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Broers MC, Wieske L, Erdag E, Gürlek C, Bunschoten C, van Doorn PA, Eftimov F, Kuitwaard K, de Vries JM, de Wit MCY, Nagtzaam MM, Franken SC, Zhu L, Paunovic M, de Wit M, Schreurs MW, Lleixà C, Martín-Aguilar L, Pascual-Goñi E, Querol L, Jacobs BC, Huizinga R, Titulaer MJ. Clinical relevance of distinguishing autoimmune nodopathies from CIDP: longitudinal assessment in a large cohort. J Neurol Neurosurg Psychiatry 2023; 95:52-60. [PMID: 37879898 DOI: 10.1136/jnnp-2023-331378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 07/28/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND The aim of this study was to determine treatment response and whether it is associated with antibody titre change in patients with autoimmune nodopathy (AN) previously diagnosed as chronic inflammatory demyelinating polyradiculoneuropathy (CIDP), and to compare clinical features and treatment response between AN and CIDP. METHODS Serum IgG antibodies to neurofascin-155 (NF155), contactin-1 (CNTN1) and contactin-associated protein 1 (CASPR1) were detected with cell-based assays in patients diagnosed with CIDP. Clinical improvement was determined using the modified Rankin scale, need for alternative and/or additional treatments and assessment of the treating neurologist. RESULTS We studied 401 patients diagnosed with CIDP and identified 21 patients with AN (10 anti-NF155, 6 anti-CNTN1, 4 anti-CASPR1 and 1 anti-NF155/anti-CASPR1 double positive). In patients with AN ataxia (68% vs 28%, p=0.001), cranial nerve involvement (34% vs 11%, p=0.012) and autonomic symptoms (47% vs 22%, p=0.025) were more frequently reported; patients with AN improved less often after intravenous immunoglobulin treatment (39% vs 80%, p=0.002) and required additional/alternative treatments more frequently (84% vs 34%, p<0.001), compared with patients with CIDP. Antibody titres decreased or became negative in patients improving on treatment. Treatment withdrawal was associated with a titre increase and clinical deterioration in four patients. CONCLUSIONS Distinguishing CIDP from AN is important, as patients with AN need a different treatment approach. Improvement and relapses were associated with changes in antibody titres, supporting the pathogenicity of these antibodies.
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Affiliation(s)
- Merel C Broers
- Department of Neurology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Luuk Wieske
- Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Ece Erdag
- Department of Neurology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Neuroscience, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Cemre Gürlek
- Department of Neurology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Carina Bunschoten
- Department of Neurology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Pieter A van Doorn
- Department of Neurology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Filip Eftimov
- Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Krista Kuitwaard
- Department of Neurology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Neurology, Albert Schweitzer Hospital, Dordrecht, The Netherlands
| | - Juna M de Vries
- Department of Neurology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Marie-Claire Y de Wit
- Department of Pediatric Neurology, Erasmus MC, Erasmus MC Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Mariska Mp Nagtzaam
- Department of Neurology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Suzanne C Franken
- Department of Neurology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Louisa Zhu
- Department of Neurology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Manuela Paunovic
- Department of Neurology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Maurice de Wit
- Department of Neurology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Marco Wj Schreurs
- Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Cinta Lleixà
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Lorena Martín-Aguilar
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elba Pascual-Goñi
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Luis Querol
- Neuromuscular Diseases Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Centro para la de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - Bart C Jacobs
- Department of Neurology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Ruth Huizinga
- Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Maarten J Titulaer
- Department of Neurology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
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Barin N, Balcioglu HE, de Heer I, de Wit M, Lamfers MLM, van Royen ME, French PJ, Accardo A. 3D-Engineered Scaffolds to Study Microtubes and Localization of Epidermal Growth Factor Receptor in Patient-Derived Glioma Cells. Small 2022; 18:e2204485. [PMID: 36207287 DOI: 10.1002/smll.202204485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/09/2022] [Indexed: 06/16/2023]
Abstract
A major obstacle in glioma research is the lack of in vitro models that can retain cellular features of glioma cells in vivo. To overcome this limitation, a 3D-engineered scaffold, fabricated by two-photon polymerization, is developed as a cell culture model system to study patient-derived glioma cells. Scanning electron microscopy, (live cell) confocal microscopy, and immunohistochemistry are employed to assess the 3D model with respect to scaffold colonization, cellular morphology, and epidermal growth factor receptor localization. Both glioma patient-derived cells and established cell lines successfully colonize the scaffolds. Compared to conventional 2D cell cultures, the 3D-engineered scaffolds more closely resemble in vivo glioma cellular features and allow better monitoring of individual cells, cellular protrusions, and intracellular trafficking. Furthermore, less random cell motility and increased stability of cellular networks is observed for cells cultured on the scaffolds. The 3D-engineered glioma scaffolds therefore represent a promising tool for studying brain cancer mechanobiology as well as for drug screening studies.
