To the editor,
Methylation-based classification stratifies supratentorial embryonal tumors into 4 distinct entities, among which, CNS-neuroblastoma,FOXR 2-activated, and neuroepithelial tumors withBCOR -alteration, have been included in the new WHO classification1,2. While the tool has emerged as an important adjunct to tumor characterization in the modern era, its performance and scope may be limited by the data used to train the classifier. We share our challenges in characterizing a supratentorial embryonal tumor that was ultimately successfully treated according to its histology.
A 5-year-old boy presented with right-focal weakness for 8-months. A 8x7x6.5-cc mass in the left-frontoparietal region (Fig.1A) was completely resected and diagnosed as CNS-neuroblastoma (Fig.1B,C). Spine, CSF and whole-body PET were clear. Methylation-based classifier failed to characterize this tumor. Unsupervised clustering grouped it closest to embryonal tumors with multi-layered rosettes (ETMR) (Fig.1D). No multi-layered rosettes were detected, LIN28 was negative, INI-1 and mismatch-repair stains were retained. Copy number aberrations (CNA) included losses in chromosomes 3p, 9 (including the CDKN2A/Blocus), 11q (partial) and 19q (partial) and focal gains on chromosome-19 (Fig.1E), but no amplification of the chromosome-19 microRNA-cluster (19MC) (Fig.1F). MYC or MYCN were not amplified. MGMT promoter was methylated (Fig.1G). Repeated attempts at sequencing failed. He was treated with craniospinal irradiation (23.4Gy, 13-fractions; tumor-bed boost 14.4Gy, 8-fractions). Adjuvant chemotherapy included vincristine, cisplatin and cyclophosphamide. The child remains in complete remission after 2-years.
CNS-neuroblastoma presents at a median age of 5-8 years, shows female preponderance, and predilection for the fronto-parietal region3,4. Radiology is heterogeneous, frequently including solid-cystic components with central necrosis and haemorrhage. Methylome analysis is the method of choice for diagnosis5. CNAs include 1q gain, aberrations/losses in 16q, 3p and 6q, and gains in chromosomes 17q and 81,5,4. Recent analyses incorporating accurate molecular analyses suggest 5-year survival >80%5. In contrast, ETMR is a tumor of infants and younger children, characterized by multi-layered pseudo-rosettes, expression of LIN28, amplification of C19MC and dismal outcomes6,7. CNAs include gain in chromosome 2 and 1q, and losses in 6q. Rare (<10%) subsets lacking C19MC amplification cluster with other ETMRs on methylome-analysis and are enriched for DICER1 variants (chromosome-14), or harbour amplifications in other micro-RNA clusters on chromosome-136.
The embryonal tumor in our patient failed characterization by methylome-analysis. While the histo-morphological best-fit was CNS-neuroblastoma, unsupervised clustering was closest to ETMR. The CNAs did not match either diagnosis. Interestingly, the MGMT promoter was methylated, which has only been rarely reported in embryonal tumors, and despite indicating sensitivity to temozolomide and lomustine, has not been predictive of survival8,9. Overall, this suggested unique biology, and that this novel entity is not currently represented in the classifier database.
As the use of methylome-based tumor classification is currently limited to specialized centers in Europe, North America and Australia, it is not surprising that rare tumor subsets from other demographic populations may be under-represented. Limitations have been apparent for rare tumors like NTRK-fused gliomas10 and those arising from germline defects like mismatch-repair deficiency11. Twinning initiatives and collaboration between centers of excellence in the West and the large-volume centers in developing countries are needed to advance this diagnostic tool and benefit the entire spectrum of children with CNS tumors.
Source of funding: AD is supported by the St. Baldrick’s Foundation International Scholar Award (with generous support from the Team Campbell Foundation; Grant number: 697257) and the SickKids Research Training Center Clinician-Scientist Training Program (Fall 2019 award).
Acknowledgements: We are grateful to Dr Martin Sill (DKFZ, Heidelberg) for analysing and confirming that methylation profile similar to the index tumor was not identified in their database.
Consent: Informed consent was obtained from the parents for publishing this case report.