Fig. 4

Medulloblastoma downregulate cell cycle and upregulate neuron differentiation related genes in response to Palbociclib treatment in a spatially dependent manner. a Volcano plots from analyses of differentially expressed (DE) genes between treatment and control samples, compared for three categories, including human, mix and mouse spots. DE genes are highlighted with red for upregulated genes, blue for downregulated genes and black for non-significant change (corrected p < 0.05). Pie charts beneath the volcano plots indicate the number of significant DE genes detected in each comparison. b Network visualisation of gene set enrichment analysis results for the human DE genes show upregulation of neuronal differentiation and downregulation of cell cycle. Each dot is annotated with the gene set term. Dot sizes indicate the number of DE genes detected within the term, and dots were coloured according to the normalised enrichment score (NES). Positive NES values (red) indicate upregulation of the term in response to treatment, while negative NES values (blue) indicate downregulation of the term in response to treatment. Edges between terms indicate overlap of the DE genes associated with the connected terms. c, d Spot-specific gene enrichment scores for E2F target genes (c) and neuron differentiation genes (d) are overlaid in the spatial context. High gene set activity is indicated by bright yellow, and low activity is indicated by dark violet; overall showing continued E2F activity at the human-mouse interface in treated samples (c) and neuronal differentiation within the tumour (d). E2F E2 family of transcription factors