Abstract
PURPOSE: To conduct a comparative metabolomic analysis of follicular fluid (FF) from patients undergoing in vitro fertilization (IVF) cycles under GnRH agonist versus antagonist protocols, aiming to identify protocol-specific metabolic signatures and explore their associations with embryological outcomes, thereby elucidating the metabolic basis for outcome differences and identifying modifiable metabolic factors to expand the scope for improving IVF outcomes. METHODS: This study included 94 patients (47 per group) propensity score-matched for age, body mass index (BMI), anti-Müllerian hormone (AMH), and antral follicle count (AFC). FF samples collected during oocyte retrieval were analyzed using gas chromatography-mass spectrometry (GC-MS). The concentrations of identified metabolites were compared between groups and correlated with key laboratory parameters including the number of retrieved oocytes, Day 3 high-quality embryos, blastocysts, and high-quality blastocysts, as well as cumulative clinical pregnancy rates. RESULTS: The patients in GnRH agonist group were found to have better ovarian response, reflected by increased numbers of retrieved oocytes. Metabolomic profiling identified 58 differentially abundant metabolites between the two protocols. The levels of three key fatty acids, 11,14,17-eicosatrienoic acid, homo-γ-linolenic acid, and pentadecanoic acid, markedly decreased in the antagonist group (fold change < 0.75, variable importance in projection > 1.5). These metabolites exhibited strong power to discriminate between the protocols (area under the curve > 80%) and showed significant positive correlations with the number of high-quality embryos (r = 0.32–0.45, P < 0.05). A trend towards a higher cumulative clinical pregnancy rate was observed in the GnRH agonist group (72.34% vs. 55.32%, P = 0.05). CONCLUSION: GnRH agonist and antagonist protocols induce distinct metabolomic profiles in FF. The GnRH agonist protocol is associated with a follicular microenvironment enriched in specific fatty acids, which may contribute to superior ovarian response and increased numbers of high-quality embryos. The identified metabolites serve as potential biomarkers for oocyte quality and provide a theoretical basis for future investigations into nutritional interventions (e.g., omega-3 fatty acid supplementation) aiming at modulating the follicular microenvironment to optimize IVF outcomes following GnRH antagonist protocols. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13048-025-01933-7.