Fig. 2
Enrichment of GBM subtypes, molecular and metabolic gene signatures in distinct GBM regions. The normalized enrichment scores (NES) of the significantly enriched (padj < 0.05) GBM subtypes are shown in distinct GBM regions and 5ALA sorted cells (A). Retrieval of gene sets specifying different GBM subtypes (Verhaak et al.) was followed by gene set enrichment analysis (GSEA). The color code indicates the differential NES values (yellow and black represent higher and lower NES, respectively). GSEA plot shows that the GBM mesenchymal subtype is significantly enriched (NES: 2.1, padj = 2.3 × 10−6) in 5ALA + cells (B). NeuN immunohistochemistry (IHC) of Core—(C), Rim (D), and Invasive margin (E) to estimate the proportion of NeuN positive (neuronal) cells (arrows). The scale bar indicates 25 µm. Differential z-scored normalized expression Log2(TPM + 1) of the significantly regulated (Limma, padj < 0.05) leading edge genes of GBM subtypes (Verhaak et al.)—Neural (F), and Mesenchymal (G)—are shown as a heatmap. Heatmap illustrating the normalized enrichment scores (NES) representing enriched cellular and metabolic states (padj < 0.05) in distinct GBM intratumor regions and 5ALA sorted cells (H). The gene signatures of cellular states (Developmental and Inflammatory wound response) and metabolic states (Glycolytic—GPM, and Mitochondrial—MTC) were retrieved and subjected to GSEA. GSEA plots represent the enrichment of GPM (I), and Inflammatory wound response (J) in 5ALA + cells compared to 5ALA − cells and Invasive margin, respectively. Heatmaps showing the differential expression of significantly regulated (Limma, padj < 0.05) leading edge genes of GPM (K) and Inflammatory wound response (L) in Core, Rim, Invasive margin, 5ALA − and 5ALA + cells. Stacked bar plot representing the transcriptional program estimates across 10 GBM samples (M). Each transcriptional program (Developmental and Inflammatory wound response) was divided into three expression-based categories based on their gene expression pattern (High, Intermediate, and Low). Each color indicates a specific expression-based category of a transcriptional program. The log10 ratios of High Inflammatory wound response and High Developmental transcriptional program in the unsorted Core region and 5ALA + cells across 10 GBM patients are shown (N). Box plots represent the median expression in Developmental and Inflammatory wound response genes enriched in cells with the high expression of different transcriptional programs (Developmental-High and Invasive margin-High) across Core and 5ALA + cell populations (O). P-values calculated from Student’s t tests are shown