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Affiliation(s)
- Nastaran Barin
- Department of Precision and Microsystems Engineering, Delft University of Technology, Mekelweg 2, Delft, 2628 CD, The Netherlands
- Department of Neurology, Erasmus MC Cancer Institute, University Medical Center, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Hayri E Balcioglu
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Iris de Heer
- Department of Neurology, Erasmus MC Cancer Institute, University Medical Center, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Maurice de Wit
- Department of Neurology, Erasmus MC Cancer Institute, University Medical Center, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Martine L M Lamfers
- Department of Neurosurgery, Erasmus MC Cancer Institute, University Medical Center, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Martin E van Royen
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Pim J French
- Department of Neurology, Erasmus MC Cancer Institute, University Medical Center, Doctor Molewaterplein 40, Rotterdam, 3015 GD, The Netherlands
| | - Angelo Accardo
- Department of Precision and Microsystems Engineering, Delft University of Technology, Mekelweg 2, Delft, 2628 CD, The Netherlands
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Mykytyn AZ, Rissmann M, Kok A, Rosu ME, Schipper D, Breugem TI, van den Doel PB, Chandler F, Bestebroer T, de Wit M, van Royen ME, Molenkamp R, Oude Munnink BB, de Vries RD, GeurtsvanKessel C, Smith DJ, Koopmans MPG, Rockx B, Lamers MM, Fouchier R, Haagmans BL. Antigenic cartography of SARS-CoV-2 reveals that Omicron BA.1 and BA.2 are antigenically distinct. Sci Immunol 2022; 7:eabq4450. [PMID: 35737747 PMCID: PMC9273038 DOI: 10.1126/sciimmunol.abq4450] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [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: 04/08/2022] [Accepted: 06/14/2022] [Indexed: 12/16/2022]
Abstract
The emergence and rapid spread of SARS-CoV-2 variants may affect vaccine efficacy substantially. The Omicron variant termed BA.2, which differs substantially from BA.1 based on genetic sequence, is currently replacing BA.1 in several countries, but its antigenic characteristics have not yet been assessed. Here, we used antigenic cartography to quantify and visualize antigenic differences between early SARS-CoV-2 variants (614G, Alpha, Beta, Gamma, Zeta, Delta, and Mu) using hamster antisera obtained after primary infection. We first verified that the choice of the cell line for the neutralization assay did not affect the topology of the map substantially. Antigenic maps generated using pseudo-typed SARS-CoV-2 on the widely used VeroE6 cell line and the human airway cell line Calu-3 generated similar maps. Maps made using authentic SARS-CoV-2 on Calu-3 cells also closely resembled those generated with pseudo-typed viruses. The antigenic maps revealed a central cluster of SARS-CoV-2 variants, which grouped on the basis of mutual spike mutations. Whereas these early variants are antigenically similar, clustering relatively close to each other in antigenic space, Omicron BA.1 and BA.2 have evolved as two distinct antigenic outliers. Our data show that BA.1 and BA.2 both escape vaccine-induced antibody responses as a result of different antigenic characteristics. Thus, antigenic cartography could be used to assess antigenic properties of future SARS-CoV-2 variants of concern that emerge and to decide on the composition of novel spike-based (booster) vaccines.
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Affiliation(s)
- Anna Z. Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Melanie Rissmann
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Adinda Kok
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Miruna E. Rosu
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Debby Schipper
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Tim I. Breugem
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Felicity Chandler
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Theo Bestebroer
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Maurice de Wit
- Department of Neurology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Martin E. van Royen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Richard Molenkamp
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Rory D. de Vries
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Derek J. Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | | | - Barry Rockx
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Mart M. Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Ron Fouchier
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
| | - Bart L. Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands
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4
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Roos FJM, van Tienderen GS, Wu H, Bordeu I, Vinke D, Albarinos LM, Monfils K, Niesten S, Smits R, Willemse J, Rosmark O, Westergren-Thorsson G, Kunz DJ, de Wit M, French PJ, Vallier L, IJzermans JNM, Bartfai R, Marks H, Simons BD, van Royen ME, Verstegen MMA, van der Laan LJW. Human branching cholangiocyte organoids recapitulate functional bile duct formation. Cell Stem Cell 2022; 29:776-794.e13. [PMID: 35523140 DOI: 10.1016/j.stem.2022.04.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 10/21/2021] [Revised: 02/25/2022] [Accepted: 04/14/2022] [Indexed: 12/13/2022]
Abstract
Human cholangiocyte organoids show great promise for regenerative therapies and in vitro modeling of bile duct development and diseases. However, the cystic organoids lack the branching morphology of intrahepatic bile ducts (IHBDs). Here, we report establishing human branching cholangiocyte organoid (BRCO) cultures. BRCOs self-organize into complex tubular structures resembling the IHBD architecture. Single-cell transcriptomics and functional analysis showed high similarity to primary cholangiocytes, and importantly, the branching growth mimics aspects of tubular development and is dependent on JAG1/NOTCH2 signaling. When applied to cholangiocarcinoma tumor organoids, the morphology changes to an in vitro morphology like primary tumors. Moreover, these branching cholangiocarcinoma organoids (BRCCAOs) better match the transcriptomic profile of primary tumors and showed increased chemoresistance to gemcitabine and cisplatin. In conclusion, BRCOs recapitulate a complex process of branching morphogenesis in vitro. This provides an improved model to study tubular formation, bile duct functionality, and associated biliary diseases.
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Affiliation(s)
- Floris J M Roos
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Gilles S van Tienderen
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Haoyu Wu
- Radboud University, Department of Molecular Biology, Nijmegen, the Netherlands
| | - Ignacio Bordeu
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Dina Vinke
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Laura Muñoz Albarinos
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Kathryn Monfils
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Sabrah Niesten
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Ron Smits
- Erasmus MC, University Medical Center Rotterdam, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands
| | - Jorke Willemse
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Oskar Rosmark
- Lung Biology, Department Experimental Medical Science, Lund University, Lund, Sweden
| | | | - Daniel J Kunz
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, University of Cambridge, Cambridge, UK
| | - Maurice de Wit
- Erasmus MC, University Medical Center Rotterdam, Department of Pathology, Rotterdam, the Netherlands
| | - Pim J French
- Erasmus MC, University Medical Center Rotterdam, Cancer Treatment Screening Facility, Department of Neurology, Rotterdam, the Netherlands
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Jan N M IJzermans
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Richard Bartfai
- Radboud University, Department of Molecular Biology, Nijmegen, the Netherlands
| | - Hendrik Marks
- Radboud University, Department of Molecular Biology, Nijmegen, the Netherlands
| | - Ben D Simons
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Martin E van Royen
- Erasmus MC, University Medical Center Rotterdam, Department of Pathology, Rotterdam, the Netherlands
| | - Monique M A Verstegen
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Luc J W van der Laan
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands.
