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Dutoit V, Migliorini D, Ranzanici G, Marinari E, Widmer V, Lobrinus JA, Momjian S, Costello J, Walker PR, Okada H, Weinschenk T, Herold-Mende C, Dietrich PY. Antigenic expression and spontaneous immune responses support the use of a selected peptide set from the IMA950 glioblastoma vaccine for immunotherapy of grade II and III glioma. Oncoimmunology 2017; 7:e1391972. [PMID: 29308320 PMCID: PMC5749651 DOI: 10.1080/2162402x.2017.1391972] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/09/2017] [Accepted: 10/09/2017] [Indexed: 01/03/2023] Open
Abstract
Gliomas are lethal brain tumors that resist standard therapeutic approaches. Immunotherapy is a promising alternative strategy mostly developed in the context of glioblastoma. However, there is a need for implementing immunotherapy for grade II/III gliomas, as these are the most common CNS tumors in young adults with a high propensity for recurrence, making them lethal despite current treatments. We recently identified HLA-A2-restricted tumor-associated antigens by peptide elution from glioblastoma and formulated a multipeptide vaccine (IMA950) evaluated in phase I/II clinical trials with promising results. Here, we investigated expression of the IMA950 antigens in patients with grade II/III astrocytoma, oligodendroglioma or ependymoma, at the mRNA, protein and peptide levels. We report that the BCAN, CSPG4, IGF2BP3, PTPRZ1 and TNC proteins are significantly over-expressed at the mRNA (n = 159) and protein (n = 36) levels in grade II/III glioma patients as compared to non-tumor samples (IGF2BP3 being absent from oligodendroglioma). Most importantly, we detected spontaneous antigen-specific T cell responses to one or more of the IMA950 antigens in 100% and 71% of grade II and grade III patients, respectively (27 patients tested). These patients displayed T cell responses of better quality (higher frequency, broader epitope targeting) than patients with glioblastoma. Detection of spontaneous T cell responses to the IMA950 antigens shows that these antigens are relevant for tumor targeting, which will be best achieved by combination with CD4 epitopes such as the IDH1R132H peptide. Altogether, we provide the rationale for using a selective set of IMA950 peptides for vaccination of patients with grade II/III glioma.
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Affiliation(s)
- Valérie Dutoit
- Department of Oncology, Geneva University Hospital, Rue Gabrielle-Perret-Gentil 4, 1204 Geneva 11, Switzerland and Department of Internal Medicine Specialties, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, 1205 Geneva Switzerland
| | - Denis Migliorini
- Department of Oncology, Geneva University Hospital, Rue Gabrielle-Perret-Gentil 4, 1204 Geneva 11, Switzerland and Department of Internal Medicine Specialties, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, 1205 Geneva Switzerland
| | - Giulia Ranzanici
- Department of Oncology, Geneva University Hospital, Rue Gabrielle-Perret-Gentil 4, 1204 Geneva 11, Switzerland and Department of Internal Medicine Specialties, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, 1205 Geneva Switzerland
| | - Eliana Marinari
- Department of Oncology, Geneva University Hospital, Rue Gabrielle-Perret-Gentil 4, 1204 Geneva 11, Switzerland and Department of Internal Medicine Specialties, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, 1205 Geneva Switzerland
| | - Valérie Widmer
- Department of Oncology, Geneva University Hospital, Rue Gabrielle-Perret-Gentil 4, 1204 Geneva 11, Switzerland and Department of Internal Medicine Specialties, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, 1205 Geneva Switzerland
| | - Johannes Alexander Lobrinus
- Division of Clinical Pathology, Geneva University Hospitals and University of Geneva, Rue Gabrielle-Perret-Gentil 4, 1204 Geneva 11, Switzerland
| | - Shahan Momjian
- Neurosurgery Service, Geneva University Hospitals and University of Geneva, Rue Gabrielle-Perret-Gentil 4, 1204 Geneva 11, Switzerland
| | - Joseph Costello
- Brain Tumor Research Centre, Department of Neurosurgery, University of California San Francisco, 505 Parnassus Ave, Room 779 M, San Francisco, CA, USA
| | - Paul R Walker
- Department of Oncology, Geneva University Hospital, Rue Gabrielle-Perret-Gentil 4, 1204 Geneva 11, Switzerland and Department of Internal Medicine Specialties, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, 1205 Geneva Switzerland
| | - Hideho Okada
- Brain Tumor Research Centre, Department of Neurosurgery, University of California San Francisco, 505 Parnassus Ave, Room 779 M, San Francisco, CA, USA.,Cancer Immunotherapy Program, University of California San Francisco and The Parker Institute for Cancer Immunotherapy, 1 Letterman Drive, Suite D3500, San Francisco, CA, USA
| | - Toni Weinschenk
- Immatics Biotechnologies GmbH, Paul-Ehrlich-Strasse 15, Tübingen, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University of Heidelberg, Im Neuenheimer Feld 400, Heidelberg, Germany
| | - Pierre-Yves Dietrich
- Department of Oncology, Geneva University Hospital, Rue Gabrielle-Perret-Gentil 4, 1204 Geneva 11, Switzerland and Department of Internal Medicine Specialties, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, 1205 Geneva Switzerland
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Olsen TK, Panagopoulos I, Meling TR, Micci F, Gorunova L, Thorsen J, Due-Tønnessen B, Scheie D, Lund-Iversen M, Krossnes B, Saxhaug C, Heim S, Brandal P. Fusion genes with ALK as recurrent partner in ependymoma-like gliomas: a new brain tumor entity? Neuro Oncol 2015; 17:1365-73. [PMID: 25795305 DOI: 10.1093/neuonc/nov039] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 02/18/2015] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND We have previously characterized 19 ependymal tumors using Giemsa banding and high-resolution comparative genomic hybridization. The aim of this study was to analyze these tumors searching for fusion genes. METHODS RNA sequencing was performed in 12 samples. Potential fusion transcripts were assessed by seed count and structural chromosomal aberrations. Transcripts of interest were validated using fluorescence in situ hybridization and PCR followed by direct sequencing. RESULTS RNA sequencing identified rearrangements of the anaplastic lymphoma kinase gene (ALK) in 2 samples. Both tumors harbored structural aberrations involving the ALK locus 2p23. Tumor 1 had an unbalanced t(2;14)(p23;q22) translocation which led to the fusion gene KTN1-ALK. Tumor 2 had an interstitial del(2)(p16p23) deletion causing the fusion of CCDC88A and ALK. In both samples, the breakpoint of ALK was located between exons 19 and 20. Both patients were infants and both tumors were supratentorial. The tumors were well demarcated from surrounding tissue and had both ependymal and astrocytic features but were diagnosed and treated as ependymomas. CONCLUSIONS By combining karyotyping and RNA sequencing, we identified the 2 first ever reported ALK rearrangements in CNS tumors. Such rearrangements may represent the hallmark of a new entity of pediatric glioma characterized by both ependymal and astrocytic features. Our findings are of particular importance because crizotinib, a selective ALK inhibitor, has demonstrated effect in patients with lung cancer harboring ALK rearrangements. Thus, ALK emerges as an interesting therapeutic target in patients with ependymal tumors carrying ALK fusions.
