RNA-Seq profiling of pre- and on-treatment tumor samples from breast cancer patients enrolled in the NeoTRIP trial.

Triple-negative breast cancer (TNBC) is immunogenic, but only a subset of patients benefits from neoadjuvant immune checkpoint inhibitors (ICIs) combined with chemotherapy. Predictive biomarkers to guide patient selection and treatment adaptation are lacking. In the NeoTRIPaPDL1 (NeoTRIP) Phase III trial, 280 high-risk TNBC patients were randomized to neoadjuvant carboplatin plus nab-paclitaxel (CT, n=142) or the same regimen with atezolizumab (CT/A, n=138). Tumor biopsies were collected at baseline and on the first day of the second cycle (D1C2). Longitudinal transcriptome sequencing and analyses of selected gene signatures were performed, including hallmark, ferroptosis-related, and immune cell type–specific signatures. Treatment-induced gene expression changes and association with pathological complete response were investigated.