Abstract PS4-01-01: Multi-omics analysis of breast cancer with subtype classification

Abstract Background: In breast cancer, changes in the fecal metabolites and gut microbiota have been shown to influence drug sensitivity and resistance; however, differences in microbial composition between subtypes and their impact on cancer risk remain poorly understood. Here, we compared the fecal metabolites and gut microbiota between healthy controls(HCs) and breast cancer(BC) patients with subtype-specific analyses. Methods: 43 HCs and 29 BC patients feces were collected. Samples from BC patients were collected before treatment initiation, when pre-treatment samples were unavailable, samples were collected during treatment. Metabolomic analysis was performed with LC-TOFMS/MS. 16S metagenomic analysis was performed and the composition was evaluated using ALDEx2. Statistical analysis was conducted using the Wilcoxon-Mann-Whitney test, and p values were adjusted for multiple comparisons using the Benjamini-Hochberg method. Results: The median age was 71 years (range: 36-95) for HCs and 57 years (range: 32-87) for BC patients. The subtypes included 18 cases of hormone receptor (HR)-positive/human epidermal growth factor receptor 2 (HER2)-negative, 6 cases of HER2-positive, and 5 cases of triple-negative breast cancer (TNBC). Concerning metabolomic analysis, the PCA plot indicated that the metabolomic profile was different between the HCs and BC patients. AMP, asparagine, diethanolamine, N-Acetylglucosamine 1-phosphate, NAD+, nicotinamide, riboflavin, terephthalate and UMP were increased in the BC patients. ROC analysis for these metabolites yielded an AUC over 0.79 in discriminating BC patients from HCs. In gut microbial analysis, β diversity assessed showed no significant difference between HCs and BC patients, while α diversity measured by the Chao1 was reduced in BC patients (q 0.001). Similarly, the HR+/HER2- group showed no significant difference in β diversity, but α diversity assessed by Chao1 was reduced in the HR+/HER2- group (p 0.05). Because the number of HER2-positive and TNBC was small, we couldn’t come to the conclusion about the difference in these two groups. ALDEx2 revealed that Clostridiales and Bacteroidales at the order level were changed when comparing HCs and BC patients (effect size 0.4, p 0.01, adjusted p = 0.27, 0.19). Furthermore, comparison between the HR+/HER2- and TNBC subtypes showed several changes in Clostridiales (effect size 0.8, p 0.05, adjusted p = 0.86). Even within the same species, the direction of change varied among subtypes. Conclusion: This study provides novel insights into the metabolome in breast cancer, highlighting as potential biomarkers. Microbial diversity was reduced in BC patients and the gut microbiota was different between breast cancer subtype. Citation Format: T. Kon, N. Shoji-Harada, H. Tokuno, Y. Hamanaka, A. Ebata, M. Iida, M. Sato, M. Yanagaki, A. Yamazaki, A. Sakamoto, M. Makita, O. Hinano, T. Abe, M. Miyashita. Multi-omics analysis of breast cancer with subtype classification 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 PS4-01-01.