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Molecular characterization of histopathological ependymoma variants

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Abstract

According to the WHO classification, ependymal tumors are classified as subependymomas, myxopapillary ependymomas, classic ependymomas, anaplastic ependymomas, and RELA-fusion-positive ependymomas (RELA-EPN). Among classic ependymomas, the WHO defines rare histological variants, i.e., the clear cell, papillary, and tanycytic ependymoma. In parallel, global DNA methylation patterns distinguish nine molecular groups, some of which tightly overlap with histopathological subgroups. However, the match of the aforementioned histological variants to DNA methylation classes remains unclear. We analyzed histomorphology, clinical parameters, and global DNA methylation of tumors with the initial histological diagnoses of tanycytic (n = 12), clear cell (n = 14), or papillary ependymoma (n = 19). Forty percent of these tumors did not match to the epigenetic profile of ependymomas, using a previously published DNA methylation-based classifier for brain tumors. Instead, they were classified as low-grade glioma (n = 3), plexus tumor (n = 2), CNS high-grade neuroepithelial tumor with MN1 alteration (n = 2), papillary tumor of the pineal region (n = 2), neurocytoma (n = 1), or did not match to any known brain tumor methylation class (n = 8). Overall, integrated diagnosis had to be changed in 35.6% of cases as compared to the initial diagnosis. Among the tumors molecularly classified as ependymoma (27/45 cases), tanycytic ependymomas were mostly located in the spine (5/7 cases) and matched to spinal or myxopapillary ependymoma. 6/8 clear cell ependymomas were found supratentorially and fell into the methylation class of RELA-EPN. Papillary ependymomas with a positive ependymoma match (12/19 cases) showed either a “papillary” (n = 5), a “trabecular” (n = 1), or a “pseudo-papillary” (n = 6) growth pattern. The papillary growth pattern was strongly associated with the methylation class B of posterior fossa ependymoma (PFB, 5/5 cases) and tumors displayed DNA methylation sites that were significantly different when compared to PFB ependymomas without papillary growth. Tumors with pseudo-papillary histology matched to the methylation class of myxopapillary ependymoma (4/6 cases), whereas the trabecular case was anatomically and molecularly a spinal ependymoma. Our results show that the diagnosis of histological ependymoma variants is challenging and epigenetic profiles may improve diagnostic accuracy of these cases. Whereas clear cell and papillary ependymomas display correlations between localization, histology, and methylation, tanycytic ependymoma does not represent a molecularly distinct subgroup.

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Acknowledgements

We thank Anne Reichstein for her dedication and excellent technical support concerning the DNA-methylation analyses. We also thank Ulrike Rumpf, Hannelore Junker-Polzin, Carolina Janko, Tasja Lempertz, and Celina Liza Soltwedel for excellent technical support with tissue sections and stainings. J.N. was supported by the Else-Kröner Fresenius Stiftung and the UKE Nachwuchsförderung. This project was generously funded by the Gert and Susanna Mayer Stiftung. U.S. was supported by the Fördergemeinschaft Kinderkrebszentrum Hamburg.

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Authors and Affiliations

  1. Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    Julia E. Neumann, Markus Glatzel & Ulrich Schüller

  2. II. Medizinische Klinik und Poliklinik, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    Michael Spohn

  3. Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    Denise Obrecht, Martin Mynarek, Stefan Rutkowski & Ulrich Schüller

  4. Institute of Neuropathology, University Hospital Münster, Münster, Germany

    Christian Thomas & Martin Hasselblatt

  5. Center for Neuropathology, Ludwig-Maximilians-University, Munich, Germany

    Mario M. Dorostkar

  6. German Center for Neurodegenerative Diseases, Munich, Germany

    Mario M. Dorostkar

  7. Department of Neuropathology, Institute of Pathology, University Hospital, Heidelberg and Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany

