Dania Zuhier Ragheb Alkhatib

In head and neck squamous cell carcinoma the partial EMT gene list is expressed by both malignant cells and fibroblasts, yet it has been scored only in bulk tumours. Dividing its 100 genes by the cells that express them shows bulk co-expression is dominated by the stromal arm, so standard pEMT scores mainly measure stroma; a single-cell pseudobulk classifier and a 12-gene malignant core recover the malignant arm in any bulk transcriptome. Among 40 patients given platinum plus cetuximab, both malignant measures were higher in those with long progression-free survival (area under the curve 0.78 and 0.82) and the stromal core was not, but the malignant arm could not be separated from the Basal subtype, which discriminated better (0.93).

In head and neck squamous cell carcinoma the partial EMT gene list is expressed by both malignant cells and fibroblasts, yet it has been scored only in bulk tumours. Dividing its 100 genes by the cells that express them shows bulk co-expression is dominated by the stromal arm, so standard pEMT scores mainly measure stroma; a single-cell pseudobulk classifier and a 12-gene malignant core recover the malignant arm in any bulk transcriptome. Among 40 patients given platinum plus cetuximab, both malignant measures were higher in those with long progression-free survival (area under the curve 0.78 and 0.82) and the stromal core was not, but the malignant arm could not be separated from the Basal subtype, which discriminated better (0.93).