Abstract
Glioblastoma (GBM) is a devastating tumor and few patients survive beyond 3 years. Defining the molecular determinants underlying long-term survival is essential for insights into tumor biology and biomarker identification. We therefore investigated homogeneously treated, IDH wt long-term (LTS, n = 10) and short-term survivors (STS, n = 6) by microarray transcription profiling. While there was no association of clinical parameters and molecular subtypes with long-term survival, STS tumors were characterized by differential polarization of infiltrating microglia with predominance of the M2 phenotype detectable both on the mRNA and protein level. Furthermore, transcriptional signatures of LTS and STS predicted patient outcome in a large, IDH wt cohort (n = 468). Interrogation of overlapping genomic alterations identified concurrent gain of chromosomes 19 and 20 as a favorable prognostic marker. The strong association of this co-gain with survival was validated by aCGH in a second, independent cohort (n = 124). Finally, FISH and gene expression data revealed gains to constitute low-amplitude, clonal events with a strong impact on transcription. In conclusion, these findings provide important insights into the manipulation of the innate immune system by particularly aggressive GBM tumors. Furthermore, we genomically characterize a previously unknown, clinically relevant subgroup of glioblastoma, which can easily be identified through modern neuropathological workup.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Alvarez S, MacGrogan D, Calasanz MJ, Nimer SD, Jhanwar SC (2001) Frequent gain of chromosome 19 in megakaryoblastic leukemias detected by comparative genomic hybridization. Genes Chromosom Cancer 32:285–293
Brennan CW, Verhaak RGW, McKenna A, Campos B, Noushmehr H, Salama SR et al (2013) The somatic genomic landscape of glioblastoma. Cell 155:462–477
Burton EC, Lamborn KR, Feuerstein BG, Prados M, Scott J, Forsyth P et al (2002) Genetic aberrations defined by comparative genomic hybridization distinguish long-term from typical survivors of glioblastoma. Cancer Res 62:6205–6210
Burton EC, Lamborn KR, Forsyth P, Scott J, O’Campo J, Uyehara-Lock J et al (2002) Aberrant p53, mdm2, and proliferation differ in glioblastomas from long-term compared with typical survivors. Clin Cancer Res 8:180–187
Capper D, Zentgraf H, Balss J, Hartmann C, Von Deimling A (2009) Monoclonal antibody specific for IDH1 R132H mutation. Acta Neuropathol 118:599–601
Carro MS, Lim WK, Alvarez MJ, Bollo RJ, Zhao X, Snyder EY et al (2010) The transcriptional network for mesenchymal transformation of brain tumours. Nature 463:318–325
Colman H, Zhang L, Sulman EP, McDonald JM, Shooshtari NL, Rivera A et al (2010) A multigene predictor of outcome in glioblastoma. Neurooncology 12:49–57
Cooper LAD, Gutman DA, Chisolm C, Appin C, Kong J, Rong Y et al (2012) The tumor microenvironment strongly impacts master transcriptional regulators and gene expression class of glioblastoma. Am J Pathol 180:2108–2119
Da Fonseca ACC, Romão L, Amaral RF, Assad Kahn S, Lobo D, Martins S et al (2012) Microglial stress inducible protein 1 promotes proliferation and migration in human glioblastoma cells. Neuroscience 200:130–141
Davis S, Meltzer PS (2007) GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics 23:1846–1847
Debus J, Abdollahi A (2014) For the next trick: new discoveries in radiobiology applied to glioblastoma. Am Soc Clin Oncol Educ Book 34:95–99
Deloukas P, Matthews LH, Ashurst J, Burton J, Gilbert JG, Jones M et al (2001) The DNA sequence and comparative analysis of human chromosome 20. Nature 414:865–871
Donson AM, Birks DK, Schittone SA, Kleinschmidt-DeMasters BK, Sun DY, Hemenway MF et al (2012) Increased immune gene expression and immune cell infiltration in high-grade astrocytoma distinguish long-term from short-term survivors. J Immunol 189:1920–1927
Engler JR, Robinson AE, Smirnov I, Hodgson JG, Berger MS, Gupta N et al (2012) Increased microglia/macrophage gene expression in a subset of adult and pediatric astrocytomas. PLoS One 7:e43339
Freije WA, Castro-Vargas FE, Fang Z, Horvath S, Cloughesy T, Liau LM et al (2004) Gene expression profiling of gliomas strongly predicts survival. Cancer Res 64:6503–6510
Gerber NK, Goenka A, Turcan S, Reyngold M, Makarov V, Kannan K et al (2014) Transcriptional diversity of long-term glioblastoma survivors. Neurooncology 16:1186–1195
Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E et al (2012) Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing. N Engl J Med 366:883–892
Glass R, Synowitz M (2014) CNS macrophages and peripheral myeloid cells in brain tumours. Acta Neuropathol 128:347–362
Greaves M, Maley CC (2012) Clonal evolution in cancer. Nature 481:306–313
Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J et al (2004) The DNA sequence and biology of human chromosome 19. Nature 428:529–535
Hartmann C, Hentschel B, Simon M, Westphal M, Schackert G, Tonn JC et al (2013) Long-term survival in primary glioblastoma with versus without isocitrate dehydrogenase mutations. Clin Cancer Res 19:5146–5157
Hartmann C, Meyer J, Balss J, Capper D, Mueller W, Christians A et al (2009) Type and frequency of IDH1 and IDH2 mutations are related to astrocytic and oligodendroglial differentiation and age: a study of 1,010 diffuse gliomas. Acta Neuropathol 118:469–474
Heimberger AB, Hlatky R, Suki D, Yang D, Weinberg J, Gilbert M et al (2005) Prognostic effect of epidermal growth factor receptor and EGFRvIII in glioblastoma multiforme patients. Clin Cancer Res 11:1462–1466
Houillier C, Lejeune J, Benouaich-Amiel A, Laigle-Donadey F, Criniere E, Mokhtari K et al (2006) Prognostic impact of molecular markers in a series of 220 primary glioblastomas. Cancer 106:2218–2223
Hovestadt V, Remke M, Kool M, Pietsch T, Northcott PA, Fischer R et al (2013) Robust molecular subgrouping and copy-number profiling of medulloblastoma from small amounts of archival tumour material using high-density DNA methylation arrays. Acta Neuropathol 125:913–916
Huber W, von Heydebreck A, Sültmann H, Poustka A, Vingron M (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18(Suppl 1):S96–104
Jones DTW, Ichimura K, Liu L, Pearson DM, Plant K, Collins VP (2006) Genomic analysis of pilocytic astrocytomas at 0.97 Mb resolution shows an increasing tendency toward chromosomal copy number change with age. J Neuropathol Exp Neurol 65:1049–1058
Kees T, Lohr J, Noack J, Mora R, Gdynia G, Tödt G et al (2012) Microglia isolated from patients with glioma gain antitumor activities on poly (I:C) stimulation. Neurooncology 14:64–78
Kim Y-W, Koul D, Kim SH, Lucio-Eterovic AK, Freire PR, Yao J et al (2013) Identification of prognostic gene signatures of glioblastoma: a study based on TCGA data analysis. Neurooncology 15:829–839
Komohara Y, Ohnishi K, Kuratsu J, Takeya M (2008) Possible involvement of the M2 anti-inflammatory macrophage phenotype in growth of human gliomas. J Pathol 216:15–24
Krex D, Klink B, Hartmann C, von Deimling A, Pietsch T, Simon M et al (2007) Long-term survival with glioblastoma multiforme. Brain 130:2596–2606
Li B, Senbabaoglu Y, Peng W, Yang M-L, Xu J, Li JZ (2012) Genomic estimates of aneuploid content in glioblastoma multiforme and improved classification. Clin Cancer Res 18:5595–5605
Lichter P, Bentz M, Joos S (1995) Detection of chromosomal aberrations by means of molecular cytogenetics: painting of chromosomes and chromosomal subregions and comparative genomic hybridization. Methods Enzymol 254:334–359
Lohr J, Ratliff T, Huppertz A, Ge Y, Dictus C, Ahmadi R et al (2011) Effector T-cell infiltration positively impacts survival of glioblastoma patients and is impaired by tumor-derived TGF-β. Clin Cancer Res 17:4296–4308
Louis DN, Ohgaki H, Wiestler OD, Cavenee WK, Burger PC, Jouvet A et al (2007) The 2007 WHO classification of tumours of the central nervous system. Acta Neuropathol 114:97–109
Marko NF, Toms SA, Barnett GH, Weil R (2008) Genomic expression patterns distinguish long-term from short-term glioblastoma survivors: a preliminary feasibility study. Genomics 91:395–406
Martinez FO, Gordon S, Locati M, Mantovani A (2006) Transcriptional profiling of the human monocyte-to-macrophage differentiation and polarization: new molecules and patterns of gene expression. J Immunol 177:7303–7311
McCabe MG, Ichimura K, Liu L, Plant K, Bäcklund LM, Pearson DM et al (2006) High-resolution array-based comparative genomic hybridization of medulloblastomas and supratentorial primitive neuroectodermal tumors. J Neuropathol Exp Neurol 65:549–561
McLendon RE, Halperin EC (2003) Is the long-term survival of patients with intracranial glioblastoma multiforme overstated? Cancer 98:1745–1748
Murray PJ, Wynn TA (2011) Protective and pathogenic functions of macrophage subsets. Nat Rev Immunol 11:723–737
Nishie A, Ono M, Shono T, Fukushi J, Otsubo M, Onoue H et al (1999) Macrophage infiltration and heme oxygenase-1 expression correlate with angiogenesis in human gliomas. Clin Cancer Res 5:1107–1113
Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K, Berman BP et al (2010) Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma. Cancer Cell 17:510–522
Petalidis LP, Oulas A, Backlund M, Wayland MT, Liu L, Plant K et al (2008) Improved grading and survival prediction of human astrocytic brain tumors by artificial neural network analysis of gene expression microarray data. Mol Cancer Ther 7:1013–1024