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5
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Hoogstrate Y, Ghisai SA, de Wit M, de Heer I, Draaisma K, van Riet J, van de Werken HJG, Bours V, Buter J, Vanden Bempt I, Eoli M, Franceschi E, Frenel JS, Gorlia T, Hanse MC, Hoeben A, Kerkhof M, Kros JM, Leenstra S, Lombardi G, Lukacova S, Robe PA, Sepulveda JM, Taal W, Taphoorn M, Vernhout RM, Walenkamp AME, Watts C, Weller M, de Vos FYF, Jenster GW, van den Bent M, French PJ. The EGFRvIII transcriptome in glioblastoma, a meta-omics analysis. Neuro Oncol 2021; 24:429-441. [PMID: 34608482 PMCID: PMC8917407 DOI: 10.1093/neuonc/noab231] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background EGFR is among the genes most frequently altered in glioblastoma, with exons 2-7 deletions (EGFRvIII) being among its most common genomic mutations. There are conflicting reports about its prognostic role and it remains unclear whether and how it differs in signaling compared with wildtype EGFR. Methods To better understand the oncogenic role of EGFRvIII, we leveraged 4 large datasets into 1 large glioblastoma transcriptome dataset (n = 741) alongside 81 whole-genome samples from 2 datasets. Results The EGFRvIII/EGFR expression ratios differ strongly between tumors and range from 1% to 95%. Interestingly, the slope of relative EGFRvIII expression is near-linear, which argues against a more positive selection pressure than EGFR wildtype. An absence of selection pressure is also suggested by the similar survival between EGFRvIII-positive and -negative glioblastoma patients. EGFRvIII levels are inversely correlated with pan-EGFR (all wildtype and mutant variants) expression, which indicates that EGFRvIII has a higher potency in downstream pathway activation. EGFRvIII-positive glioblastomas have a lower CDK4 or MDM2 amplification incidence than EGFRvIII-negative (P = .007), which may point toward crosstalk between these pathways. EGFRvIII-expressing tumors have an upregulation of “classical” subtype genes compared to those with EGFR-amplification only (P = 3.873e−6). Genomic breakpoints of the EGFRvIII deletions have a preference toward the 3′-end of the large intron-1. These preferred breakpoints preserve a cryptic exon resulting in a novel EGFRvIII variant and preserve an intronic enhancer. Conclusions These data provide deeper insights into the complex EGFRvIII biology and provide new insights for targeting EGFRvIII mutated tumors.
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Affiliation(s)
- Youri Hoogstrate
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
- Cancer Computational Biology Center, Erasmus MC, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC, Rotterdam, The Netherlands
- Corresponding Author: Youri Hoogstrate, PhD, Department of Neurology, Erasmus MC, PO Box 2040, 3000CA Rotterdam, the Netherlands ()
| | | | - Maurice de Wit
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
| | - Iris de Heer
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
| | - Kaspar Draaisma
- Department of Neurosurgery, UMC Utrecht, Utrecht, The Netherlands
| | - Job van Riet
- Cancer Computational Biology Center, Erasmus MC, Rotterdam, The Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC, Rotterdam, The Netherlands
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Vincent Bours
- Department of Human Genetics, Université de Liège, Liège, Belgium
| | - Jan Buter
- Department of Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Marica Eoli
- Unit of Molecular Neuro-Oncology, Besta-IRCCS, Milan, Italy
| | - Enrico Franceschi
- IRCCS Istituto Scienze Neurologiche di Bologna, Nervous System Medical Oncology Department, Bologna, Italy
| | | | | | - Monique C Hanse
- Department of Neurology, Catharina Hospital, Eindhoven, The Netherlands
| | - Ann Hoeben
- Department of Medical Oncology, Maastricht UMC+, Maastricht, The Netherlands
| | - Melissa Kerkhof
- Department of Neurology, Haaglanden Medical Center, The Hague, The Netherlands
| | - Johan M Kros
- Department of Medical Oncology, Erasmus MC, Rotterdam, The Netherlands
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Sieger Leenstra
- Department of Neurosurgery, Erasmus MC, Rotterdam, The Netherlands
| | | | - Slávka Lukacova
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Pierre A Robe
- Department of Neurosurgery, UMC Utrecht, Utrecht, The Netherlands
| | | | - Walter Taal
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
| | - Martin Taphoorn
- Department of Neurology, Haaglanden Medical Center, The Hague, The Netherlands
| | - René M Vernhout
- Department of Radiotherapy, Erasmus MC, Rotterdam, The Netherlands
| | | | - Colin Watts
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Michael Weller
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland
| | - Filip Y F de Vos
- Department of Medical Oncology, UMC Utrecht, Utrecht, The Netherlands
| | - Guido W Jenster
- Department of Urology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Pim J French
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
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6
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Tesileanu CMS, Vallentgoed WR, Sanson M, Taal W, Clement PM, Wick W, Brandes AA, Baurain JF, Chinot OL, Wheeler H, Gill S, Griffin M, Rogers L, Rudà R, Weller M, McBain C, Reijneveld J, Enting RH, Caparrotti F, Lesimple T, Clenton S, Gijtenbeek A, Lim E, de Vos F, Mulholland PJ, Taphoorn MJB, de Heer I, Hoogstrate Y, de Wit M, Boggiani L, Venneker S, Oosting J, Bovée JVMG, Erridge S, Vogelbaum MA, Nowak AK, Mason WP, Kros JM, Wesseling P, Aldape K, Jenkins RB, Dubbink HJ, Baumert B, Golfinopoulos V, Gorlia T, van den Bent M, French PJ. Non-IDH1-R132H IDH1/2 mutations are associated with increased DNA methylation and improved survival in astrocytomas, compared to IDH1-R132H mutations. Acta Neuropathol 2021; 141:945-957. [PMID: 33740099 PMCID: PMC8113211 DOI: 10.1007/s00401-021-02291-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 12/30/2020] [Revised: 02/05/2021] [Accepted: 02/23/2021] [Indexed: 02/06/2023]
