Gene expression profile of endometrium in receptive state in women with adenomyosis

Nižja stopnja zanositve pri ženskah z adenomiozo maternice se povezuje z ovirano endometrijsko receptivnostjo za vgnezdenje zarodka. Pripadajoči molekularni vzroki so slabo raziskani zaradi preteklih tehnoloških omejitev neinvazivnih diagnostičnih metod za odkrivanje adenomioze. S pristopi sistemske biologije smo zato identificirali kandidatne biološke poti/gene spremenjene endometrijske receptivnosti pri adenomiozi. Izvedli smo analizo RNA sekvenciranja (RNA-seq) endometrija v pričakovanem stanju receptivnosti ženskam z (n = 10) in brez (n = 10) ultrazvočnih znakov adenomioze. Identificirane spremenjeno izražene gene smo dalje integrirali s podatki iz pregleda literature, da bi razumeli njihov pomen v povezavi z molekularno biologijo endometrija. Zbrali smo poročane transkripte in proteine, povezane z endometrijsko receptivnostjo pri adenomiozi, pri sorodni, a bolje raziskani endometriozi in pri zdravi maternici, ter poenotili njihovo poimenovanje po genski nomeklaturi zbirke HGNC. S primerjavo podatkov RNA-seq samo potrjeno receptivnih vzorcev (8 adenomioznih in 5 kontrolnih) smo zaznali 382 spremenjeno izraženih genov (p 0,05), kar bi lahko bila posledica nizkega števila uporabljenih vzorcev. Na podlagi analize podatkov iz dosedanje literature in lastnih rezultatov RNA-seq sklepamo, da je endometrijska receptivnost pri ženskah z adenomiozo spremenjena na ravni signalizacije s citokini imunskega sistema.Lower pregnancy rate in women with uterine adenomyosis is associated with impaired endometrial receptivity for embryo implantation. The underlying molecular causes are poorly understood due to past technological limitations of non-invasive methods to diagnose adenomyosis. We therefore applied systems biology approaches to identify candidate biological pathways/genes of altered endometrial receptivity in adenomyosis. We performed RNA sequencing (RNA-seq) analysis of the endometrium in the expected receptive state in women with (n = 10) and without (n = 10) ultrasound signs of adenomyosis. The identified differentially expressed genes were further integrated with data from the literature mining to understand their relevance in the context of endometrial molecular biology. We gathered reported transcripts and proteins associated with endometrial receptivity in adenomyosis, in related but better-studied endometriosis and in healthy uterus, and adopted their gene nomenclature according to the HGNC database. The comparison of RNA-seq data of only confirmed receptive samples (8 adenomyosis and 5 controls) identified 382 differentially expressed genes (p 0.05), which may be due to the small sample size. Based on the analysis of existing literature and own RNA-seq results, we conclude that endometrial receptivity in adenomyosis is altered at the level of immune cytokine signalling

Determining the molecular background of endometrial receptivity in adenomyosis

Background: Adenomyosis is a gynaecological condition with limited evidence of negative impact to endometrial receptivity. It is commonly associated with endometriosis, which has been shown to alter endometrial expression patterns. Therefore, the candidate genes identified in endometriosis could serve as a source to study endometrial function in adenomyosis. Methods: Transcripts/proteins associated with endometrial receptivity in women with adenomyosis or endometriosis and healthy women were obtained from publications and their nomenclature was adopted according to the HUGO Gene Nomenclature Committee (HGNC). Retrieved genes were analysed for enriched pathways using Cytoscape/Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Reactome tools to prioritise candidates for endometrial receptivity. These were used for validation on women with (n = 9) and without (n = 13) adenomyosis. Results: Functional enrichment analysis of 173, 42 and 151 genes associated with endometriosis, adenomyosis and healthy women, respectively, revealed signalling by interleukins and interleukin-4 and interleukin-13 signalling pathways, from which annotated LIF, JUNB, IL6, FOS, IL10 and SOCS3 were prioritised. Selected genes showed downregulated expression levels in adenomyosis compared to the control group, but without statistical significance. Conclusion: This is the first integrative study providing putative candidate genes and pathways characterising endometrial receptivity in women with adenomyosis in comparison to healthy women and women with endometriosis

Determining the Molecular Background of Endometrial Receptivity in Adenomyosis

Background: Adenomyosis is a gynaecological condition with limited evidence of negative impact to endometrial receptivity. It is commonly associated with endometriosis, which has been shown to alter endometrial expression patterns. Therefore, the candidate genes identified in endometriosis could serve as a source to study endometrial function in adenomyosis. Methods: Transcripts/proteins associated with endometrial receptivity in women with adenomyosis or endometriosis and healthy women were obtained from publications and their nomenclature was adopted according to the HUGO Gene Nomenclature Committee (HGNC). Retrieved genes were analysed for enriched pathways using Cytoscape/Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Reactome tools to prioritise candidates for endometrial receptivity. These were used for validation on women with (n = 9) and without (n = 13) adenomyosis. Results: Functional enrichment analysis of 173, 42 and 151 genes associated with endometriosis, adenomyosis and healthy women, respectively, revealed signalling by interleukins and interleukin-4 and interleukin-13 signalling pathways, from which annotated LIF, JUNB, IL6, FOS, IL10 and SOCS3 were prioritised. Selected genes showed downregulated expression levels in adenomyosis compared to the control group, but without statistical significance. Conclusion: This is the first integrative study providing putative candidate genes and pathways characterising endometrial receptivity in women with adenomyosis in comparison to healthy women and women with endometriosis

Transcriptomics of receptive endometrium in women with sonographic features of adenomyosis

Background: Women with uterine adenomyosis seeking assisted reproduction have been associated with compromised endometrial receptivity to embryo implantation. To understand the mechanisms involved in this process, we aimed to compare endometrial transcriptome profles during the window of implantation (WOI) between women with and without adenomyosis. Methods: 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 classifcation with a molecular tool for menstrual cycle phase dating (beREADY®, 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 identifed diferentially 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. Results: 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<0.05nonsignifcant after adjusted p value) in the adenomyosis group but only 4 enriched pathways (Bonferroni p value < 0.05). The analysis of 13 samples only dated to the receptive phase provided suggestive 382 DEGs (p<0.05nonsignifcant after adjusted p value) in the adenomyosis group, leading to 33 enriched pathways (Bonferroni p value <0.05). These included pathways were already associated with endometrial biology, such as “Expression of interferon (IFN)-induced genes” and “Response to IFN-alpha”. Data integration revealed pathways indicating a unique efect of adenomyosis on endometrial molecular organization (e.g., “Expression of IFN-induced genes”) and its interference with endometrial receptivity establishment (e.g., “Extracellular matrix organization” and “Tumour necrosis factor production”). Conclusions: Accurate endometrial dating and RNA-seq analysis resulted in the identifcation of altered response to IFN signalling as the most promising candidate of impaired uterine receptivity in adenomyosis