Integrated single-cell and spatial transcriptomics reveal divergent immunological and stromal programs in peritoneal versus ovarian endometriosis

Background Endometriosis encompasses heterogeneous lesions, primarily peritoneal and ovarian subtypes, with distinct immunological and fibrotic features. The subtype-specific roles of the immune microenvironment in pathogenesis remain unclear. Integrated analysis combining high-resolution cellular atlases with spatial context is needed to decipher these mechanisms.

We performed an integrative analysis of published single-cell RNA sequencing (n = 81,676 cells) from control endometrium (Ctrl), eutopic endometrium (EuE), peritoneal endometriosis (EcP), and ovarian endometriosis (EcO), and spatial transcriptomic (n = 60 segments) data from Ecp and match EuE. Analytical pipelines include cellular atlas construction, differential expression, spatial co-expression, and cell-cell communication inference.

Our single-cell atlas revealed fundamentally distinct cellular ecosystems. EcP was enriched for CCL19 + perivascular cells (6.4-fold vs. control) and immune-active niches, whereas EcO exhibited pronounced smooth muscle differentiation and NNMT upregulation. Spatial analysis compartmentalized these programs, with the CCL19-CCR7 chemokine axis localized to stromal niches in EcP strongly correlated (ρ = 0.872). In contrast, EcO showed enhanced smooth muscle gene expression (MYH11, log₂FC = 3.87). Cell-cell communication networks diverged, with EcP dominated by chemokine and TGF-β signaling, and EcO dominated by smooth muscle and PDGF pathways. Therapeutic target analysis revealed subtype-specific patterns: immune checkpoints (CTLA4 and PDCD1) were upregulated in EcP, whereas MMP9 was dramatically downregulated in EcO.

EcP and EcO exhibit fundamentally divergent programs. We propose to conceptualize these as an ‘immune-hot’, chemokine-driven inflammatory niche (EcP) versus an ‘immune-cold’, fibromuscular survival niche (EcO). These findings underscore that lesion-specific immune-stromal crosstalk may dictates pathogenesis and suggest a potential paradigm shift toward immunologically-informed, subtype-specific precision therapeutics, which warrant further experimental validation. Similar content being viewed by others Data availability All the data analyzed in this study were available from public repositories. ScRNA-seq data are available under GEO accession number GSE179640. Spatial transcriptomic data are available under GEO accession GSE263897. Processed data and analysis codes will be made available in the GitHub repository upon publication. Abbreviations - EcP: - Peritoneal endometriosis - EcO: - Ovarian endometriosis - EuE: - Eutopic endometrium - Ctrl: - Control endometrium - scRNA-seq: - Single-cell RNA sequencing - UMAP: - Uniform Manifold Approximation and Projection - PCA: - Principal Component Analysis - GO: - Gene Ontology - CAF: - Cancer-associated fibroblast - MDSC: - Myeloid-derived suppressor cell

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We would like to thank Editage (www.edita ge.cn) for the English language editing. Funding This study was supported by the Joint Funds for the Innovation of Science and Technology, Fujian Province (2023Y9359 and 2024Y9538), Qihang Fund of Fujian Medical University (2023QH1190 and 2023QH1193), and Fujian Provincial Health Technology Project (2024GGA057). 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 Contributions Fangjie He : Conceptualization, Data curation, Formal analysis, Funding acquisition, Project administration, Supervision, Writing – original draft, Writing – review & editing. Shuiling Zu : Data curation, Formal analysis, Funding acquisition, Project administration, Visualization, Writing – original draft. Yan Lin : Data curation, Formal analysis, Visualization, Writing – original draft. Jun Shi : Data curation, Writing – review & editing. Shunhe Lin : Conceptualization, Funding acquisition, Project administration, Supervision, Writing – review & editing. Corresponding authors Ethics declarations Ethics approval and consent to participate This study only utilized publicly available anonymized datasets. Original studies involving human participants were reviewed and approved by their respective Institutional Review Boards. As this work involved the re-analysis of existing de-identified data, it did not constitute human subject research requiring additional ethical approval. 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 4.0 International License, which permits use, sharing, adaptation, 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 changes were made. 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/4.0/. About this article Cite this article He, F., Zu, S., Lin, Y. et al. Integrated single-cell and spatial transcriptomics reveal divergent immunological and stromal programs in peritoneal versus ovarian endometriosis. BMC Women's Health (2026). https://doi.org/10.1186/s12905-026-04456-5 Received: Accepted: Published: DOI: https://doi.org/10.1186/s12905-026-04456-5