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To understand the mechanisms involved in this process, we aimed to compare endometrial transcriptome profiles during the window of implantation (WOI) between women with and without adenomyosis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We obtained endometrial biopsies LH-timed to the WOI from women with sonographic features of adenomyosis (n=10) and controls (n=10). Isolated RNA samples were subjected to RNA sequencing (RNA-seq) by the Illumina NovaSeq 6000 platform and endometrial receptivity classification with a molecular tool for menstrual cycle phase dating (beREADY\u00ae, CCHT). The program language R and Bioconductor packages were applied to analyse RNA-seq data in the setting of the result of accurate endometrial dating. To suggest robust candidate pathways, the identified differentially expressed genes (DEGs) associated with the adenomyosis group in the receptive phase were further integrated with 151, 173 and 42 extracted genes from published studies that were related to endometrial receptivity in healthy uterus, endometriosis and adenomyosis, respectively. Enrichment analyses were performed using Cytoscape ClueGO and CluePedia apps.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Out of 20 endometrial samples, 2 were dated to the early receptive phase, 13 to the receptive phase and 5 to the late receptive phase. Comparison of the transcriptomics data from all 20 samples provided 909 DEGs (p&lt;0.05; nonsignificant after adjusted p value) in the adenomyosis group but only 4 enriched pathways (Bonferroni p value &lt; 0.05). The analysis of 13 samples only dated to the receptive phase provided suggestive 382 DEGs (p&lt;0.05; nonsignificant after adjusted p value) in the adenomyosis group, leading to 33 enriched pathways (Bonferroni p value &lt; 0.05). These included pathways were already associated with endometrial biology, such as \u201cExpression of interferon (IFN)-induced genes\u201d and \u201cResponse to IFN-alpha\u201d. Data integration revealed pathways indicating a unique effect of adenomyosis on endometrial molecular organization (e.g., \u201cExpression of IFN-induced genes\u201d) and its interference with endometrial receptivity establishment (e.g., \u201cExtracellular matrix organization\u201d and \u201cTumour necrosis factor production\u201d).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Accurate endometrial dating and RNA-seq analysis resulted in the identification of altered response to IFN signalling as the most promising candidate of impaired uterine receptivity in adenomyosis.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12958-021-00871-5","type":"journal-article","created":{"date-parts":[[2022,1,3]],"date-time":"2022-01-03T01:02:41Z","timestamp":1641171761000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Transcriptomics of receptive endometrium in women with sonographic features of adenomyosis"],"prefix":"10.1186","volume":"20","author":[{"given":"Erika","family":"Pra\u0161nikar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanja","family":"Kunej","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mario","family":"Gorenjak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Uro\u0161","family":"Poto\u010dnik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Borut","family":"Kova\u010di\u010d","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3543-5920","authenticated-orcid":false,"given":"Jure","family":"Knez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,1,3]]},"reference":[{"key":"871_CR1","doi-asserted-by":"publisher","unstructured":"Andres MP, Borrelli GM, Ribeiro J, Baracat EC, Abr\u00e3o MS, Kho RM. 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