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Despite the increasing prevalence of endometriosis, there has been limited research on genetic effects, and its molecular mechanisms remain unclear. This study aimed to investigate the mechanisms underlying the development of endometriosis and to identify new genetic targets for endometriosis by integrating data from gene chips, single-cell mapping, and genome-wide association study databases.\u00a0Using the Gene Expression Omnibus database, we downloaded data on normal endometrium, eutopic endometrium, and ectopic lesion tissues to explore the differentially expressed genes (DEGs) between normal and eutopic endometrium, and between eutopic and ectopic endometrium. Assessment of the relationships between DEGs and endometriosis involved differential expression, expression quantitative trait loci (eQTL), and Mendelian randomization (MR) analyses. Two single-cell atlas datasets were then analyzed to explore the mechanisms underlying disease development and progression.\u00a0Intersection of MR results with DEGs between normal and eutopic endometrium highlighted 28 candidate biomarker genes (17 upregulated and 11 downregulated). Similarly, we identified two additional candidate biomarker genes by intersecting the DEGs between eutopic and ectopic endometrium with MR results. Among these 30 candidates, further filtering using single-cell datasets revealed that the histamine N-methyltransferase (\n                      <jats:italic>HNMT<\/jats:italic>\n                      ), coiled-coil domain containing 28\u00a0A (\n                      <jats:italic>CCDC28A<\/jats:italic>\n                      ), fatty acid desaturase 1 (\n                      <jats:italic>FADS1<\/jats:italic>\n                      ) and mahogunin ring finger 1 (\n                      <jats:italic>MGRN1<\/jats:italic>\n                      ) genes were differentially expressed between the normal and eutopic groups, consistent with transcriptomic and MR results. Our findings suggested that eutopic endometrium exhibits epithelial-mesenchymal transition (EMT). Cell communication analysis focused on ciliated epithelial cells expressing\n                      <jats:italic>CDH1<\/jats:italic>\n                      and\n                      <jats:italic>KRT23<\/jats:italic>\n                      revealed that, in the eutopic endometrium, ciliated epithelial cells are strongly correlated and interact with natural killer cells, T cells, and B cells.\u00a0We identified four novel biomarker genes and found evidence for EMT in the eutopic endometrium. The mechanism of endometriosis progression may be closely related to EMT and changes in the immune microenvironment triggered by damage to ciliated epithelial cells.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1007\/s10142-025-01543-y","type":"journal-article","created":{"date-parts":[[2025,3,29]],"date-time":"2025-03-29T17:40:22Z","timestamp":1743270022000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["A new perspective on endometriosis: Integrating eQTL mendelian randomization with transcriptomics and single-cell data analyses"],"prefix":"10.1007","volume":"25","author":[{"given":"Sheng","family":"Dou","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zongyun","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fenglian","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuechang","family":"Cen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjing","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haimei","family":"Qin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junli","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,3,26]]},"reference":[{"key":"1543_CR1","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1165\/rcmb.2014-0493OC","volume":"53","author":"S Anvari","year":"2015","unstructured":"Anvari S, Vyhlidal CA, Dai H, Jones BL (2015) Genetic variation along the histamine pathway in children with allergic versus nonallergic asthma. 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