Fig. 2: Transcriptomic characterization and molecular subtypes of CNS SFTs.

A Volcano plot comparing gene expression between CNS and peripheral SFT tumors. The names of the genes marked in red are genes that are highly expressed in the nervous system. Differential analysis was performed using the R package DESeq2, and the p-value was calculated using the two-sided Wald test and corrected with FDR. B–D Representative IHC staining results for Synaptotagmin and Decorin in CNS SFT (n = 6) and peripheral SFT (n = 11) (B) and their quantitative results (C, D). Data are presented as mean ± SEM. ****, p < 0.0001 (Student’s t-test, two-sided). E GO enrichment analysis of differentially expressed genes between WHO grade 3 and WHO grade 1 SFT. F GO enrichment analysis of differentially expressed genes between CNS SFT and meningioma (a merged dataset of GSE136661 and GSE189672). Term Enrichment is performed by R package clusterProfiler. P-value was calculated by two-sided Kolmogorov–Smirnov test and adjusted by FDR. G Sankey plot illustrating the relationship between WHO grade and molecular subtypes. H Heatmap showing significantly activated signaling pathways across four molecular subtypes. I–K The maximum percentage of Ki67% (I), the log10-transformed tumor volume (J) and the frequency of cystic necrosis according to radiographic result (K) in different molecular subtypes of CNS SFT. Neural-like (n = 13), Classical (n = 37), Inflamed (n = 13), Migratory (n = 17). Data are presented as mean ± SEM. *, p < 0.05; **, p < 0.01 (For (I) and (J) Student’s t-test, two-sided; for (K) Chi-square test, two-sided). Source data are provided as a Source Data file.