Phillips HS, Kharbanda S, Chen R, Forrest WF, Soriano RH, Wu TD et al (2006) Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell 9:157–173
Prosniak M, Harshyne LA, Andrews DW, Kenyon LC, Bedelbaeva K, Apanasovich TV et al (2013) Glioma grade is associated with the accumulation and activity of cells bearing M2 monocyte markers. Clin Cancer Res 19:3776–3786
Reifenberger G, Weber RG, Riehmer V, Kaulich K, Willscher E, Wirth H et al (2014) Molecular characterization of long-term survivors of glioblastoma using genome- and transcriptome-wide profiling. Int J Cancer 135:1822–1831
Shinawi T, Hill VK, Krex D, Schackert G, Gentle D, Morris MR et al (2013) DNA methylation profiles of long- and short-term glioblastoma survivors. Epigenetics 8:149–156
Shinojima N, Tada K, Shiraishi S, Kamiryo T, Kochi M, Nakamura H et al (2003) Prognostic value of epidermal growth factor receptor in patients with glioblastoma multiforme. Cancer Res 63:6962–6970
Stupp R, Hegi ME, Mason WP, van den Bent MJ, Taphoorn MJB, Janzer RC et al (2009) Effects of radiotherapy with concomitant and adjuvant temozolomide versus radiotherapy alone on survival in glioblastoma in a randomised phase III study: 5-year analysis of the EORTC-NCIC trial. Lancet Oncol 10:459–466
Stupp R, Mason WP, van den Bent MJ, Weller M, Fisher B, Taphoorn MJB et al (2005) Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma. N Engl J Med 352:987–996
Sturm D, Bender S, Jones DTW, Lichter P, Grill J, Becher O et al (2014) Paediatric and adult glioblastoma: multiform (epi)genomic culprits emerge. Nat Rev Cancer 14:92–107
Sturm D, Witt H, Hovestadt V, Khuong-Quang D-A, Jones DTW, Konermann C et al (2012) Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. Cancer Cell 22:425–437
The R Development Core Team (2008) R: a language and environment for statistical computing
Turcan S, Rohle D, Goenka A, Walsh LA, Fang F, Yilmaz E et al (2012) IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype. Nature 483:479–483
Verhaak RGW, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD et al (2010) Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 17:98–110
Wesolowska A, Kwiatkowska A, Slomnicki L, Dembinski M, Master A, Sliwa M et al (2008) Microglia-derived TGF-beta as an important regulator of glioblastoma invasion–an inhibition of TGF-beta-dependent effects by shRNA against human TGF-beta type II receptor. Oncogene 27:918–930
Xu W, Yang H, Liu Y, Yang Y, Wang P, Kim S-H et al (2011) Oncometabolite 2-Hydroxyglutarate Is a Competitive Inhibitor of α-Ketoglutarate-Dependent Dioxygenases. Cancer Cell 19:17–30
Yamanaka R, Arao T, Yajima N, Tsuchiya N, Homma J, Tanaka R et al (2006) Identification of expressed genes characterizing long-term survival in malignant glioma patients. Oncogene 25:5994–6002
Yan H, Parsons DW, Jin G, McLendon R, Rasheed BA, Yuan W et al (2009) IDH1 and IDH2 mutations in gliomas. N Engl J Med 360:765–773
Acknowledgments
We thank Steffen Dettling and Saskia Rösch for proofreading of the manuscript as well as Anja Metzner and Daniela Zito for review of patient data. Furthermore, we thank Farzaneh Kashfi, Hildegard Göltzer, Ilka Hearn and Melanie Greibich as well as Barbara Schwager and Claudia Rittmüller for their excellent technical assistance. This study has been funded in part by a grant from the Anni Hofmann Stiftung to CHM and the German Federal Ministry of Research and Education (BMBF) to BB (01GS0883).
Conflict of interest
The authors declare that they have no conflict of interest.
Ethical approval
This article does not contain any studies with animals performed by any of the authors. All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. Informed consent was obtained from all individual participants included in the study.
Author information
Authors and Affiliations
Corresponding author
Additional information
C. Geisenberger, A. Mock, A. Abdollahi and C. Herold-Mende have contributed equally to this work.
Electronic supplementary material
Below is the link to the electronic supplementary material.
401_2015_1427_MOESM1_ESM.pdf
Fig. S1 TCGA subtypes in LTS/STS discovery cohort. Fig. S2 Principal Component Analysis of LTS and STS gene expression data. Fig. S3 Microglial infiltration in LTS and STS tumors. Fig. S4 Correlation of TCGA expression data and microglia signature. Fig. S5 Survival for combined „LTS-like“-status and chr. 19/20 co-gain. Fig. S6 Study cohort for chromosome 19/20 FISH validation (PDF 968 kb)
Rights and permissions
About this article
Cite this article
Geisenberger, C., Mock, A., Warta, R. et al. Molecular profiling of long-term survivors identifies a subgroup of glioblastoma characterized by chromosome 19/20 co-gain. Acta Neuropathol 130, 419–434 (2015). https://doi.org/10.1007/s00401-015-1427-y
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00401-015-1427-y