Longitudinal tissue biopsies (pretreatment and after two cycles) and surgical specimens were collected in the PROMIX trial (Fig. 1a), thus a multi-omics cohort of 150 HER2-negative breast cancer patients was established (Fig. 1b): bulk microarray gene expression profiling (GEP) (122 patients, 275 samples), single nucleus RNA-seq (snRNA-seq) (8 patients, 20 samples), whole-exome sequencing (WES) (20 patients, 50 tumor samples), multiplex fluorescent (mf) immunohistochemistry (IHC) (6 patients, 16 tumor samples), and MS-based proteomics (29 patients, 53 samples). Here, ERBB2 is linked to breast cancer.