DNA methylation-based classification and molecular characteristics of spinal cord gliomas with wildtype histone H3 reveal differences between adult and pediatric pilocytic astrocytoma

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Abstract

OBJECTIVE: Spinal cord gliomas with wildtype histone H3 (H3WT-SCGs) are rare but heterogeneous tumors for which pathological classification is challenging. Our aim was to characterize a methylation-based molecular classification of H3WT-SCGs. METHODS: We characterized H3WT-SCGs from 55 patients using data from DNA methylation arrays, whole-exome/transcriptome sequencing, proteomics, phosphoproteomics, single-cell RNA sequencing, and multiplex staining. Another 31 cases with DNA methylation data were used for validation. RESULTS: Using DNA methylation data, we identified six spinal cord methylation (SCM) subtypes: pilocytic astrocytoma (PA), PA-immune enriched (PA-IME), diffuse leptomeningeal glioneuronal tumor (DLGNT), subependymoma (SUBEPN), glioblastoma-like (GBM), and pleomorphic xanthoastrocytoma-like (PXA). These SCM subtypes exhibited a distinction from the traditional histology classification in 58.2% of the study cases. In comparison to histology, SCM subtyping better correlates with independent molecular features, as evidenced by significant enrichment of BRAF fusions in the PA and DLGNT classes, and notable enrichment of chromosome 1p losses and 1q gains in DLGNT. SCM-PA can be further divided into pediatric (SCM-PA-P) and adult (SCM-PA-A) subgroups. In comparison to SCM-PA-P, SCM-PA-A was associated with lower BRAF fusion frequency (P < 0.01), smaller tumor size (P < 0.01), and longer progression-free survival (P = 0.036; all patients alive). Neoplastic cells in SCM-PA-A exhibited a less differentiated status with higher expression of neuronal markers and lower expression of cytokines and chemokines in comparison to SCM-PA-P. In addition, SCM-PA-A had a lower senescence-associated secretory phenotype, lower infiltration of immunosuppressive monocyte-derived macrophages, and less proliferative myeloid cells in comparison to SCM-PA-P. CONCLUSIONS: This study defined clinically relevant H3WT-SCG molecular classes that reflect patient prognosis and molecular characteristics for potential therapeutic strategies.

Abstract as published, via PubMed.