwa JY, Koudijs MJ, Verwiel ETP, Kester LA, van Tuil M, Strengman E, Buijs A, Kranendonk MEG, Hiemcke-Jiwa LS, de Haas V, van de Geer E, de Leng W, van der Lugt J, Lijnzaad P, Holstege FCP, Kemmeren P, Tops BBJ. Improved Gene Fusion Detection in Childhood Cancer Diagnostics Using RNA Sequencing. JCO Precis Oncol 2022; 6:e2000504. [PMID: 35085008 PMCID: PMC8830514 DOI: 10.1200/po.20.00504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 08/27/2021] [Accepted: 12/03/2021] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Gene fusions play a significant role in cancer etiology, making their detection crucial for accurate diagnosis, prognosis, and determining therapeutic targets. Current diagnostic methods largely focus on either targeted or low-resolution genome-wide techniques, which may be unable to capture rare events or both fusion partners. We investigate if RNA sequencing can overcome current limitations with traditional diagnostic techniques to identify gene fusion events. METHODS We first performed RNA sequencing on a validation cohort of 24 samples with a known gene fusion event, after which a prospective pan-pediatric cancer cohort (n = 244) was tested by RNA sequencing in parallel to existing diagnostic procedures. This cohort included hematologic malignancies, tumors of the CNS, solid tumors, and suspected neoplastic samples. All samples were processed in the routine diagnostic workflow and analyzed for gene fusions using standard-of-care methods and RNA sequencing. RESULTS We identified a clinically relevant gene fusion in 83 of 244 cases in the prospective cohort. Sixty fusions were detected by both routine diagnostic techniques and RNA sequencing, and one fusion was detected only in routine diagnostics, but an additional 24 fusions were detected solely by RNA sequencing. RNA sequencing, therefore, increased the diagnostic yield by 38%-39%. In addition, RNA sequencing identified both gene partners involved in the gene fusion, in contrast to most routine techniques. For two patients, the newly identified fusion by RNA sequencing resulted in treatment with targeted agents. CONCLUSION We show that RNA sequencing is sufficiently robust for gene fusion detection in routine diagnostics of childhood cancers and can make a difference in treatment decisions.
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Affiliation(s)
| | - Marco J. Koudijs
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Department of Laboratories, Pharmacy and Biomedical Genetics, Section of Genome Diagnostics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Lennart A. Kester
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Marc van Tuil
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Eric Strengman
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Arjan Buijs
- Department of Laboratories, Pharmacy and Biomedical Genetics, Section of Genome Diagnostics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | - Valerie de Haas
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ellen van de Geer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Wendy de Leng
- Department of Laboratories, Pharmacy and Biomedical Genetics, Section Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Philip Lijnzaad
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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Vallentgoed W, Niers A, van Garderen K, van den Bent M, Draaisma K, de Heer I, Kouwenhoven M, Kros J, Martin I, Robe P, Smits M, Tesileanu M, van Thuijl H, Verhaak R, Westerman B, van de Wiel M, Ylstra B, de Leng W, Wesseling P, French P. EPCO-17. METHYLATION ANALYSIS OF MATCHED PRIMARY AND RECURRENT IDHmt ASTROCYTOMA; AN UPDATE FROM THE GLIOMA LONGITUDINAL ANALYSIS NL (GLASS-NL) CONSORTIUM. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.016] [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: 11/14/2022] Open
Abstract
Abstract
The GLASS-NL consortium, was initiated to gain insight into the molecular mechanisms underlying glioma evolution and to identify markers of progression in IDH-mutant astrocytomas. Here, we present the first results of genome-wide DNA-methylation profiling of GLASS-NL samples. 110 adult patients were identified with an IDH-mutant astrocytoma at first diagnosis. All patients underwent a surgical resection of the tumor at least twice, separated by at least 6 months (median 40.9 months (IQR: 24.0, 64.7). In 37% and 18% of the cases, patients were treated with radiotherapy or chemotherapy respectively, before surgical resection of the recurrent tumor. DNA-methylation profiling was done on 235 samples from 103 patients (102 1st, 101 2nd, 29 3rd, and 3 4th resection). Copy number variations were also extracted from these data. Methylation classes were determined according to Capper et al. Overall survival (OS) was measured from date of first surgery. Of all primary tumors, the methylation-classifier assigned 85 (87%) to the low grade subclass and 10 (10%) to the high grade subclass. The relative proportion of high grade tumors increased ~three-fold at tumor recurrence (32/101, 32%) and even further in the second recurrence (15/29, 52%). Methylation classes were prognostic, both in primary and recurrent tumors. The overall DNA-methylation levels of recurrent samples was lower than that of primary samples. This difference is explained by the increased number of high grade samples at recurrence, since near identical DNA-methylation levels were observed in samples that remained low grade. In an unsupervised analysis, DNA-methylation data derived from primary and first recurrence samples of individual patients mostly (79%) cluster together. Recurrent samples that do not cluster with their primary tumor, form a separate group with relatively low genome-wide DNA-methylation. Our data demonstrate that methylation profiling identifies a shift towards a higher grade at tumor progression coinciding with reduced genome-wide DNA-methylation levels.
