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Loss of 5-hydroxymethylcytosine and intratumoral heterogeneity as an epigenomic hallmark of glioblastoma

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Tumor Biology

Abstract

Glioblastoma (GBM) is the most malignant neoplasm with predominant astrocytic differentiation and the most frequent primary brain tumor of the adult. Here, we investigated 170 human GBM specimens deriving from 162 patients, as well as 66 healthy control tissue specimens deriving from 27 patients, and analyzed the amount of 5-hydroxymethylcytosine (5hmC) in GBMs compared to normal brain and tumor infiltration zones. Additionally, we correlated the amount of 5hmC with two different proliferation markers, Ki67 and H3S10p. Genetic characterization of GBMs enabled us to analyze the effect of isocitrate dehydrogenase 1 (IDH1) mutations, O6-methylguanin-DNA-methyltransferase (MGMT) promoter methylation, and loss of heterozygosity of chromosome 1p and 19q (LOH1p/19q) on 5hmC amount. We found that GBMs show a tremendous loss of 5hmC, and we observed that even the infiltration zones show reduced amounts of 5hmC. Interestingly, the amount of 5hmC was inversely proportional to the two investigated proliferation markers, Ki67 and H3S10p. Correlation of 5hmC amount and molecular genetic markers of GBMs showed that there are no correlations of 5hmC amount and IDH1 mutations, MGMT promoter methylation, and LOH1p/19q. Furthermore, we evaluated the intratumoral distribution of 5hmC in compact and infiltrating areas and found that the quantification of the 5hmC amount is a useful tool in evaluation of tumor infiltration. In summary, our data emphasize that GBMs show a disturbed hydroxymethylome that is disrupted by IDH1 independent pathways, and that loss of 5hmC shows astonishing intratumoral heterogeneity.

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Acknowledgments

The authors thank the BrainBank Munich (Thomas Arzberger) for providing control tissue.

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Authors and Affiliations

  1. Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University, Feodor-Lynen-Str. 23, Munich, D-81377, Germany

    Theo F. J. Kraus, Gesa Kolck, Andrea Greiner, Katharina Schierl, Virginie Guibourt & Hans A. Kretzschmar

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  1. Theo F. J. Kraus
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  2. Gesa Kolck
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  3. Andrea Greiner
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  4. Katharina Schierl
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Corresponding author

Correspondence to Theo F. J. Kraus.

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Supplementary Fig. S1

Molecular genetic status of investigated GBMs. We analyzed MGMT promoter methylation status (a), IDH1/2 mutation status (b), and LOH1p/19q status (c) of tumors. MGMT methylation: 0, unmethylated MGMT promoter sequence; 1, methylated MGMT promoter sequence; 2, partially methylated MGMT promoter sequence; 9, not determined due to tissue limitations. IDH mutations: 0, IDH1 no mutation and IDH2 no mutation; 1, IDH1 mutation and IDH2 no mutation; 2, IDH1 no mutation and IDH2 mutation; 3, IDH1 mutation and IDH2 mutation; 9, not determined due to tissue limitations. LOH1p/19q: 0, no LOH1p/19q; 1, loss of 1p; 2, loss of 19q: 3, LOH1p/19q; 4, other aberrations; 9, not determined due to tissue limitations. (TIFF 444 kb)

High Resolution (GIF 740 kb)

Supplementary Table S1

Overview of GBM patients. We investigated solid tumor regions of 162 GBMs as well as 10 tumor infiltration regions. Mean age of GBM patients was 59 years with a median age of 62 years. Sixty-four percent of patients were male and 36 % were female with a male to female ratio of 1.7. Details on the molecular genetic status of GBM can be found in Supplementary Fig. S1. (XLSX 17 kb)

Supplementary Table S2

Overview of control patients. Sixty-six control tissues derived from 27 different patients were investigated. Mean age of controls was 62 years with a median age of 61 years. Sixty-three percent of patients were male and 37 % were female with a male to female ratio of 1.7. n.a. not available. (XLSX 14 kb)

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Kraus, T.F.J., Kolck, G., Greiner, A. et al. Loss of 5-hydroxymethylcytosine and intratumoral heterogeneity as an epigenomic hallmark of glioblastoma. Tumor Biol. 36, 8439–8446 (2015). https://doi.org/10.1007/s13277-015-3606-9

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  • DOI: https://doi.org/10.1007/s13277-015-3606-9

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