Abstract
Somatic mutations in the isocitrate dehydrogenase genes IDH1 and IDH2 occur at high frequency in several tumour types. Even though these mutations are confined to distinct hotspots, we show that gliomas are the only tumour type with an exceptionally high percentage of IDH1R132H mutations. Patients harbouring IDH1R132H mutated tumours have lower levels of genome-wide DNA-methylation, and an associated increased gene expression, compared to tumours with other IDH1/2 mutations ("non-R132H IDH1/2 mutations"). This reduced methylation is seen in multiple tumour types and thus appears independent of the site of origin. For 1p/19q non-codeleted glioma (astrocytoma) patients, we show that this difference is clinically relevant: in samples of the randomised phase III CATNON trial, patients harbouring tumours with IDH mutations other than IDH1R132H have a better outcome (hazard ratio 0.41, 95% CI [0.24, 0.71], p = 0.0013). Such non-R132H IDH1/2-mutated tumours also had a significantly lower proportion of tumours assigned to prognostically poor DNA-methylation classes (p < 0.001). IDH mutation-type was independent in a multivariable model containing known clinical and molecular prognostic factors. To confirm these observations, we validated the prognostic effect of IDH mutation type on a large independent dataset. The observation that non-R132H IDH1/2-mutated astrocytomas have a more favourable prognosis than their IDH1R132H mutated counterpart indicates that not all IDH-mutations are identical. This difference is clinically relevant and should be taken into account for patient prognostication.
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7
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de Wit M, Gao Y, Mercieca D, de Heer I, Valkenburg B, van Royen ME, Aerts J, Sillevis Smitt P, French P. Mutation and drug-specific intracellular accumulation of EGFR predict clinical responses to tyrosine kinase inhibitors. EBioMedicine 2020; 56:102796. [PMID: 32512509 PMCID: PMC7276512 DOI: 10.1016/j.ebiom.2020.102796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 11/20/2019] [Revised: 03/19/2020] [Accepted: 04/27/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Clinical responses to EGFR tyrosine kinase inhibitors (TKIs) are restricted to tumors harboring specific activating mutations and even then, not all tyrosine kinase inhibitors provide clinical benefit. All TKIs however, effectively inhibit EGFR phosphorylation regardless of the mutation present. METHODS High-throughput, high-content imaging analysis, western blot, Reversed phase protein arrays, mass spectrometry and RT-qPCR. FINDINGS We show that the addition of TKIs results in a strong and rapid intracellular accumulation of EGFR. This accumulation mimicked clinical efficacy as it was observed only in the context of the combination of a TKI-sensitive mutation with a clinically effective (type I) TKI. Intracellular accumulation of EGFR was able to predict response to gefitinib in a panel of cell-lines with different EGFR mutations. Our assay also predicted clinical benefit to EGFR TKIs on a cohort of pulmonary adenocarcinoma patients (hazard ratio 0.21, P=0.0004 [Cox proportional hazard model]) and could predict the clinical response in patients harboring rare mutations with unknown TKI-sensitivity. All investigated TKIs, regardless of clinical efficacy, inhibited EGFR phosphorylation and downstream pathway activation, irrespective of the mutation present. Intracellular accumulation of EGFR depended on a continued presence of TKI indicating (type I) TKIs remain associated with the protein even after its dephosphorylation. Accumulation therefore is likely caused by two consecutive conformational changes, induced by both activating mutation and TKI, that combined block EGFR-membrane recycling. INTERPRETATION We report on an assay that mimics the discrepancy between molecular and clinical activity of EGFR-TKIs, which may allow response prediction in vitro and helps understand the mechanism of effective inhibitors.
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Affiliation(s)
- Maurice de Wit
- Department of Neurology, Erasmus MC, PO Box 2040,Rotterdam, CA 3000, the Netherlands; Cancer Treatment Screening Facility (CTSF), Erasmus MC, Rotterdam, the Netherlands
| | - Ya Gao
- Department of Neurology, Erasmus MC, PO Box 2040,Rotterdam, CA 3000, the Netherlands
| | - Darlene Mercieca
- Department of Pulmonary Diseases, Erasmus MC, Rotterdam, the Netherlands
| | - Iris de Heer
- Department of Neurology, Erasmus MC, PO Box 2040,Rotterdam, CA 3000, the Netherlands
| | - Bart Valkenburg
- Department of Neurology, Erasmus MC, PO Box 2040,Rotterdam, CA 3000, the Netherlands
| | - Martin E van Royen
- Cancer Treatment Screening Facility (CTSF), Erasmus MC, Rotterdam, the Netherlands; Erasmus Optical Imaging Centre (OIC), Erasmus MC, Rotterdam, the Netherlands; Department of Pathology, Erasmus MC, Rotterdam, the Netherlands
| | - Joachim Aerts
- Department of Pulmonary Diseases, Erasmus MC, Rotterdam, the Netherlands
| | - Peter Sillevis Smitt
- Department of Neurology, Erasmus MC, PO Box 2040,Rotterdam, CA 3000, the Netherlands
| | - Pim French
- Department of Neurology, Erasmus MC, PO Box 2040,Rotterdam, CA 3000, the Netherlands; Cancer Treatment Screening Facility (CTSF), Erasmus MC, Rotterdam, the Netherlands.
