Tumor-intrinsic B4GALNT3 expression drives a protective immune microenvironment in endometriosis-associated ovarian cancer

Background Although endometriosis-associated ovarian cancer (EAOC) is considered a separate clinical entity, no specific prognostic biomarkers aid in its management. This has, therefore, been among the factors hindering the development of tailored treatments. We aim to develop a robust, histotype-aware biomarker for EAOC through an integrative computational approach to explain its association with the tumor immune microenvironment. Methods A multi-stage bioinformatics approach using multiple independent Gene Expression Omnibus (GEO) cohorts was employed. We extracted consensus differentially expressed genes (DEGs) from three discovery datasets (EAOC vs. non-malignant tissue). These DEGs were further distilled into high-confidence hub genes using two machine learning algorithms. The pan-cancer prognostic potential was assessed via meta-analysis and tested for validity in an independent, EAOC-enriched cohort (GSE65986). The derived immune context was assessed using CIBERSORTx deconvolution in a pure EAOC cohort (GSE226870), while the cellular origin of our candidate was determined using an independent ovarian clear cell carcinoma (OCCC) single-cell RNA sequencing (scRNA-seq) dataset (GSE224334). Results From our analysis, we identified 75 consensus DEGs distilled into five hub genes. Among these, B4GALNT3 was the key candidate. While the pan-ovarian cancer meta-analysis showed a non-significant protective trend, we confirmed in our EAOC-enriched validation cohort that high B4GALNT3 expression was significantly associated with improved overall survival [hazard ratio (HR) =0.350, P=0.04]. It showed robust diagnostic potential with an overall area under the curve (AUC) of 0.962 [95% confidence interval (CI): 0.923–0.993] in leave-one-dataset-out cross-validation among discovery datasets. Immune deconvolution revealed that B4GALNT3 expression correlated with an anti-tumor microenvironment composed of increased levels of plasma B cells, memory B cells, and activated dendritic cells, with decreased regulatory T cells and M2 macrophages. Finally, scRNA-seq analysis confirmed that B4GALNT3 was intrinsically highly expressed in malignant and epithelial cells, with low expression in immune lineages. Conclusions B4GALNT3 is a novel, subtype-specific protective biomarker in EAOC. Our findings support a mechanism by which tumor-cell-intrinsic expression of B4GALNT3 drives protection from immune microenvironments. This work identifies B4GALNT3 as a promising prognostic factor and potential target for further mechanistic studies and protein-level validation in EAOC.