Fig. 1

mRNA hypertranscription is associated with poor prognosis and tumor progression in HNSCC. a UMAP projection of all single cells from 12 HNSCC samples, annotated by major cell types. b Dot plot showing the average expression and detection frequency of canonical marker genes used for cell type identification. c Aneuploid and diploid cell prediction using copyKAT analysis. d UMAP of reclustered epithelial tumor cells (n = 18,798), defining 11 subpopulations (epi_0-epi_10). e mRNA hypertranscription status (low, medium, and high) overlaid on the tumor UMAP. f Scatter plot showing the correlation between the normalized total UMI count and the number of expressed genes. g Box plot comparing the CytoTRACE scores among the hypertranscription groups; higher scores reflect lower differentiation. Statistical significance was assessed using the Wilcoxon rank-sum test (all p < 0.001). h Heatmap of differentially expressed genes across mRNA hypertranscription groups. i Heatmap showing enrichment scores of the top 20 hallmark pathways across transcriptional states