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Hoogstrate Y, Vallentgoed W, Kros JM, de Heer I, de Wit M, Eoli M, Sepulveda JM, Walenkamp AME, Frenel JS, Franceschi E, Clement PM, Weller M, van Royen ME, Ansell P, Looman J, Bain E, Morfouace M, Gorlia T, Golfinopoulos V, van den Bent M, French PJ. EGFR mutations are associated with response to depatux-m in combination with temozolomide and result in a receptor that is hypersensitive to ligand. Neurooncol Adv 2019; 2:vdz051. [PMID: 32642719 PMCID: PMC7212878 DOI: 10.1093/noajnl/vdz051] [Citation(s) in RCA: 4] [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] [Indexed: 01/24/2023] Open
Abstract
Background The randomized phase II INTELLANCE-2/EORTC_1410 trial on EGFR-amplified recurrent glioblastomas showed a trend towards improved overall survival when patients were treated with depatux-m plus temozolomide compared with the control arm of alkylating chemotherapy only. We here performed translational research on material derived from this clinical trial to identify patients that benefit from this treatment. Methods Targeted DNA-sequencing and whole transcriptome analysis was performed on clinical trial samples. High-throughput, high-content imaging analysis was done to understand the molecular mechanism underlying the survival benefit. Results We first define the tumor genomic landscape in this well-annotated patient population. We find that tumors harboring EGFR single-nucleotide variations (SNVs) have improved outcome in the depatux-m + TMZ combination arm. Such SNVs are common to the extracellular domain of the receptor and functionally result in a receptor that is hypersensitive to low-affinity EGFR ligands. These hypersensitizing SNVs and the ligand-independent EGFRvIII variant are inversely correlated, indicating two distinct modes of evolution to increase EGFR signaling in glioblastomas. Ligand hypersensitivity can explain the therapeutic efficacy of depatux-m as increased ligand-induced activation will result in increased exposure of the epitope to the antibody-drug conjugate. We also identified tumors harboring mutations sensitive to "classical" EGFR tyrosine-kinase inhibitors, providing a potential alternative treatment strategy. Conclusions These data can help guide treatment for recurrent glioblastoma patients and increase our understanding into the molecular mechanisms underlying EGFR signaling in these tumors.
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Affiliation(s)
- Youri Hoogstrate
- Departments of Neurology, Erasmus MC, Rotterdam, The Netherlands.,Urology, Erasmus MC, Rotterdam, The Netherlands
| | - Wies Vallentgoed
- Departments of Neurology, Erasmus MC, Rotterdam, The Netherlands
| | - Johan M Kros
- Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Iris de Heer
- Departments of Neurology, Erasmus MC, Rotterdam, The Netherlands
| | - Maurice de Wit
- Departments of Neurology, Erasmus MC, Rotterdam, The Netherlands
| | | | | | | | | | | | | | - Micheal Weller
- Department of Neurology, University Hospital and University of Zurich, Switzerland
| | - Martin E van Royen
- Pathology, Erasmus MC, Rotterdam, The Netherlands.,Cancer Treatment Screening Facility, Erasmus MC, Rotterdam, The Netherlands
| | | | - Jim Looman
- AbbVie, North Chicago, Illinois, Belgium
| | - Earle Bain
- AbbVie, North Chicago, Illinois, Belgium
| | | | | | | | | | - Pim J French
- Departments of Neurology, Erasmus MC, Rotterdam, The Netherlands.,Cancer Treatment Screening Facility, Erasmus MC, Rotterdam, The Netherlands
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French P, de Wit M, de Heer I, van Royen M, Vallentgoed W, Hoogstrate Y, Sillevis Smitt P. CSIG-08. EXTRACELLULAR DOMAIN MUTATIONS IN EGFR RESULT IN A HYPERSENSITIVE RECEPTOR. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.179] [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: 11/13/2022] Open
Abstract
Abstract
INTRODUCTION
The Epidermal Growth Factor Receptor (EGFR) is a driver gene that is amplified in more than half of all glioblastomas. After the initial high copy-number amplification, secondary missense mutations in the extracellular, ligand binding domain of EGFR can evolve. We here performed analysis on these mutations to better understand their function.
METHODS
Activation of EGFR-mutation constructs was measured by western blot and high-throughput quantitative image analysis using EGFR and phospho-EGFR specific antibodies.
RESULTS
Amphiregulin (AREG) is a low affinity EGFR ligand and was able to only marginally activate EGFRwt at high concentrations. In contrast however, AREG strongly activated all extracellular domain (ECD) mutation constructs (R108K, A289V and G598V). As expected, EGF-stimulation resulted in a strong activation in both EGFRwt and ECD mutation constructs. Further dose response analysis showed that in EGFRwt, all high affinity EGFR ligands (EGF, TGFa, HB-EGF and BTC) resulted in a strong activation and all low affinity ligands AREG, EREG and EPGN resulted in a markedly weaker activation. All ECD mutations however, showed strong activation towards all EGFR ligands, including the low affinity ligands (40%-80% of EGF stimulation). The constitutively active, ligand independent EGFRvIII mutation did not respond to any of the ligands and was mainly found to have an intracellular localization. Interestingly, the presence of ECD mutations and EGFRvIII are inversely correlated: in three large datasets (TCGA, Belob and Intellance 2), the majority of samples expressing EGFRvIII do not express additional ECD mutations and vice versa. ECD mutations likely affect stability of the tethered, inactive conformation thereby increasing exposure of the dimerization domain (II), resulting in increased ligand-sensitivity.
CONCLUSION
These experiments show that EGFR containing extracellular missense mutations render the receptor more sensitive to stimulation by low affinity ligands. Glioblastomas evolve to either become independent of ligand (EGFRvIII) or become ligand-hypersensitive (ECD mutations).