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Affiliation(s)
| | - Anneke Niers
- Amsterdam University Medical Centers/VUmc, Amsterdam, Noord-Holland, Netherlands
| | | | | | - Kaspar Draaisma
- University Medical Center Utrecht, Utrecht, Utrecht, Netherlands
| | - Iris de Heer
- Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Mathilde Kouwenhoven
- Brain Tumor Center Amsterdam, Amsterdam University Medical Centers/VUmc, Amsterdam, Netherlands
| | - Johan Kros
- Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Ivonne Martin
- Amsterdam University Medical Centers/VUmc, Amsterdam, Noord-Holland, Netherlands
| | - Pierre Robe
- University Medical Center Utrecht, Utrecht, Utrecht, Netherlands
| | - Marion Smits
- Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | | | | | - Roel Verhaak
- The Jackson Laboratory For Genomic Medicine, Farmington, CT, USA
| | - Bart Westerman
- Amsterdam University Medical Centers/VUmc, Amsterdam, Noord-Holland, Netherlands
| | - Mark van de Wiel
- Amsterdam University Medical Centers/VUmc, Amsterdam, Noord-Holland, Netherlands
| | - Bauke Ylstra
- Amsterdam University Medical Centers/VUmc, Amsterdam, Noord-Holland, Netherlands
| | - Wendy de Leng
- University Medical Center Utrecht, Utrecht, Utrecht, Netherlands
| | | | - Pim French
- Erasmus MC, Dept of Neuro-Oncology, Rotterdam, Netherlands
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Velasco A, Tokat F, Bonde J, Trim N, Bauer E, Meeney A, de Leng W, Chong G, Dalstein V, Kis LL, Lorentzen JA, Tomić S, Thwaites K, Putzová M, Birnbaum A, Qazi R, Primmer V, Dockhorn-Dworniczak B, Hernández-Losa J, Soares FA, Gertler AA, Kalman M, Wong C, Carraro DM, Sousa AC, Reis RM, Fox SB, Fassan M, Brevet M, Merkelbach-Bruse S, Colling R, Soilleux E, Teo RYW, D'Haene N, Nolet S, Ristimäki A, Väisänen T, Chapusot C, Soruri A, Unger T, Wecgowiec J, Biscuola M, Frattini M, Long A, Campregher PV, Matias-Guiu X. Multi-center real-world comparison of the fully automated Idylla™ microsatellite instability assay with routine molecular methods and immunohistochemistry on formalin-fixed paraffin-embedded tissue of colorectal cancer. Virchows Arch 2020; 478:851-863. [PMID: 33170334 PMCID: PMC8099763 DOI: 10.1007/s00428-020-02962-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/14/2020] [Accepted: 10/30/2020] [Indexed: 12/24/2022]
Abstract
Microsatellite instability (MSI) is present in 15–20% of primary colorectal cancers. MSI status is assessed to detect Lynch syndrome, guide adjuvant chemotherapy, determine prognosis, and use as a companion test for checkpoint blockade inhibitors. Traditionally, MSI status is determined by immunohistochemistry or molecular methods. The Idylla™ MSI Assay is a fully automated molecular method (including automated result interpretation), using seven novel MSI biomarkers (ACVR2A, BTBD7, DIDO1, MRE11, RYR3, SEC31A, SULF2) and not requiring matched normal tissue. In this real-world global study, 44 clinical centers performed Idylla™ testing on a total of 1301 archived colorectal cancer formalin-fixed, paraffin-embedded (FFPE) tissue sections and compared Idylla™ results against available results from routine diagnostic testing in those sites. MSI mutations detected with the Idylla™ MSI Assay were equally distributed over the seven biomarkers, and 84.48% of the MSI-high samples had ≥ 5 mutated biomarkers, while 98.25% of the microsatellite-stable samples had zero mutated biomarkers. The concordance level between the Idylla™ MSI Assay and immunohistochemistry was 96.39% (988/1025); 17/37 discordant samples were found to be concordant when a third method was used. Compared with routine molecular methods, the concordance level was 98.01% (789/805); third-method analysis found concordance for 8/16 discordant samples. The failure rate of the Idylla™ MSI Assay (0.23%; 3/1301) was lower than that of referenced immunohistochemistry (4.37%; 47/1075) or molecular assays (0.86%; 7/812). In conclusion, lower failure rates and high concordance levels were found between the Idylla™ MSI Assay and routine tests.
