Comprehensive profiling of paediatric chordoma: poorly differentiated and conventional subtypes

Chordoma in children is rare and inadequately characterized. This study aims to provide a comprehensive characterization of the clinicopathological and (epi)genetic features of chordomas in children, particularly the poorly differentiated chordomas (PDC). We established a cohort of seven PDCs and 28 conventional chordomas (CC). Besides characterizing the clinical and histopathological features, we performed comprehensive immunohistochemical staining for markers enabling diagnosis of chordoma and members of the sonic hedgehog signalling pathway. Using DNA methylation analysis, we characterized the molecular subtypes among chordomas in children and the SMARCB1 (INI1)-deficient tumours, which was further complemented by fluorescence in situ hybridization and targeted exome sequencing. Paediatric patients with PDC showed poorer prognosis compared with paediatric patients with CC. PDC tumours occurred more frequently in younger children and typically located at the clivus. Histologically, PDC tumours exhibited large polygonal/epithelioid cells or chubby spindle cells, with positive staining for cytokeratins and brachyury, but loss of expression of SMARCB1 (INI1) protein, and a high Ki-67 index. PDC samples showed promiscuous staining of sonic hedgehog pathway members, which contrasts the homogenous staining of sonic hedgehog pathway members in CC samples. Unsupervised hierarchical clustering and t-distributed stochastic neighbour embedding analyses of DNA methylation data showed that paediatric PDCs formed a distinct methylation cluster in comparison with the samples of CC, atypical teratoid/rhabdoid tumours and bone fide extracranial proximal epithelioid sarcoma. Whereas PDCs harboured relatively stable karyotype, frequent chromosomal gains or losses were observed in CCs. Mutational profiling identified different sets of genes in PDCs versus CCs. Loss of SMARCB1 (INI1) expression in PDCs was predominantly due to locus deletion. In summary, our findings support the differential diagnosis between paediatric PDC and CC. Further, our findings suggest that besides distinct methylome profiles, paediatric PDC and CC are likely driven by distinct pathogenic pathways.