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Affiliation(s)
- Pim French
- Erasmus MC Cancer Institute, Rotterdam, Netherlands
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10
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French P, Gao Y, Wit MD, Mercieca D, Heer ID, Valkenburg B, Royen MV, Aerts J, Smitt PS. Abstract 2071: Protein aggregate formation predicts clinical responses to EGFR tyrosine kinase inhibitors. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2071] [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
Although many tumours depend on EGFR signalling for growth, benefit from EGFR tyrosine kinase inhibitors (TKIs) is restricted to patients harboring specific activating mutations and even then restricted to specific TKIs only. We here performed functional analysis on EGFR to understand why only specific mutation-TKI combinations respond. We find that the addition of TKIs (n=5 inhibitors tested) to mutated-EGFR expressing cells resulted in a rapid and massive formation of protein aggregates, but only with EGFR-mutations where clinical responses have been documented (L858R, ΔE746-A750) and only with TKIs with proven clinical benefit (n=4). No aggregates are formed with inhibitors that are clinically inactive (lapatinib) or with clinically unresponsive mutations (EGFRvIII, EGFRwt). Constructs harboring secondary resistance mutations only formed aggregates in the presence of osimertinib. Western blot, quantitative imaging analysis, revers phase phosphoprotein arrays (RPPA) and RT-qPCR was performed on five different lung cancer cell lines to demonstrate that all TKIs effectively inhibit EGFR phosphorylation and downstream pathway activation. Aggregate formation therefore occurs in addition to EGFR dephosphorylation. We next tested whether our assay is able to predict clinical responses to EGFR TKIs. For this, we first generated eleven different mutation constructs and show that our in-vitro assay directly correlates with cell survival in eleven different EGFR-mutated cell-lines, with striking concordance of IC50 values. We then generated more mutation constructs (total n=31) to show that our in-vitro assay predicts clinical benefit to EGFR TKIs in pulmonary adenocarcinoma patients (median survival 7.0 vs 13 months, HR 0.21, P=0.0004), including prediction of mutations where the response to inhibitors has thus-far not been documented (n=7). Our in-vitro assay therefore provides a clinically important asset to predict whether a tumor harboring an unknown mutation will respond to EGFR-TKIs, and if so, which TKI is most effective. We propose a model whereby only clinically effective inhibitors induce a conformational change, which occurs only in the context of specific activating mutations and in addition to EGFR dephosphorylation. Since this model only depends on the mutation present and the inhibitor used, response to EGFR TKIs is largely independent of the genetic background of the tumor. All patients with sensitive EGFR mutations should, regardless of the type of tumor, be considered for treatment with EGFR-TKIs.
Citation Format: Pim French, Ya Gao, Maurice de Wit, Darlene Mercieca, Iris de Heer, Bart Valkenburg, Martin van Royen, Joachim Aerts, Peter Sillevis Smitt. Protein aggregate formation predicts clinical responses to EGFR tyrosine kinase inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2071.
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Affiliation(s)
| | - Ya Gao
- Erasmus MC, Rotterdam, Netherlands
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French P, Gao Y, de Wit M, Mercieca D, de Heer I, van Royen M, Aerts J, Sillevis Smitt P. DRES-14. PROTEIN AGGREGATE FORMATION PREDICTS CLINICAL RESPONSES TO EGFR TKIs. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.321] [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: 11/12/2022] Open
Affiliation(s)
- Pim French
- Dept. of Neurology, Brain Tumor Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Ya Gao
- Dept. of Neurology, Brain Tumor Center, Erasmus Medical Center, Rotterdam, Netherlands
| | | | | | - Iris de Heer
- Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | | | - Joachim Aerts
- Erasmus MC, Pulmonary Diseases, Rotterdam, Netherlands
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Gao Y, de Wit M, Struys EA, van der Linde HCZ, Salomons GS, Lamfers MLM, Willemsen R, Sillevis Smitt PAE, French PJ. IDH1-mutated transgenic zebrafish lines: An in-vivo model for drug screening and functional analysis. PLoS One 2018; 13:e0199737. [PMID: 29953513 PMCID: PMC6023169 DOI: 10.1371/journal.pone.0199737] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/13/2018] [Indexed: 01/04/2023] Open
Abstract
Introduction The gene encoding isocitrate dehydrogenase 1 (IDH1) is frequently mutated in several tumor types including gliomas. The most prevalent mutation in gliomas is a missense mutation leading to a substitution of arginine with histidine at the residue 132 (R132H). Wild type IDH1 catalyzes oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG) whereas mutant IDH1 converts α-KG into D2-hydroxyglutarate (D2HG). Unfortunately, there are few in vivo model systems for IDH-mutated tumors to study the effects of IDH1 mutations in tumor development. We have therefore created transgenic zebrafish lines that express various IDH1 mutants. Materials and methods IDH1 mutations (IDH1R132H, IDH1R132C and loss-of-function mutation IDH1G70D), IDH1wildtype or eGFP were cloned into constructs with several brain-specific promoters (Nestin, Gfap or Gata2). These constructs were injected into fertilized zebrafish eggs at the one-cell stage. Results In total more than ten transgenic zebrafish lines expressing various brain-specific IDH1 mutations were created. A significant increase in the level of D2HG was observed in all transgenic lines expressing IDH1R132C or IDH1R132H, but not in any of the lines expressing IDH1wildtype, IDH1G70D or eGFP. No differences in 5-hydroxymethyl cytosine and mature collagen IV levels were observed between wildtype and mutant IDH1 transgenic fish. To our surprise, we failed to identify any strong phenotype, despite increased levels of the oncometabolite D2HG. No tumors were observed, even when backcrossing with tp53-mutant fish which suggests that additional transforming events are required for tumor formation. Elevated D2HG levels could be lowered by treatment of the transgenic zebrafish with an inhibitor of mutant IDH1 activity. Conclusions We have generated a transgenic zebrafish model system for mutations in IDH1 that can be used for functional analysis and drug screening. Our model systems help understand the biology of IDH1 mutations and its role in tumor formation.
