Molecular determinants of neoadjuvant chemotherapy resistance in breast cancer: An analysis of gene expression and tumor microenvironment

Neoadjuvant chemotherapy (NAC) is a critical component of breast cancer treatment, but the molecular mechanisms underlying resistance remain poorly understood. This study aimed to identify transcriptomic changes associated with NAC resistance across four breast cancer subtypes: Luminal A, Luminal B/HER2-positive, Luminal B/HER2-negative, and Triple-Negative Breast Cancer (TNBC). RNA-seq analysis was performed on paired pre- and post-NAC breast cancer samples from 35 non-responders. Differentially expressed genes (DEGs) were identified, and functional enrichment analyses were conducted. Protein-protein interaction (PPI) networks were constructed to identify hub genes. Tumor microenvironment (TME) infiltration was estimated using deconvolution algorithms. The results revealed distinct gene expression profiles between pre- and post-NAC samples, with FOS and NR4A1 being common DEGs across all subtypes. Enriched pathways varied among subtypes, including signal transduction, estrogen biosynthesis, extracellular matrix organization, dendritic cell activation, and B cell activation. TME analysis showed increased infiltration of specific immune cell populations after NAC, including CD4 memory T cells, regulatory T cells, neutrophils, macrophages, and mast cells, varying by subtype. These findings suggest that NAC modulates gene expression, cellular activity, and TME interactions, potentially contributing to treatment resistance. Understanding the molecular determinants of NAC resistance is crucial for developing targeted therapeutic strategies and improving outcomes for breast cancer patients. Overall design: After obtaining informed consent, patients with a histologically confirmed diagnosis of breast cancer and scheduled chemotherapy were recruited for this study. Histopathological review of pre- and post-chemotherapy biopsies was performed by an expert pathologist who reviewed the slides and outlined the tumor tissue. Following completion of the neoadjuvant regimen, treatment response was evaluated using surgical specimens obtained by a pathologist. A pCR was established according to the most accepted definition: the absence of infiltrating components in the breast and lymph nodes (ypT0/is or ypN0). Patients were classified as responders if they showed pCR and non-responders if they did not present with pCR. RNA sequencing was performed on formalin-fixed paraffin-embedded pretreatment (baseline) and posttreatment (FollowUp) tissues from 35 non-responder patients . Differentially expressed genes (DEGs) were identified between the FollowUp and Baseline samples for molecular subtypes.