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Affiliation(s)
- Ana Velasco
- Departments of Pathology and Molecular Genetics, Hospital U Arnau de Vilanova and Hospital U de Bellvitge, University of Lleida, IRBLLEIDA, IDIBELL, CIBERONC, Av. Alcalde Rovira Roure, 80 25198, Lleida, Spain.
| | - Fatma Tokat
- Department of Pathology, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - Jesper Bonde
- Molecular Pathology Laboratory, Department of Pathology, afs. 134, Hvidovre Hospital, Hvidovre, Denmark
| | - Nicola Trim
- Molecular Pathology Diagnostic Service, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Elisabeth Bauer
- Städtisches Klinikum Karlsruhe gGmbH, Institut für Pathologie, Karlsruhe, Germany
| | - Adam Meeney
- Ophthalmic Pathology Laboratory Histopathology, Royal Hallamshire Hospital, Glossop Road, Sheffield, UK
| | - Wendy de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - George Chong
- Molecular Pathology Centre, Jewish General Hospital-McGill University, Montreal, Quebec, Canada
| | - Véronique Dalstein
- Laboratoire de Biopathologie, Unité INSERM UMR-S 1250, CHU Reims, Reims, France
| | - Lorand L Kis
- Department of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Jon A Lorentzen
- Molecular Pathology Unit, Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Snjezana Tomić
- Department of Pathology, Forensic Medicine and Cytology, University Hospital Split, Split, Croatia
| | - Keeley Thwaites
- Histopathology Department, Barking, Havering and Redbridge University Hospitals NHS Trust, Queen's Hospital, Romford, UK
| | - Martina Putzová
- Bioptická laboratoř s.r.o., Laboratory of Molecular Genetics, Plzeň, Czech Republic.,ÚBLG FN Motol, Praha, Czech Republic.,LF UK, Plzeň, Czech Republic
| | | | - Romena Qazi
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital & Research Centre, Johr Town, Lahore, Pakistan
| | - Vanessa Primmer
- Pathologisch-Bakteriologisches Institut Kaiser-Franz-Josef-Spital, Vienna, Austria
| | | | - Javier Hernández-Losa
- Department of Pathology, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain
| | | | - Asaf A Gertler
- Department of Pathology, Hadassah Medical Center, Jerusalem, Israel
| | - Michal Kalman
- Department of Pathologic Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic.,Martin's Biopsy Center Ltd., Martin, Slovak Republic
| | - Chris Wong
- Hong Kong Molecular Pathology Diagnostic Centre, Hong Kong Special Administrative Region of the People's Republic of China, Hong Kong, People's Republic of China
| | - Dirce M Carraro
- Genomics and Molecular Biology Group, International Research Center/CIPE, A. C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Ana C Sousa
- GenoMed, Diagnósticos de Medicina Molecular, SA, Lisbon, Portugal
| | - Rui M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Stephen B Fox
- Pathology, Peter MacCallum Cancer Centre and University of Melbourne, Vic, Australia
| | - Matteo Fassan
- Surgical Pathology Unit, Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Marie Brevet
- Department of Pathology, Hospices Civils de Lyon, Université Lyon 1, Bron, France & Cypath, Villeurbanne, France
| | | | - Richard Colling
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Ryan Yee Wei Teo
- Department of Pathology, Tan Tock Seng Hospital, Novena, Republic of Singapore
| | - Nicky D'Haene
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Serge Nolet
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, Québec, Canada
| | - Ari Ristimäki
- Department of Pathology, Research Programs Unit and HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Timo Väisänen
- Oulu University Hospital and Department of Pathology, Cancer and Translational Medicine Research Unit, University of Oulu, Oulu, Finland
