Serum Proteome Profiling Identifies N-cadherin and c-Met as Candidates for the Early Detection of therapeutic Response to Neoadjuvant Chemotherapy in Breast Cancer: A retrospective Study

Background: Neoadjuvant chemotherapy (NACT) for non-metastatic breast cancer is often preferred over adjuvant chemotherapy to shrink tumours and facilitate surgical removal. NACT typically comprises 8 cycles over 20–24 weeks: 4 cycles of anthracycline with cyclophosphamide followed by 4 cycles of paclitaxel. After surgery, the therapeutic response is assessed histopathologically using the TNM classification, where ypT0 indicates pathological complete remission (PCR) and residual tumour cells (> ypT0) indicate non-complete remission (non-PCR). Currently, imaging techniques such as ultrasound are used during NACT to assess clinical response. Liquid biopsy-based methods may complement imaging by enabling early response monitoring. In this study, we used serum proteomics to identify marker candidates associated with PCR as early as after the second NACT cycle. Methods: Longitudinal, retrospective serum proteomic analyses were performed on 22 breast cancer patients (11 PCR, 11 non-PCR) and 21 age-matched healthy controls. Serum samples were collected pre-therapy and after two and six NACT cycles. Proteins were analysed using liquid chromatography–tandem mass spectrometry (LC–MS/MS) following immunoaffinity depletion, trypsin digestion, tandem mass tag labelling, and fractionation. Protein quantitation was performed with MaxQuant software, and abundance analysis utilised linear models of microarray analysis. Tumour-resident expression of a candidate marker was evaluated via immunohistochemistry in an independent cohort of 37 cases. Results: Across 84 samples, >390 proteins were consistently identified and quantified. Pre-therapy serum proteomes showed no significant differences between PCR and non-PCR groups. Longitudinal analysis revealed that serum levels of c-Met and N-cadherin could distinguish responders after the second NACT cycle with high predictive value (AUC 0.93). More pronounced changes were observed after the sixth cycle, including significant alterations in centrosomal protein, sex hormone-binding globulin, and cholinesterase levels. Additionally, N-cadherin expression was elevated in therapy-naïve tumour samples from patients achieving PCR. Conclusions: This study highlights the potential of serum proteomics for identifying markers to assess NACT efficacy in breast cancer. Soluble N-cadherin and c-Met may serve as promising serum markers for PCR, particularly when combined with (immune)histochemical tumour characterisation.