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Affiliation(s)
- Thale Kristin Olsen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., S.H.); Department of Neurosurgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway (T.R.M., B.D.-T.); Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway (M.L.-I., B.K.); Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (C.S.); Department of Pathology, Rigshospitalet, Copenhagen, Denmark (D.S.); Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (P.B.)
| | - Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., S.H.); Department of Neurosurgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway (T.R.M., B.D.-T.); Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway (M.L.-I., B.K.); Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (C.S.); Department of Pathology, Rigshospitalet, Copenhagen, Denmark (D.S.); Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (P.B.)
| | - Torstein R Meling
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., S.H.); Department of Neurosurgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway (T.R.M., B.D.-T.); Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway (M.L.-I., B.K.); Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (C.S.); Department of Pathology, Rigshospitalet, Copenhagen, Denmark (D.S.); Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (P.B.)
| | - Francesca Micci
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., S.H.); Department of Neurosurgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway (T.R.M., B.D.-T.); Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway (M.L.-I., B.K.); Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (C.S.); Department of Pathology, Rigshospitalet, Copenhagen, Denmark (D.S.); Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (P.B.)
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., S.H.); Department of Neurosurgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway (T.R.M., B.D.-T.); Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway (M.L.-I., B.K.); Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (C.S.); Department of Pathology, Rigshospitalet, Copenhagen, Denmark (D.S.); Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (P.B.)
| | - Jim Thorsen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., S.H.); Department of Neurosurgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway (T.R.M., B.D.-T.); Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway (M.L.-I., B.K.); Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (C.S.); Department of Pathology, Rigshospitalet, Copenhagen, Denmark (D.S.); Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (P.B.)
| | - Bernt Due-Tønnessen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., S.H.); Department of Neurosurgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway (T.R.M., B.D.-T.); Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway (M.L.-I., B.K.); Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (C.S.); Department of Pathology, Rigshospitalet, Copenhagen, Denmark (D.S.); Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (P.B.)
| | - David Scheie
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., S.H.); Department of Neurosurgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway (T.R.M., B.D.-T.); Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway (M.L.-I., B.K.); Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (C.S.); Department of Pathology, Rigshospitalet, Copenhagen, Denmark (D.S.); Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (P.B.)
| | - Marius Lund-Iversen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., S.H.); Department of Neurosurgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway (T.R.M., B.D.-T.); Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway (M.L.-I., B.K.); Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (C.S.); Department of Pathology, Rigshospitalet, Copenhagen, Denmark (D.S.); Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (P.B.)
| | - Bård Krossnes
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., S.H.); Department of Neurosurgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway (T.R.M., B.D.-T.); Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway (M.L.-I., B.K.); Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (C.S.); Department of Pathology, Rigshospitalet, Copenhagen, Denmark (D.S.); Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (P.B.)
| | - Cathrine Saxhaug
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., S.H.); Department of Neurosurgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway (T.R.M., B.D.-T.); Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway (M.L.-I., B.K.); Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (C.S.); Department of Pathology, Rigshospitalet, Copenhagen, Denmark (D.S.); Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (P.B.)
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., S.H.); Department of Neurosurgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway (T.R.M., B.D.-T.); Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway (M.L.-I., B.K.); Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (C.S.); Department of Pathology, Rigshospitalet, Copenhagen, Denmark (D.S.); Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (P.B.)
| | - Petter Brandal
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., I.P., F.M., L.G., J.T., S.H., P.B.); Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway (T.K.O., S.H.); Department of Neurosurgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway (T.R.M., B.D.-T.); Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway (M.L.-I., B.K.); Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (C.S.); Department of Pathology, Rigshospitalet, Copenhagen, Denmark (D.S.); Department of Oncology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway (P.B.)
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