| | | | - Afsaneh Soruri
- Institut für Pathologie und Molekularpathologie, Pforzheim, Germany
| | - Tina Unger
- Institut für Pathologie, University of Leipzig, Leipzig, Germany
| | - Johanna Wecgowiec
- Institut für Pathologie, Evangelisches Krankenhaus BETHESDA Zu Duisburg GmbH, Duisburg, Germany
| | - Michele Biscuola
- Department of Pathology, Molecular Pathology Laboratory, Hospital Universitario Virgen del Rocío-IBIS, Seville, Spain
| | - Milo Frattini
- Laboratory of Molecular Pathology, Institute of Pathology, Locarno, Switzerland
| | - Anna Long
- Cellular Pathology, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Xavier Matias-Guiu
- Departments of Pathology and Molecular Genetics, Hospital U Arnau de Vilanova and Hospital U de Bellvitge, University of Lleida, IRBLLEIDA, IDIBELL, CIBERONC, Av. Alcalde Rovira Roure, 80 25198, Lleida, Spain
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5
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Verduin M, Compter I, Primakov S, van Kuijk S, te Dorsthorst M, Revenich E, ter Laan M, Pegge S, Meijer A, Beckervordersandforth J, Jan Speel E, Jochems A, de Leng W, Anten M, Broen M, Ackermans L, Schijns O, Vooijs M, Tjan-Heijnen V, Lambin P, Eekers D, Jacobi-Postma L, Hoeben A. NIMG-65. PREDICTING PROGNOSIS AND CANCER HOTSPOT MUTATIONS USING QUALITATIVE MR IMAGING ANALYSIS IN GLIOBLASTOMA. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.734] [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: 11/12/2022] Open
Abstract
Abstract
INTRODUCTION
Tumor heterogeneity poses one of the major limitations in improving the treatment for glioblastoma (GBM), which calls for new clinically relevant predictive models. This study aims to investigate non-invasive diagnostic methods, including patient characteristics and qualitative imaging analysis as a prognostic classifier and predictor for druggable oncogenes.
METHODS
We performed a retrospective analysis on 143 GBM patients (discovery cohort). Diagnostic MRIs were re-analyzed for qualitative imaging features (VASARI features). DNA was extracted from formalin-fixed, paraffin-embedded GBM tissue of the discovery cohort for next-generation sequencing (Ion Torrent Cancer Hotspot panel v2Plus), TERT-promoter mutation and MGMT-methylation analysis. Multivariable regression analysis was used to determine the prognostic and predictive value of VASARI features.
RESULTS
Of the 143 patients, median age was 61.4 years (range 15.5–84.6) with a median overall survival of 12 months (range 0–142). We observed IDH1 R132H mutation in 8.5%, MGMT-promotor methylation in 26.1%, TERT-promotor mutation (C250T;C228T) in 69.5%, EGFR mutation in 20.3% and EGFR amplification in 37.5% of all patients. A set of eight VASARI features was identified to be associated with overall survival (p< 0.001), which is currently being validated in an external dataset (n= 184). Interestingly, VASARI features appeared to be associated with IDH1-mutation (four features, p=0.004), TERT-promotor mutation (five features, p-value < 0.001), EGFR mutation (five features, p-value < 0.001) and EGFR amplification (seven features, p-value < 0.001) but not with MGMT-methylation (two features, p-value=0.054). Additional cancer hotspots are currently being analyzed and internal validation is ongoing.
CONCLUSION AND FUTURE PERSPECTIVES
We propose an integrated prognostic classifier comprising MRI features, also associated with GBM-specific molecular alterations. Additionally, quantitative MRI radiomics features are being extracted from the discovery and validation set and incorporated in the prognostic classifier. Subsequently, radiomics and VASARI features will be correlated to intratumoral heterogeneity, assessed by tissue micro-array analysis of the discovery cohort.
