Fig. 1: The study schematics.

a. Tumour tissue samples underwent (i) Whole-exome sequencing (WES) for mutation and clonality detection followed by neoantigen prediction; (ii) Nanostring gene expression profiling; and (iii) stromal TILs counting. Our goal was to select samples that passed quality control and perform the temporal characterisation of the mutational, gene expression and TILs in serial primary HER2-negative breast cancers that were good responders or poor responders to eribulin. DNA sequencing (WES) was performed in 88 primary invasive breast cancers and matched the normal DNA of each patient. Of these, 66 tumour samples were used for mutational and clonality analyses. RNA-Nanostring gene expression profiling was performed in 96 primary invasive breast cancers. From the DNA sequencing data, candidate neoantigens were predicted. Stromal TILs were counted from the H&E slides in 91 out of 105 tumour specimens. Clinical features and the PAM50 intrinsic molecular subtypes of each of the sequential primary tumour’s biopsies were examined. TMB tumour mutation burden, ORR overall response rate. b Schematics of the clinical trial. Temporal tumour sampling and a number of samples included in each analysis and time point are depicted. Distribution of PAM50 molecular intrinsic breast cancer subtypes at V1 (diagnostic biopsy), and ORR at V3 (surgery). E eribulin administration, V1 visit one, V2 visit two, V3 visit three, VR visit recurrence, CR complete response, PR partial response, SD stable disease, PD progressive disease.