Integrated lipidomics and transcriptomics reveal the key role of ceramides in the development of endometriosis.

Endometriosis (EMs) is a chronic gynecological disease with poorly understood pathogenesis. This study integrated lipidomics and transcriptomics to systematically investigate aberrant sphingolipid metabolism in EMs, aiming to identify pathogenic mechanisms and therapeutic targets. Differential metabolites and genes in EMs lesions were identified through multi-omics profiling, followed by gene-metabolite network construction via MetaboAnalyst. EMs mouse models were established by intraperitoneal endometrial transplantation. Mice received ceramide (Cer) or EMs therapeutics for 2 weeks. Lesion size, cytokines, Cer levels, apoptosis, SMPD3 expression, and CD206+ macrophage infiltration were assessed using ELISA, TUNEL, western blot, RT‑qPCR, flow cytometry, and dual immunofluorescence. Integrated analysis revealed substantial metabolic and transcriptional alterations in EMs lesions. Sphingomyelin (SM) emerged as a central network hub, while Cer, generated via SMPD3-mediated SM hydrolysis, was markedly accumulated in lesions. In vivo, exogenous Cer(d18:1/20:0) supplementation exacerbated Cer accumulation, enhanced anti-apoptotic capacity, intensified inflammatory responses, and promoted CD206+ macrophage infiltration. Conversely, effective EMs therapeutics suppressed Cer accumulation, downregulated macrophage SMPD3 expression, and reduced CD206+ macrophage infiltration. Collectively, we identify the SM-SMPD3-Cer axis as a novel metabolic driver of EMs progression. Pathological Cer accumulation facilitates lesion development by promoting inflammation, enhancing CD206+ macrophage polarization, and suppressing apoptosis. These findings provide new metabolic insights and a theoretical foundation for Cer-targeted therapeutic strategies in endometriosis.