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Affiliation(s)
- Maikel Verduin
- Department of Medical Oncology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Inge Compter
- Department of Radiotherapy (MAASTRO), School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Sergey Primakov
- The-D-Lab: Decision Support for Precision Medicine, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Sander van Kuijk
- Department of Clinical Epidemiology and Medical Technology Assessment, Maastricht University Medical Center, Maastricht, Netherlands
| | - Maarten te Dorsthorst
- Department of Neurosurgery, Radboud University Medical Center, Nijmegen, Netherlands
| | - Elles Revenich
- Department of Medical Oncology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Mark ter Laan
- Department of Neurosurgery, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sjoert Pegge
- Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Anton Meijer
- Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Ernst Jan Speel
- Department of Pathology, Maastricht University Medical Center+, Maastricht, Netherlands
| | - Arthur Jochems
- The-D-Lab: Decision Support for Precision Medicine, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Wendy de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Monique Anten
- Department of Neurology, Maastricht University Medical Center+, Maastricht, Netherlands
| | - Martijn Broen
- Department of Neurology, Maastricht University Medical Center+, Maastricht, Netherlands
| | - Linda Ackermans
- Department of Neurosurgery, Maastricht University Medical Center+, Maastricht, Netherlands
| | - Olaf Schijns
- Department of Neurosurgery, Maastricht University Medical Center+, Maastricht, Netherlands
| | - Marc Vooijs
- Department of Radiotherapy (MAASTRO), School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Vivianne Tjan-Heijnen
- Department of Medical Oncology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Philippe Lambin
- The-D-Lab: Decision Support for Precision Medicine, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Danielle Eekers
- Department of Radiotherapy (MAASTRO), School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Linda Jacobi-Postma
- Department of Radiology and Nuclear Medicine, School for Mental Health and Neuroscience, Maastricht University Medical Center+, Maastricht, Netherlands
| | - Ann Hoeben
- Department of Medical Oncology, School for Oncology and Developmental Biology (GROW), Maastricht University Medical Centre+, Maastricht, Netherlands
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Wesseling P, Priesterbach-Ackley L, Plasschaert S, Hoving E, Küsters B, Schoots M, Aronica E, Tops B, de Leng W. TBIO-17. IMPLEMENTATION OF METHYLATION PROFILING FOR CNS TUMOR DIAGNOSIS IN THE PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY, THE NETHERLANDS. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Pieter Wesseling
- Dept. of Pathology, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Dept. of Pathology, VU Univ. Med. Ctr., Amsterdam, The Netherlands
| | | | - Sabine Plasschaert
- Dept. of Pediatric Oncology, Princess Máxima Center, Utrecht, The Netherlands
| | - Eelco Hoving
- Dept. of Neurosurgery, Univ. Med. Ctr. Utrecht, Utrecht, The Netherlands
| | - Benno Küsters
- Dept. of Pathology, Radboud Univ. Med. Ctr., Nijmegen, The Netherlands
| | - Mirthe Schoots
- Dept. of Pathology, Univ. Med. Ctr. Groningen, Groningen, The Netherlands
| | - Eleonora Aronica
- Dept. of (Neuro)Pathology, Academic Medical Center, Amsterdam, The Netherlands
| | - Bas Tops
- Dept. of Pathology, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Wendy de Leng
- Dept. of Pathology, Univ. Med. Ctr. Utrecht, Utrecht, The Netherlands
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Robe P, Jansen JEM, Spliet WM, de Leng W. Histologic characterization of the immune infiltrate in isocitrate dehydrogenase wild-type and mutant World Health Organization Grade II and III gliomas. Glioma 2018. [DOI: 10.4103/glioma.glioma_42_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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de Leng W, Hoskam A, van Kuik J, Spliet W, Van Hecke W, Robe P, de Vos F. PATH-11. DESIGNING A DIAGNOSTIC FGFR3-TACC3 FUSION ASSAY USING RT-PCR FOR GLIOBLASTOMA MULTIFORME PATIENTS. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox168.702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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9
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Heerma van Voss MR, Vesuna F, Trumpi K, Brilliant J, Berlinicke C, de Leng W, Kranenburg O, Offerhaus GJ, Bürger H, van der Wall E, van Diest PJ, Raman V. Identification of the DEAD box RNA helicase DDX3 as a therapeutic target in colorectal cancer. Oncotarget 2016; 6:28312-26. [PMID: 26311743 PMCID: PMC4695062 DOI: 10.18632/oncotarget.4873] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/09/2015] [Indexed: 02/06/2023] Open
Abstract
