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Comprehensive profiling of paediatric chordoma: poorly differentiated and conventional subtypes
Zejun Duan1, Jing Feng1, Haidan Wang2
1Department of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing 100018, China.
Brain Communications
|June 15, 2026
Summary
Poorly differentiated chordomas (PDCs) in children have a worse prognosis than conventional chordomas (CCs), with distinct genetic and methylation profiles. These findings aid in differentiating pediatric chordoma subtypes and understanding their unique pathogenic pathways.
Area of Science:
- Pediatric oncology
- Molecular pathology
- Cancer genomics
Background:
- Chordoma is a rare bone tumor, particularly in children, with poorly understood subtypes.
- Distinguishing between poorly differentiated chordoma (PDC) and conventional chordoma (CC) in pediatric patients is crucial for prognosis and treatment.
Purpose of the Study:
- To comprehensively characterize the clinicopathological and (epi)genetic features of pediatric chordomas, focusing on PDCs.
- To identify molecular differences that distinguish PDCs from CCs and other rare tumors.
Main Methods:
- Established a cohort of 7 PDCs and 28 CCs for analysis.
- Performed immunohistochemistry, DNA methylation analysis, fluorescence in situ hybridization, and targeted exome sequencing.
- Analyzed clinical, histopathological, and molecular data, including sonic hedgehog pathway markers and SMARCB1 (INI1) expression.
Main Results:
- PDCs showed poorer prognosis, occurred in younger children, and were often clival, unlike CCs.
- PDCs exhibited characteristic histology, loss of SMARCB1 (INI1) expression, and promiscuous sonic hedgehog pathway staining.
- DNA methylation analysis revealed a distinct cluster for pediatric PDCs, separate from CCs and other tumor types.
- PDCs had stable karyotypes, while CCs showed frequent chromosomal gains/losses; mutational profiling identified distinct gene sets.
Conclusions:
- Findings support differential diagnosis between pediatric PDC and CC.
- Paediatric PDCs and CCs are likely driven by distinct pathogenic pathways, supported by unique methylome profiles.
- Loss of SMARCB1 (INI1) in PDCs is primarily due to locus deletion.
