Abstract PS2-10-14: Blood-based metabolomic profiling and transcriptomic analysis of circulating cd3+ t cells reveal associations with treatment response and immune activation in early breast cancer (ebc)

Abstract Background: Pathological complete response (pCR) is a strong predictor of long-term outcomes in early breast cancer (eBC), establishing neoadjuvant chemotherapy (NACT) as the standard of care for aggressive BC subtypes. Recently, targeting host and tumor metabolism has emerged as a promising approach to boost antitumor immunity and improve NACT efficacy. However, the specific metabolic biomarkers involved, and their immunological effects remain poorly defined. Methods: We performed untargeted metabolomics on baseline plasma from 84 eBC patients undergoing NACT at our institution between 2021-2023 (22% luminal, 36% HER2+, 42% triple-negative; 48% achieved pCR). Data were analysed using univariate (t-test), multivariate (PLS-DA), and pathway enrichment approaches. In a subset of 49 patients (58%), bulk RNA was extracted from sorted CD3+ circulating T cells for gene expression analysis. Gene Ontology enrichment analysis was used to characterize upregulated pathways in T cells. Results: Pathway enrichment analysis of metabolomic data identified alpha-linolenic acid (ALA, omega-3)and linoleic acid (LA, omega-6) metabolism as top pathways associated with pCR and residual disease, respectively. Specifically, the VIP score analysis showed that docosahexaenoic acid (DHA, along-chain omega-3 derived from ALA) and dihomo-gamma-linolenic acid (DGLA, a downstreamomega-6 derived from LA) has the strongest association with pCR and RD respectively. Additional top ranked metabolites at VIP analysis included palmitoleic acid (POA, an omega-7 lipokine with immunomodulatory role) and conjugated linoleic acid (CLA, an omega-6 known to counteract the inflammatory effects of classical non-conjugated omega-6). We developed an “Omega Signature” tracking the balance between anti-inflammatory omega-3/6/7 and pro-inflammatory omega-6 asPOA + [(DHA + CLA)/DGLA]. This signature was significantly associated with pCR in a multivariate logistic regression model adjusted for age and BMI (OR 1.53, 95% CI 1.33-1.88, p < 0.0001). To assess whether the Omega Signature reflects T cells polarization, we performed transcriptomic profiling of circulating T lymphocytes in 49/84 patients. Patients with high Omega Signature (above the median)showed upregulation of gene pathways involved in T cell activation and adaptive immune responses compared to those with low scores. Conclusion: Our findings reveal that a specific circulating fatty acid profile seems to be associated with treatment response and immune activation in eBC. This signature reflects a favorable balance of immunomodulatory lipids and may serve as a non-invasive biomarker to identify patients more likely to achieve pCR. Correlation analyses with tissue metabolomics and gene expression data are ongoing will be presented at the Congress. Citation Format: V. Martini, B. Conte, L. Negrini, M. Manfredi, B. Elettra, S. D'Alfonso, M. Mellai, D. Corà, F. Favero, T. Landolfo, I. Taglialatela, B. Ruffilli, S. Nardin, V. Rossi, F. D'Avanzo, S. Gobbato, M. Bitrus, A. Turky, C. Branni, J. Gennari, A. Gennari. Blood-based metabolomic profiling and transcriptomic analysis of circulating cd3+ t cells reveal associations with treatment response and immune activation in early breast cancer (ebc) [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 PS2-10-14.