Article,
Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology
Contributors
Kresbach, Catena
0000-0002-6004-7332
[1]
[2]
[3]
Englinger, Bernhard
0000-0002-9701-2600
[11]
[12]
[13]
[14]
[15]
Gojo, Johannes
0000-0002-8113-3416
[15]
Pietsch, Torsten
0000-0003-0763-6506
[20]
Schueller, Ulrich
0000-0002-8731-1121
(Corresponding author)
[1]
[2]
[3]
Affiliations
- [1] Univ Med Ctr Hamburg Eppendorf, Dept Pediat Hematol & Oncol, Hamburg, Germany [NORA names: Germany; Europe, EU; OECD];
- [2] Univ Med Ctr Hamburg Eppendorf, Dept Pediat Hematol & Oncol, Hamburg, Germany [NORA names: Germany; Europe, EU; OECD];
- [3] Res Inst Childrens Canc Ctr, Hamburg, Germany [NORA names: Germany; Europe, EU; OECD];
- [4] Aarhus Univ Hosp, Dept Pediat & Adolescent Med, Aarhus, Denmark [NORA names: AU Aarhus University; University; Denmark; Europe, EU; Nordic; OECD];
- [5] Free Univ Berlin, Humboldt Univ Berlin, Berlin Inst Hlth, Berlin, Germany [NORA names: Germany; Europe, EU; OECD];
(... more)
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 (pPFS = 0.0026, pOS < 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.