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Affiliation(s)
- Ya Gao
- Department of Neurology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Maurice de Wit
- Department of Neurology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Eduard A. Struys
- Department of Clinical Chemistry, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Gajja S. Salomons
- Department of Clinical Chemistry, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Rob Willemsen
- Department of Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Pim J. French
- Department of Neurology, Erasmus Medical Center, Rotterdam, the Netherlands
- * E-mail:
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Gao YD, de Wit M, Struys EA, Lamfers ML, Salomons GS, Sillevis Smitt PA, French PJ. Abstract 4170: A transgenic zebrafish model for gliomas with mutations in isocitrate dehydrogenase 1. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4170] [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
The gene encoding Isocitrate dehydrogenase 1 (IDH1) is frequently mutated in gliomas, chondrosarcomas, acute myeloid leukemia and intrahepatic cholangiocarcinomas. As there are few in-vivo model systems for IDH-mutated tumors we have created a transgenic zebrafish (Danio rerio) model expressing mutant IDH1. We have chosen the zebrafish as a model because they are transparent (allowing monitoring of the transgene in-vivo) and drug screening assays are straightforward (they are simply added to the aquarium).
IDH1R132H and IDH1R132C, mutations found in tumors that both produce D-2-hydroxyglutarate (D2HG) instead of alpha ketoglutarate, were cloned into an expression construct that is driven either by the Nestin or GFAP promoter. IDH1G70D (a loss of function mutation), IDH1wildtype and GFP were used as control. All IDH1 constructs were fused to GFP for visualization. These constructs were injected into fertilized zebrafish eggs at the one-cell stage.
All of our transgenic zebrafish lines remain healthy and produce offspring. Transgene expression was detected in the mid/hindbrain of the central nervous system by immunohistochemistry, Western blot and RT-QPCR. A significant increase in the level of D2HG was observed in all transgenic lines expressing IDH1R132C or IDH1R132H, but not in any of the lines expressing control constructs (IDH1wildtype, IDH1G70D or GFP). In contrast to reported, we failed to detect any differences in hydroxymethyl cytosine (the first step in DNA-demethylation) and mature collagen IV levels between wildtype and mutant IDH1 transgenic fish. We also performed microinjections on fertilized eggs to screen for early developmental effects of IDH1R132H and IDH1R132C. Despite of the high expression of the transgene, no developmental effects were found. Our observations therefore suggest that elevated levels of D2HG are insufficient to initiate tumorigenesis or other phenotypic effects in our fish. Treatment of the transgenic zebrafish with an IDH1 mutant inhibitor, AGI-5198, resulted in a reduction in the D2HG level in the mutant zebrafish. The L2HG level was not affected by AGI-5198. As no tumors were formed in our transgenic zebrafish lines, we backcrossed them with Tp53 mutant fish. Analysis of these lines is currently being performed.
In summary, we have generated a transgenic zebrafish model system that expresses mutated IDH1 that can be used to study effects of mutant IDH1 (or elevated levels of D2HG) in vivo and can be used for drug screening.
Citation Format: Ya D. Gao, Maurice de Wit, Eduard A. Struys, Martine L.M. Lamfers, Gajja S. Salomons, Peter A.E. Sillevis Smitt, Pim J. French. A transgenic zebrafish model for gliomas with mutations in isocitrate dehydrogenase 1. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4170.
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Affiliation(s)
- Ya D. Gao
- 1Department of Neurology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Maurice de Wit
- 1Department of Neurology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Eduard A. Struys
- 2Department of Clinical Chemistry, VU University Medical Center, Amsterdam, Netherlands
| | | | - Gajja S. Salomons
- 2Department of Clinical Chemistry, VU University Medical Center, Amsterdam, Netherlands
| | | | - Pim J. French
- 1Department of Neurology, Erasmus Medical Center, Rotterdam, Netherlands
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14
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Erdem-Eraslan L, van den Bent MJ, Hoogstrate Y, Naz-Khan H, Stubbs A, van der Spek P, Böttcher R, Gao Y, de Wit M, Taal W, Oosterkamp HM, Walenkamp A, Beerepoot LV, Hanse MCJ, Buter J, Honkoop AH, van der Holt B, Vernhout RM, Sillevis Smitt PAE, Kros JM, French PJ. Identification of Patients with Recurrent Glioblastoma Who May Benefit from Combined Bevacizumab and CCNU Therapy: A Report from the BELOB Trial. Cancer Res 2016; 76:525-34. [PMID: 26762204 DOI: 10.1158/0008-5472.can-15-0776] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 10/08/2015] [Indexed: 11/16/2022]
Abstract
The results from the randomized phase II BELOB trial provided evidence for a potential benefit of bevacizumab (beva), a humanized monoclonal antibody against circulating VEGF-A, when added to CCNU chemotherapy in patients with recurrent glioblastoma (GBM). In this study, we performed gene expression profiling (DASL and RNA-seq) of formalin-fixed, paraffin-embedded tumor material from participants of the BELOB trial to identify patients with recurrent GBM who benefitted most from beva+CCNU treatment. We demonstrate that tumors assigned to the IGS-18 or "classical" subtype and treated with beva+CCNU showed a significant benefit in progression-free survival and a trend toward benefit in overall survival, whereas other subtypes did not exhibit such benefit. In particular, expression of FMO4 and OSBPL3 was associated with treatment response. Importantly, the improved outcome in the beva+CCNU treatment arm was not explained by an uneven distribution of prognostically favorable subtypes as all molecular glioma subtypes were evenly distributed along the different study arms. The RNA-seq analysis also highlighted genetic alterations, including mutations, gene fusions, and copy number changes, within this well-defined cohort of tumors that may serve as useful predictive or prognostic biomarkers of patient outcome. Further validation of the identified molecular markers may enable the future stratification of recurrent GBM patients into appropriate treatment regimens.
