Dissecting the cell microenvironment of ovarian endometrioma through single-cell RNA sequencing

Ovarian endometrioma (OE), also known as “chocolate cysts,” is a cystic mass that develops in the ovaries due to endometriosis and is a common gynecological condition characterized by the growth of endometrial tissue outside the uterus, leading to symptoms such as dysmenorrhea, pelvic pain, and infertility. However, the precise molecular and cellular mechanisms driving this pathophysiology remain largely unknown, posing challenges for diagnosis and treatment. Here, we employed integrated single-cell transcriptomic profiling of over 52,000 individual cells from endometrial tissues of OE patients and healthy donors and identified twelve major cell populations. We identified notable alterations in cell type-specific proportions and molecular signatures associated with OE. Notably, the activation of IGFBP5+ macrophages with pro-inflammatory properties, NK cell exhaustion, and aberrant proliferation of IQCG+ and KLF2+ epithelium are key features and may be the potential mechanisms underlying the pathogenesis of OE. Collectively, our data contribute to a better understanding of OE at the single cell level and may pave the way for the development of novel therapeutic strategies. Similar content being viewed by others Data availability All the sequencing data have been deposited in the Genome Sequence Archive (GSA) (https://bigd.big.ac.cn/gsa/) with the accession number OMIX004497.

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This work is supported from Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences (CI2023D003, CI2021B014), the National Key Research and Development Program of China (2022YFC2303600, 2020YFA0908000), the Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine (ZYYCXTD-C-202002), the CACMS Innovation Fund (CI2023E002, CI2021A05101, CI2021A05104), the Science and Technology Foundation of Shenzhen (JCYJ20210324115800001), the Science and Technology Foundation of Shenzhen (Shenzhen Clinical Medical Research Center for Geriatric Diseases); the Shenzhen Medical Research Fund (B2302051), the National Natural Science Foundation of China (82201786), Guangdong Basic and Applied Basic Research Foundation (2021A1515110646), Guangdong-Dongguan Joint Fund Regional Cultivation Project (2021B1515140033), and Dongguan Science and Technology of Social Development Program (20211800904742, 20221800905732, 20221800904462). Author information Authors and Affiliations Corresponding authors Ethics declarations The authors declare that they have no conflict of interest. Electronic supplementary material Rights and permissions About this article Cite this article Wu, J., Xia, S., Ye, W. et al. Dissecting the cell microenvironment of ovarian endometrioma through single-cell RNA sequencing. Sci. China Life Sci. 68, 116–129 (2025). https://doi.org/10.1007/s11427-024-2638-9 Received: Accepted: Published: Version of record: Issue date: DOI: https://doi.org/10.1007/s11427-024-2638-9