Abstract 3044: Butyrate modulates key oncogenic pathways in triple-negative breast cancer: insights from transcriptomic profiling
Authors: Gabriel Borges Vélez, Diego N. Bracero-Sánchez, Liah M. Román-Calderón, Ariana S. García-Lopez, Angel Amaral-Maisonet, Jeannette Salgado-Montilla, Esther A. Peterson-Peguero, Josué Pérez-Santiago
Journal: Cancer Research (2025)

Abstract Introduction: Triple-negative breast cancer (TNBC) is a highly aggressive subtype with a poor prognosis, affecting approximately 5% of breast cancer patients and lacking targeted therapies. Recent studies highlight the potential of short-chain fatty acids (SCFAs), metabolic byproducts of the microbiome, as anticancer agents. Among these, butyrate exhibits anti-inflammatory, immunomodulatory, and antineoplastic effects in several cancer types. Our preliminary data shows that butyrate exerts cytotoxic, anti-migratory, and antiproliferative effects on TNBC cells. However, to understand molecular mechanisms related to butyrate treatment and investigate its therapeutic potential in TNBC, this study measured transcriptomic changes after butyrate treatment of TNBC. Methods: MDA-MB-231 cells (TNCB cell model) were treated with 5 mM butyrate for 24 hours. RNA was extracted, quantified, and assessed for integrity before sequencing on the Illumina NextSeq 550. Bioinformatics workflows included quality control (FastQC), trimming (Trimmomatic), and alignment to the GRCh38 human genome using STAR. Read quantification was performed with RSEM, and differential gene expression was analyzed using R statistical software (tximport and DESeq2 packages). Functional annotation, pathway enrichment, and protein interaction analyses of significantly differentially expressed genes were conducted using Metascape and STRING (adj. p-value&amp;lt;0.05). Results: Butyrate treatment significantly altered the expression of 4, 352 transcripts in MDA-MB-231 cells. The most upregulated transcript, DHRS2, a cell cycle regulator with tumor suppressor properties, exhibited an 8.8-fold increase. Conversely, ZNF709, a zinc finger protein frequently overexpressed in cancers, showed a 7.8-fold decrease. Pathway analysis revealed that affected transcripts are involved in critical oncogenic processes, including cell adhesion, cytokine signaling, wound healing, regulation of cell migration, and MAPK signaling. STRING analysis identified clusters of proteins significantly associated with protein phosphorylation regulation, along with binding-related molecular functions and phosphoprotein. Conclusions: Our results demonstrate that butyrate modulates the transcriptome of MDA-MB-231 cells, targeting pathways involved in oncogenic processes such as cell adhesion, migration, and signaling, which is consistent with our cellular results. Key transcripts, such as DHRS2 and ZNF709, are novel prognostic markers for prostate and gastric cancer respectively, highlighting butyrate's capacity to regulate tumor suppressor and oncogenic pathways. These findings support butyrate's potential as a microbiome-derived therapeutic for TNBC. Citation Format: Gabriel Borges Vélez, Diego N. Bracero-Sánchez, Liah M. Román-Calderón, Ariana S. García-Lopez, Angel Amaral-Maisonet, Jeannette Salgado-Montilla, Esther A. Peterson-Peguero, Josué Pérez-Santiago. Butyrate modulates key oncogenic pathways in triple-negative breast cancer: insights from transcriptomic profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3044.