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Affiliation(s)
- Lale Erdem-Eraslan
- Department of Neurology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | - Youri Hoogstrate
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands. Bioinformatics, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Hina Naz-Khan
- Bioinformatics, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Andrew Stubbs
- Bioinformatics, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | - René Böttcher
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Ya Gao
- Department of Neurology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Maurice de Wit
- Department of Neurology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Walter Taal
- Department of Neurology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Hendrika M Oosterkamp
- Department of Medical Oncology, Medical Center Haaglanden, The Hague, the Netherlands
| | - Annemiek Walenkamp
- Department of Medical Oncology, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Monique C J Hanse
- Department of Neurology, Catharina Hospital Eindhoven, the Netherlands
| | - Jan Buter
- Department of Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Aafke H Honkoop
- Department of Internal Medicine, Isala Kliniek, Zwolle, the Netherlands
| | - Bronno van der Holt
- Clinical Trial Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - René M Vernhout
- Clinical Trial Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | - Johan M Kros
- Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Pim J French
- Department of Neurology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
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Erdem-Eraslan L, Heijsman D, de Wit M, Kremer A, Sacchetti A, van der Spek PJ, Smitt PAES, French PJ. Tumor-specific mutations in low-frequency genes affect their functional properties. J Neurooncol 2015; 122:461-70. [PMID: 25694352 PMCID: PMC4436689 DOI: 10.1007/s11060-015-1741-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 10/01/2014] [Accepted: 02/01/2015] [Indexed: 12/16/2022]
Abstract
Causal genetic changes in oligodendrogliomas (OD) with 1p/19q co-deletion include mutations in IDH1, IDH2, CIC, FUBP1, TERT promoter and NOTCH1. However, it is generally assumed that more somatic mutations are required for tumorigenesis. This study aimed to establish whether genes mutated at low frequency can be involved in OD initiation and/or progression. We performed whole-genome sequencing on three anaplastic ODs with 1p/19q co-deletion. To estimate mutation frequency, we performed targeted resequencing on an additional 39 ODs. Whole-genome sequencing identified a total of 55 coding mutations (range 8-32 mutations per tumor), including known abnormalities in IDH1, IDH2, CIC and FUBP1. We also identified mutations in genes, most of which were previously not implicated in ODs. Targeted resequencing on 39 additional ODs confirmed that these genes are mutated at low frequency. Most of the mutations identified were predicted to have a deleterious functional effect. Functional analysis on a subset of these genes (e.g. NTN4 and MAGEH1) showed that the mutation affects the subcellular localization of the protein (n = 2/12). In addition, HOG cells stably expressing mutant GDI1 or XPO7 showed altered cell proliferation compared to those expressing wildtype constructs. Similarly, HOG cells expressing mutant SASH3 or GDI1 showed altered migration. The significantly higher rate of predicted deleterious mutations, the changes in subcellular localization and the effects on proliferation and/or migration indicate that many of these genes functionally may contribute to gliomagenesis and/or progression. These low-frequency genes and their affected pathways may provide new treatment targets for this tumor type.
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Affiliation(s)
- Lale Erdem-Eraslan
- Department of Neurology, Be 430A, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Daphne Heijsman
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Maurice de Wit
- Department of Neurology, Be 430A, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Andreas Kremer
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Andrea Sacchetti
- Department of Pathology, Josephine Nefkens Institute, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Peter A. E. Sillevis Smitt
- Department of Neurology, Be 430A, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Pim J. French
- Department of Neurology, Be 430A, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
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Erdem-Eraslan L, de Wit M, Heijsman D, Kremer A, van der Spek PJ, Sillevis Smitt PA, French PJ. Abstract 3142: Whole genome sequencing of oligodendrogliomas identifies genes mutated at a low frequency that contribute to tumor formation. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-3142] [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: Causal genetic changes in oligodendrogliomas (OD) with 1p/19q codeletion include mutations in IDH1, IDH2, CIC and FUBP1. Here, we have performed whole genome sequencing on three ODs to determine whether additional genetic changes contribute to tumor formation.
Methods: We performed whole genome sequencing of DNA from 3 ODs grade III with 1p/19q codeletion and matched germline DNA. Targeted resequencing of identified genes was performed in an additional 32 ODs with 1p19q LOH (28/32) or partial loss of 1p (2/32), 19q (2/32). All mutations were validated by Sanger sequencing. Constructs of wildtype and mutated genes were subsequently generated (n=13), fused to GFP for visualization. Established cell lines were created to perform functional analysis.
Results: Whole genome sequencing identified a total of 55 mutations in coding exons (range 8-32 mutations per tumor), including the known molecular abnormalities in IDH1 (2/3), IDH2 (1/3), CIC (2/3) and FUBP1 (1/3). Mutations in the ATRX gene were not identified. In addition to these known genes, we identified mutations in additional genes, most of which were previously not implicated in ODs. We first examined the mutation frequency of these genes in an additional 32 tumors. No additional mutations were identified. We then performed functional analysis on a subset of these mutations. For ZNF238, we observed a difference in the sub cellular localization between wildtype and mutant contructs; the wildtype protein localized to the nucleus while the mutant protein is present in the cytoplasm. In addition, stably transfected ZNF238 mutant cell line shows increased proliferation compared to wildtype.
Conclusion: Our results confirm that mutations in IDH, CIC and FUBP1 are present at high frequency in oligodendrogliomas with 1p/19q loss. Functional analysis of infrequently mutated genes provide evidence that they contribute to oncogenesis.
Citation Format: Lale Erdem-Eraslan, Maurice de Wit, Daphne Heijsman, Andreas Kremer, Peter J. van der Spek, Peter A.E. Sillevis Smitt, Pim J. French. Whole genome sequencing of oligodendrogliomas identifies genes mutated at a low frequency that contribute to tumor formation. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3142. doi:10.1158/1538-7445.AM2013-3142
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