Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology

Swenja Gödicke; Catena Kresbach; Max Ehlert; Denise Obrecht; Lea Altendorf; Karoline Hack; Katja von Hoff; Helena Carén; Viktoria Melcher; Kornelius Kerl; Bernhard Englinger; Mariella Filbin; Kristian W Pajtler; Johannes Gojo; Torsten Pietsch; Stefan Rutkowski; Ulrich Schüller

doi:10.1007/s00401-023-02682-x

Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology

Acta Neuropathol. 2024 Jan 24;147(1):23. doi: 10.1007/s00401-023-02682-x.

Authors

Swenja Gödicke^{1

2}, Catena Kresbach^{1

2

3}, Max Ehlert^{1

2}, Denise Obrecht¹, Lea Altendorf^{1

2}, Karoline Hack^{1

2}, Katja von Hoff^{4

5}, Helena Carén⁶, Viktoria Melcher⁷, Kornelius Kerl⁷, Bernhard Englinger^{8

9

10

11}, Mariella Filbin^{8

9}, Kristian W Pajtler^{12

13

14}, Johannes Gojo¹⁵, Torsten Pietsch¹⁶, Stefan Rutkowski¹, Ulrich Schüller^{17

18

19}

Affiliations

¹ Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
² Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany.
³ Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
⁴ Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health, Berlin, Germany.
⁵ Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark.
⁶ Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Center for Cancer Research, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden.
⁷ Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany.
⁸ Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA.
⁹ Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
¹⁰ Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria.
¹¹ Center for Cancer Research and Comprehensive Cancer Center, Medical University Vienna, 1090, Vienna, Austria.
¹² Hopp Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.
¹³ Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
¹⁴ Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, 69120, Heidelberg, Germany.
¹⁵ Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria.
¹⁶ Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn Medical Center, Bonn, Germany.
¹⁷ Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. u.schueller@uke.de.
¹⁸ Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany. u.schueller@uke.de.
¹⁹ Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany. u.schueller@uke.de.

Abstract

Posterior fossa type A (PF-EPN-A, PFA) ependymoma are aggressive tumors that mainly affect children and have a poor prognosis. Histopathology shows significant intratumoral heterogeneity, ranging from loose tissue to often sharply demarcated, extremely cell-dense tumor areas. To determine molecular differences in morphologically different areas and to understand their clinical significance, we analyzed 113 PF-EPN-A samples, including 40 corresponding relapse samples. Cell-dense areas ranged from 0 to 100% of the tumor area and displayed a higher proportion of proliferating tumor cells (p < 0.01). Clinically, cell density was associated with poor progression-free and overall survival (p_PFS = 0.0026, p_OS < 0.01). Molecularly, tumor areas with low and high cell density showed diverging DNA methylation profiles regarding their similarity to distinct previously discovered PF-EPN-A subtypes in 9/21 cases. Prognostically relevant chromosomal changes at 1q and 6q showed spatial heterogeneity within single tumors and were significantly enriched in cell-dense tumor areas as shown by single-cell RNA (scRNA)-sequencing as well as copy number profiling and fluorescence in situ hybridization (FISH) analyses of different tumor areas. Finally, spatial transcriptomics revealed cell-dense areas of different tumors to be more similar than various different areas of the same tumor. High-density areas distinctly overexpressed genes encoding histone proteins, WNT5A, TGFB1, or IGF2. Relapsing tumors displayed a higher proportion of cell-dense areas (p = 0.036), a change in PF-EPN-A methylation subtypes (13/32 patients), and novel chromosome 1q gains and 6q losses (12/32 cases) compared to corresponding primary tumors. Our data suggest that PF-EPN-A ependymomas habor a previously unrecognized intratumoral heterogeneity with clinical implications, which has to be accounted for when selecting diagnostic material, inter alia, by histological evaluation of the proportion of cell-dense areas.

Keywords: 1q gain; 6q loss; DNA methylation; Ependymoma; Intratumoral heterogeneity; Morphology.

MeSH terms

Child
Ependymoma*
Gene Expression Profiling
Histones
Humans
In Situ Hybridization, Fluorescence
Neoplasm Recurrence, Local*

Substances

Histones