Abstract
Eutopic endometrium appears to be crucial for endometriosis development. Despite of the evident importance, data regarding the cellular microenvironment remain unclear. Our objective was to explore the tissue microenvironment heterogeneity, transcripts, and pathways that are enriched in all phases of the menstrual cycle by analysing publicly deposited data derived from whole transcriptome microarrays of eutopic endometria of women with and without endometriosis. A meta-analysis of the transcriptome microarrays was performed using raw data available from a public database. Eligibility criteria included eutopic endometrium samples from women with endometriosis and healthy controls without any pathological condition reported the presence of an adequately reported normal menstrual phase, and samples containing both glandular and stromal components. Raw data were processed using a robust multiarray average method to provide background correction, normalisation, and summarisation. The batch effect was estimated by principal variant component analysis and removed using an empirical Bayes method. Cellular tissue heterogeneity was inferred using the xCell package. Differentially expressed genes were identified based on a 5% adjusted p value and a 2.0-fold change. Pathways were identified by functional enrichment based on the Molecular Signatures Database, a p value of < 5%, and an FDR q value of ≤ 25%. Genes that were more frequently found in pathways were identified using leading edge analysis. In a manner independent of cycle phase, the subpopulations of activated dendritic cells, CD4 T effector memory phenotype cells, eosinophils, macrophages M1, and natural killer T cells (NKT) were all higher in stage I-II endometriosis compared to those in healthy controls. The subpopulations of M2 macrophages and natural killer T cells were elevated in eutopic endometriums from women with stage III-IV endometriosis, and smooth muscle cells were always more prevalent in healthy eutopic endometriums. Among the differently expressed genes, FOS, FOSB, JUNB, and EGR1 were the most frequently mapped within the interaction networks, and this was independent of stage and cycle phase. The enriched pathways were directly related to immune surveillance, stem cell self-renewal, and epithelial mesenchymal transition. PI3K AKT mTOR, TGF signalling, and interferon alpha/gamma responses were enriched exclusively in stage III-IV endometriosis. The cellular microenvironments and immune cell profiles were different between eutopic endometriums from women with stage I-II and stage III-IV endometriosis, and these differences were independent of the hormonal milieu. Specifically, a pro-inflammatory profile was predominant in stage I-II endometriosis, and M1-M2 polarization into eutopic endometrium may be crucial for the progression of the disease. The higher prevalence of NKT cells in eutopic endometriums from women with endometriosis that was independent of cycle phase or staging suggested a sustained stress and/or damage to these eutopic endometriums. Based on this, the results of this meta-analysis are important for identifying challenges and opportunities for future research.
Highlights
Www.nature.com/scientificreports was independent of cycle phase or staging suggested a sustained stress and/or damage to these eutopic endometriums
Throughout each cycle phase, subpopulations of activated dendritic cells, CD4 T effector memory phenotype cells (CD4 TEM), eosinophils, macrophages M1, natural killer T cells (NKT), and myocites were predominant in stage I-II endometriosis compared to levels observed in healthy controls, while common lymphoid progenitors (CLP) were predominant in these lasts
Within the eutopic endometria obtained from women with stage I-II endometriosis there was a predominance of several cell subtypes; this difference was less significant in the endometria obtained from women with stage III-IV endometriosis, which predominantly contained only M2 macrophages and NKT
Summary
Www.nature.com/scientificreports was independent of cycle phase or staging suggested a sustained stress and/or damage to these eutopic endometriums. At least two additional pivotal mechanisms appear to be fundamental for disease development, and these include immune system dysfunction and genetic susceptibility[11] Despite these uncertainties, a reasonable amount of information available within the literature indicates that the eutopic endometrium in women with endometriosis is different from that of healthy women. Microarray analysis quantifies the expression of a preselected number of probes/genes determined by certain platforms, while RNA sequencing incorporates high-throughput sequencing to identify all expressed sequences[14] Despite their strengths and limitations, both methods are reproducible[15], and because of this, microarray techniques provide researchers with fast, cheap and reproducible results when studying known genes. Exploring transcriptome data using a meta-analytical approach can provide the scientific community with substantial, integrated, and confirmatory information regarding the tissue microenvironment and the genes and pathways underlying endometriosis The results of these studies will aid researchers in the design of future studies. The rigorous selection of healthy controls and the use of menstrual phase identification enabled us to identify the most important cell types, transcripts, and pathways that are enriched in eutopic endometria from women with and without endometriosis
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