Fig. 4: Early treatment-induced molecular changes.

A Heatmap of genes differentially expressed at Day14 compared to baseline. The comparison was carried out in the overall population and separately for the two trial cohorts. Manually selected representative genes are highlighted. Gene to cell type annotation based on an external HER2+ scRNA-seq dataset²² is reported. Only genes with |logFC | >1 are reported, * = FDR < 10%. An extended version, reporting all genes with FDR < 10% in at least one comparison, is presented in Supplementary Fig. 8. B Heatmap of genesets significantly enriched in either the overall population or one of the two treatment cohorts, * = gene permutation FDR < 0.1%. C Evaluation of changes in sTILs at Day14 compared to baseline in the overall population and separately for the Fulv and NoFulv cohorts, two-sided Student’s t-test. D Evaluation of changes in iTILs at Day14 compared to baseline in the overall population and separately for the Fulv and NoFulv cohorts, two-sided Student’s t-test. All boxplots are defined as follow: centre line = median; box limits = upper and lower quartiles; whiskers = 1.5x interquartile range; points = outliers. sTILs = stromal tumour infiltrating lymphocytes; iTILs = intra-tumoral infiltrating lymphocytes. Source data are provided as a Source Data file.