Abstract PS2-10-22: Proteomic analysis of residual disease identifies potential prognostic biomarkers of triple-negative breast cancer after neoadjuvant chemotherapy

Abstract Background: Triple negative breast cancer(TNBC) patients with residual disease after neoadjuvant chemotherapy have a poor prognosis. However, not all such patients have a bad outcome. Residual cancer burden (RCB) can provide some prognostic information, but there is still a lack of effective molecular markers. This study is aimed at exploring the prognostic biomarkers in TNBC patients with residual disease after neoadjuvant therapy from the perspective of proteomics. Methods: TNBC patients with residual disease after neoadjuvant chemotherapy were divided into a short-term recurrence group (recurrence free survival≤3 years) and a non-recurrence group (recurrence free survival 3 years), and baseline characteristics between the two groups were matched. Sixty residual tumor samples from patients were selected for whole proteome analysis using Liquid Chromatography-Mass Spectrometry (LC-MS). Differential protein screening, pathway enrichment analysis, protein - protein interaction network analysis, and immune infiltration analysis were performed between the two groups. Finally, the expression of differential proteins was validated at the immunohistochemical(IHC) level. Results: A total of 60 postoperative residual tumor samples were tested, with 30 in the recurrence group and 30 in the non-recurrence group, and baseline characteristics were balanced between the two groups. A total of 49 up-regulated and 237 down-regulated proteins were identified when comparing the recurrence and non-recurrence groups. GO enrichment analysis indicated that the down-regulated proteins were mainly enriched in pathways related to leukocyte-mediated immune response, T cell activation, and mitochondrial metabolism. KEGG enrichment analysis showed that the down-regulated proteins were enriched in the T cell receptor signaling pathway and osteoclast differentiation pathway. Both pathway enrichment analyses revealed that immune-related proteins, especially those in the T cell pathway, were significantly down-regulated in recurrent patients compared to non-recurrent patients. Protein-protein interaction network analysis identified 25 key proteins, several of which are immune-related, including CD1C, CD247, CD2, CD300A, CD3D, CD40, CD68, CD84, GZMB, CD20, and CD150. Survival analysis based on these 25 key proteins showed that down-regulation of CD68 and CD40 most significantly affected patient survival. Immune infiltration analysis revealed down-regulated immune cell-related expression in recurrent patients compared to non-recurrent patients, with decreased expression of CD4+ effector T cells, dendritic cells, macrophages, M2 macrophages, naive B cells and plasmacytoid dendritic cells in the recurrence group. Based on the analysis of key differential proteins and immune infiltration, IHC was used to verify the expression of CD4, CD40, and CD68 in recurrence and non-recurrence groups. Results showed that the recurrence group had significantly lower expression levels. The tumor-infiltrating lymphocytes in the recurrence group were also significantly lower than in the non-recurrence group (median 10% vs. 20%, P0.001). Conclusion: The study found that in patients with residual disease after neoadjuvant therapy for TNBC, the downregulation of immune-related proteins, particularly in the T cell pathway, is closely associated with short term recurrence. Immunohistochemistry confirmed that CD4, CD40, and CD68 are downregulated in the recurrent group. Our study preliminarily confirms that the downregulation of immune-related proteins is an important prognostic factor for TNBC patients with residual disease, offering valuable insights for future research and clinical practice. Citation Format: X. Chen, L. Ji, H. Lv, G. Song, Q. Li, J. Wang, Y. Fan, Y. Luo, B. Lan, S. Chen, R. Cai, F. Ma, B. Xu, P. Zhang. Proteomic analysis of residual disease identifies potential prognostic biomarkers of triple-negative breast cancer after neoadjuvant chemotherapy abstract. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS2-10-22.