Response to neoadjuvant chemotherapy in early breast cancers is associated with epithelial-mesenchymal transition and tumor-infiltrating lymphocytes

Epithelial-mesenchymal transition (EMT) and tumor-infiltrating lymphocytes (TILs) play a central role in early-stage breast cancer (BC) and are associated with chemoresistance, stemness, and invasion. The objective of this study was two fold: (a) by investigating the predictive value of EMT and TILs, we aimed to estimate the chance of achieving a response after neoadjuvant chemotherapy (NAC) and (b) to evaluate the potential changes of EMT and TILs in BC upon NAC. Using bulk RNA sequencing and immunofluorescence (IF) for EMT (E-cadherin and vimentin) and lymphocyte markers (CD3, CD8, FOXP3), we analyzed pre- and post-NAC tumor samples from 100 early-BC patients treated with NAC. For each BC molecular subtype, we compared the expression of EMT and TILs, at the RNA and protein level, between responding and non-responding tumors. Paired analysis of pre- and post-NAC samples was performed for patients with residual disease after NAC. RNA sequencing of pre- and post-NAC samples identified significant differences in EMT-related and inflammation-related gene expression between non-responding (RCB-II/III) and responding (RCB-0/I) tumors. Increased EMT-related marker expression was observed after NAC in cases with residual disease, in particular in the luminal subtype. Characterization of TILs in pre-NAC samples showed substantially more CD3 + CD8-FOXP3-lymphocytes in responding HER2+ tumors compared with non-responding. Paired analyses of pre- and post-NAC samples demonstrated higher levels of CD3 + CD8 + FOXP3-lymphocytes in residual luminal and triple-negative BC and higher levels of CD3 + CD8-FOXP3-lymphocytes in residual triple-negative BC compared with other subtypes of lymphocytes. We found that there is an unmet clinical need for reliable biomarkers to predict response to NAC in BC. Our results suggest that an upregulation of the EMT gene signature in diagnostic biopsies is associated with poor response to NAC in early BC, across all subtypes. Additionally, changes in EMT and in the TIL population occur in residual tumors after NAC. These findings could help to personalize future NAC and adjuvant treatment regimens.