Figure 1.

snRNA-seq identifies gene expression programs driving cell states in IDH-mutant gliomas

(A) Clinical and molecular characteristics of the IDH-mutant glioma cohort for single-nuclei sequencing.

(B and C) UMAP representation and initial cluster assignments for integrated snRNA-seq samples of oligodendrogliomas (n = 8) (B) and astrocytomas (n = 6) (C). Nuclei labeled as “excluded” in (B) are omitted from downstream analyses due to technical reasons (tumor cells clustering with microglia and originating from a single patient). UMAP1, x axis; UMAP2, y axis. Colors indicate cell-type assignments.

(D and E) Pearson’s correlation scores for individual NMF programs in oligodendrogliomas (n = 8) (D) and astrocytomas (n = 6) (E). Metaprograms were identified by hierarchical clustering of individual NMF programs.

(F) Dot plot displaying five marker genes for each tumor population.

(G and H) UMAP embedding of oligodendrogliomas (G) and astrocytomas (H), colored by NMF metaprograms, gradient cells, and TME (dark gray).

(I) Bar plot showing tumor population proportions across individual samples, grouped by subtype and grade. Bars are arranged by descending RE proportion.

(J) Representative IHC staining for H&E and two RE population markers, EEF2 and EEF1A1, for oligodendroglioma and astrocytoma samples, separated by grade. Oligodendroglioma (OD) n = 22 (11 grade 2, 11 grade 3); astrocytoma (AS) n = 15 (10 grade 2, 5 grade 3). Scale bars represent 50 μm.

(K) Spatial distribution of EEF2 and EEF1A1 (40×). Scale bars represent 50 μm.

(L) Plots showing semi-quantitative histological scores (0 = 0%, 1 = 0%–5%, 2 = 6%–29%, 3 = 30%–69%, and 4 >70% positive staining) for EEF2 (top) and EEF1A1 (bottom). Top: a qualitative increase in EEF2 staining in grade 3 compared with grade 2 AS tumors. Bottom: a qualitative increase in EEF1A1 staining in grade 2 OD tumors compared with grade 2 AS tumors. Wilcoxon rank-sum test was performed to test for significance, ∗p < 0.05.