    Annika K. Wefers

  8. Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany

    Annika K. Wefers

  9. Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany

    Annika K. Wefers, Hendrik Witt, Marcel Kool & Kristian W. Pajtler

  10. Institute of Pathology, University of Basel, Basel, Switzerland

    Stephan Frank

  11. Department of Neuropathology, Institute of Pathology, University of Würzburg, Würzburg, Germany

    Camelia-Maria Monoranu

  12. Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany

    Arend Koch

  13. Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany

    Hendrik Witt, Marcel Kool & Kristian W. Pajtler

  14. Department of Pediatric Oncology and Hematology, University Hospital Heidelberg, Heidelberg, Germany

    Hendrik Witt & Kristian W. Pajtler

  15. Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany

    Michael Spohn & Ulrich Schüller

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Supplementary Fig. 1: t-SNE plot including the 45 cases analyzed in this study that were plotted with brain tumor samples of 82 published CNS tumor methylation classes and with cases of nine control tissue methylation classes (n = 2801 [3]). Supplementary Fig. 2: Histomorphology of cases diagnosed as tanycytic ependymoma that did not match to any molecular ependymoma group based on DNA methylation. (a–d) H&E stainings. Scale bar in a is 50 μm for a–d. (a) Case #9 showed astrocytic tumor cells arranged around vessels. No clear pseudorosettes were detected. (b) Case #10 was suggestive of a low-grade glioma with abundant and evenly distributed small round calcifications (see arrows). (c) Case #11 impressed as an ependymoma with tanycytic morphology. (d) Case #12 showed a fibrillary tanycytic pattern with hyalinized vessels (see arrows). Supplementary Fig. 3: Histomorphology of cases diagnosed as clear cell ependymoma that did not match to any molecular ependymoma group based on DNA methylation. (a–f) H&E stainings. Scale bar in a is 50 μm for a–f. (a) Case #21 showed slightly pleomorphic tumor cells with clear cell morphology (left panel) and areas with ependymal pseudorosettes (right panel), being compatible with a clear cell ependymoma. (b) Case 22 showed thin capillaries, small oligodendroglia-like cells and some larger cells suggestive of “floating neurons” (see arrow). (c,d) Cases #23 and #24 impressed as uniformly clear cell tumors without papillary structures. (e) Clear cells with accentuated cell boundaries and nuclei free vascular spaces. (f) Uniform round cells and calcifications (see arrow), well compatible with a neurocytoma. Supplementary Fig. 4: Molecular characteristics of RELA-fusion-positive ependymoma comparing cases with (n = 6) or without clear cell morphology (n = 65). (a) Unsupervised hierarchical clustering of RELA-fusion-positive ependymoma cases with or without clear cell morphology based on 3 significantly differentially methylated CpG sites (FDR < 0.1, delta beta value ≥ 0.2) did not reveal distinct clusters. Details on all 4 significantly differentially methylated CpG sites can be found in supplementary Table 1. (b) t-SNE plot of RELA-fusion-positive ependymomas. Cases with clear cell morphology (n = 6) located scattered among cases without clear cell morphology (n = 65) (c) Stacked integrated copy number plots of cases with or without clear cell morphology showed similar chromosomal alterations. RELA, NCCM = RELA-fusion-positive ependymoma, clear cell morphology. RELA, NCCM = RELA-fusion-positive ependymoma, no clear cell morphology. FDR = false discovery rate. Supplementary Fig. 5: Histomorphology of cases diagnosed as papillary ependymoma that did not match to any molecular ependymoma group based on DNA methylation. (a–g) H&E stainings. Scale bar in a is 50 μm for a–g. (a,d,e) Cases #39, 42 and 43 showed a pseudo-papillary picture with hyalizined vessels being present in cases #42 and 43. (b) Papillary growing tumor, slightly suggestive of plexus tissue, well compatible with a plexus tumor. (c) Case #41 was a highly vascularized tumor with nuclei free areas and circular arrangement of tumor cells around vessels. (f) Case #44 showed abundant trabecular structures resembling ependymal canals. (g) Case #45 showed tumor cell nests within a myxoid matrix. Supplementary Fig. 6: Molecular characteristics of posterior fossa group B ependymoma, comparing papillary morphology (n = 5) with non-papillary morphology (n = 15). (a) t-SNE plot showing cases with papillary morphology or non-papillary morphology including a data set of published posterior fossa group B ependymoma [5]. Histomorphology was not associated with one of the published 5 subtypes of posterior fossa group B ependymoma [5]. (b) Stacked integrated copy number plots of cases with papillary morphology or non-papillary morphology showed common chromosomal alterations but papillary ependymomas lacked gain of chromosome 11. PFB1-5 = posterior fossa group B ependymoma, subtypes 1-5. (PDF 50941 kb)

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Neumann, J.E., Spohn, M., Obrecht, D. et al. Molecular characterization of histopathological ependymoma variants. Acta Neuropathol 139, 305–318 (2020). https://doi.org/10.1007/s00401-019-02090-0

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