Single-cell atlas reveals immune microenvironment heterogeneity in endometriosis subtypes

Background Endometriosis affects an estimated 10% of women within the reproductive age group globally, causing chronic pelvic pain and infertility. Nevertheless, its cellular and molecular pathogenic mechanisms remain poorly understood.

This research performed a systematic analysis of three eutopic endometrium specimens, three ovarian endometriosis specimens, and three deep infiltrating endometriosis specimens, utilizing the GSE213216 single-cell RNA sequencing dataset. The study successfully established a detailed single-cell atlas that delineates the cellular composition of endometrial epithelial cells, stromal cells, and diverse immune cell populations.

This study demonstrates tissue-specific heterogeneity in cell-subset distribution and transcriptional states, reflecting profound cellular remodeling and reprogramming in disease. Endometriotic microenvironments exhibit robust immune activation; most pronounced in deep infiltrating endometriosis. Epithelial cells upregulate antigen presentation and oxidative phosphorylation. Cell crosstalk is subtype-dependent: immune cells predominantly interact with ciliated epithelial cells in ovarian endometriosis and with glandular secretory cells in deep infiltrating endometriosis. We further identify increased infiltration of TAGLN⁺ fibroblasts linked to tissue fibrosis.

This investigation comprehensively elucidates the intricate complexity and substantial heterogeneity of the immune microenvironment across distinct endometriosis subtypes through single-cell resolution analysis. The single-cell dissection reveals inter-subtype microenvironmental complexity, providing mechanistic insights and theoretical basis to advance precise diagnosis and targeted therapies for endometriosis. Similar content being viewed by others

We thank Department of Gynecology, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University that supported this work. Funding This study was supported by the Joint Funds for the Innovation of Science and Technology, Fujian province (2023Y9384), the Fujian provincial health technology project (2025QNGGA010), the Natural Science Foundation of Fujian Province, China (2025J011157), the National Major Research and Development Program, China (2024YFA1107202), the Technology Innovation Startup Fund of Fujian Maternity and Child Health Hospital (YCXY23-06), the Fujian Provincial Natural Science Foundation of China (2025J01321510), and the Fujian Provincial Natural Science Foundation of China (Grant No. 2023J05231). The sponsors had no involvement in the study design, collection, analysis, and interpretation of data, writing of the report, or decision to submit the article for publication. Author information Authors and Affiliations Corresponding authors Ethics declarations Ethics approval and consent to participate All participants agreed to participate in this study and signed the informed consent form. The study was conducted in accordance with the Declaration of Helsinki and approved by the Ethics Committee of Fujian Maternity and Child Health Hospital (Approval Number: 2024KY180). Competing interests The authors declare no competing interests. Additional information Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Supplementary Information Rights and permissions Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/. About this article Cite this article Huang, P., Zhang, X., Jiang, S. et al. Single-cell atlas reveals immune microenvironment heterogeneity in endometriosis subtypes. BMC Women's Health (2026). https://doi.org/10.1186/s12905-026-04969-z Received: Accepted: Published: DOI: https://doi.org/10.1186/s12905-026-04969-z