Identifying druggable targets in the Wnt-signaling pathway can optimize colorectal cancer treatment. Recent studies have identified a member of the RNA helicase family DDX3 (DDX3X) as a multilevel activator of Wnt signaling in cells without activating mutations in the Wnt-signaling pathway. In this study, we evaluated whether DDX3 plays a role in the constitutively active Wnt pathway that drives colorectal cancer. We determined DDX3 expression levels in 303 colorectal cancers by immunohistochemistry. 39% of tumors overexpressed DDX3. High cytoplasmic DDX3 expression correlated with nuclear β-catenin expression, a marker of activated Wnt signaling. Functionally, we validated this finding in vitro and found that inhibition of DDX3 with siRNA resulted in reduced TCF4-reporter activity and lowered the mRNA expression levels of downstream TCF4-regulated genes. In addition, DDX3 knockdown in colorectal cancer cell lines reduced proliferation and caused a G1 arrest, supporting a potential oncogenic role of DDX3 in colorectal cancer. RK-33 is a small molecule inhibitor designed to bind to the ATP-binding site of DDX3. Treatment of colorectal cancer cell lines and patient-derived 3D cultures with RK-33 inhibited growth and promoted cell death with IC50 values ranging from 2.5 to 8 μM. The highest RK-33 sensitivity was observed in tumors with wild-type APC-status and a mutation in CTNNB1. Based on these results, we conclude that DDX3 has an oncogenic role in colorectal cancer. Inhibition of DDX3 with the small molecule inhibitor RK-33 causes inhibition of Wnt signaling and may therefore be a promising future treatment strategy for a subset of colorectal cancers.
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Affiliation(s)
- Marise R Heerma van Voss
- Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.,Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Farhad Vesuna
- Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Kari Trumpi
- Department of Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Justin Brilliant
- Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Cynthia Berlinicke
- Wilmer Eye Institute, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Wendy de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Onno Kranenburg
- Department of Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - G Johan Offerhaus
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Elsken van der Wall
- Department of Internal Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Venu Raman
- Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.,Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Oncology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
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Veiga G, de Leng W, Cachucho R, Ketelaar L, Kok JN, Knobbe A, Neto C, Rieffe C. Social Competence at the Playground: Preschoolers During Recess. Inf Child Dev 2016. [DOI: 10.1002/icd.1957] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Guida Veiga
- Departamento de Desporto e Saúde; Escola de Ciências e Tecnologia; Universidade de Évora; Évora Portugal
- Laboratory of Motor Behavior; Faculdade de Motricidade Humana; Universidade de Lisboa; Lisboa Portugal
| | - Wendy de Leng
- Developmental Psychology; Leiden University; Leiden The Netherlands
| | - Ricardo Cachucho
- Leiden Institute for Advanced Computer Science; Leiden University; Leiden The Netherlands
| | - Lizet Ketelaar
- Developmental Psychology; Leiden University; Leiden The Netherlands
- Dutch Foundation for the Deaf and Hard of Hearing Child; Amsterdam The Netherlands
| | - Joost N. Kok
- Leiden Institute for Advanced Computer Science; Leiden University; Leiden The Netherlands
| | - Arno Knobbe
- Leiden Institute for Advanced Computer Science; Leiden University; Leiden The Netherlands
| | - Carlos Neto
- Laboratory of Motor Behavior, CIPER; Faculdade de Motricidade Humana, Universidade de Lisboa; Lisboa Portugal
| | - Carolien Rieffe
- Developmental Psychology; Leiden University; Leiden The Netherlands
- Dutch Foundation for the Deaf and Hard of Hearing Child; Amsterdam The Netherlands
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Langeveld D, Jansen M, Brosens L, Morsink F, Offerhaus GJ, de Leng W. Diversity counts. Visualizing pretumor progression in the gastrointestinal tract. Am J Clin Pathol 2011; 135:878-88. [PMID: 21571961 DOI: 10.1309/ajcpp3i5hdywmhja] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Tumor progression is critically dependent on the selection of genetic alterations. This clonal evolution can be traced to the stage preceding visible tumor formation called pretumor progression, in which genetic change occurs without visible change. Recently, the identification of intestinal stem cell markers in animal models has made visualization of stem cells possible in vivo. Translating this work to the clinical setting by visualizing stem cells in patient material may allow us to understand differences in patients' vulnerability to cancer development and target preventive measures to high-risk groups. In this review article, we examine some of the analytic methods currently used in research settings tracing stem cell dynamics.
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