Fig. 3: Transcriptomic analysis demonstrates considerable ITH underlying convergent immune phenotypes.

a Volcano plot of differentially expressed genes comparing high vs. low immune infiltrate regions across the tumor core and margins. Vertical red lines indicate a minimum twofold change in expression value; horizontal red line indicates the adjusted p-value threshold of <1e-8. b Representative IHC sections demonstrating matched tumor content (SOX10 stain, above) and immune infiltration (CD8 stain, below) illustrating substantial variation of local CD8 T-cell content ranging from low (arrows) to high (arrowheads). c Gene connection network of genes upregulated in immune-infiltrated samples that contribute to highly enriched GO terms/pathways, showing substantial connectivity. d Functional enrichment network showing diverse representation of immune cell pathways and functions in the immune infiltrate-derived differentially expressed genes, dominated by highly inter-connected T and B-lymphocyte-related terms. e Representative IHC images of a para-tumoral lymphoid structure present in section 1B, demonstrating absence of tumor cells (SOX10) but mixed populations of CD4+, CD8+, and PAX5+ lymphocytes. Magnification ×10. f Single-sample gene-set enrichment analysis demonstrating spatially discontiguous enrichment of functionally relevant gene sets throughout the tumor. IHC-based estimate of immune infiltrate (top) and sample location (bottom) are indicated. g Immunostained tumor tissue revealing restriction of tumor cell phospho-ERK1/2 expression (brown staining) to cells located at or immediately subjacent to the tumor cell surface. Arrowheads: tumor-surrounding tissue interface. Magnification ×10.