{"paper_id":"d593fd86-479f-4712-ac94-cd7ac1b10e5e","body_text":"Content uploaded by Nazli Ece Gungor\nAuthor content\nAll content in this area was uploaded by Nazli Ece Gungor on Feb 09, 2025\nContent may be subject to copyright.\nBioinformatic approach highlights cellular compositions in endometriosis organoids (EOs)\nTurkiye\nIntroduction/Background\nEndometriosis affects 5–10% of reproductive-age women, with current treatments offering only\ntemporary relief. Understanding its mechanisms remains limited. This study focuses on patient-\nderived endometriosis organoids (EOs) to explore cellular composition using bioinformatics,\naiming to uncover key interactions between endometrial and immune cells and improve\nunderstanding of disease pathogenesis.\nMaterials and Methods\nBy obtaining published bulk RNA sequencing data of two menstrual fluid (MFO), two non-\ntreated endometrial biopsies (EMO-N), and three hormone-treated endometrial biopsy-derived\n(EMO-H) organoids, we established a reference gene matrix from a published single-cell RNA\nsequencing (scRNAseq) collection of healthy eutopic endometrium, eutopic endometrium (EuE),\nectopic peritoneal lesions (EcP) and the adjacent regions to these (EcPA), and ectopic ovarian\nlesions (EcO) for the deconvolution of major cell types in organoid models.\nResults\nWe performed scRNAseq analysis on 31 samples, identifying 58,072 evaluable single cells after\nfiltering and doublet removal. Cells were classified into epithelial, endothelial, stromal, myeloid,\nand lymphocyte types using 325 marker genes. The major cell types varied by tissue condition:\nlymphocytes and stromal cells were most abundant in EuE, EcO, and healthy endometrium. The\norganoid models (MFOs) showed distinct cellular composition, resembling healthy endometrium\nmore than EuE, with 53% lymphocytes, 24% stromal, 10% epithelial, 8% myeloid, and 5%\nendothelial cells. EMOs had 25% lymphocytes, 27% epithelial, 24% stromal, 16% endothelial,\nand 8% myeloid cells. Subclassifying EMOs into EMO-N (higher epithelial fraction, 30%) and\nEMO-H (25%) revealed differences in epithelial content, with EMO-Ns showing a greater\nepithelial proportion.\nConclusion\nWe suggest highlighting cellular heterogeneity within the EOs and revealing that the method of\nsample collection and patient-specific factors might affect the distribution of major cell types\nrepresented in EOs. Furthermore, the presence of non-epithelial cells in EOs should be\nconsidered when treatment tests are done using EOs.\nKey words\nEndometrial organoids, single-cell sequencing, cell heterogeneity","source_license":"CC0","license_restricted":false}