Transcriptomic Changes During the Pre-Receptive to Receptive Transition in Human Endometrium Detected by RNA-Seq

Hu, Shuanggang; Yao, Guangxin; Wang, Yang; Xu, Haijing; Ji, Xiaowei; He, Yang; Zhu, Qinling; Chen, Zi‐Jiang; Sun, Yun

doi:10.1210/jc.2014-2155

Cited by 106 publications

(77 citation statements)

References 40 publications

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“…In order to overcome these limitations, we directly analysed lists of differentially expressed genes from nine published studies involving a total of 164 endometrial biopsy samples from healthy women. Using a method that has been specifically designed for comparison of gene lists and identification of commonly overlapping genes in various studies, including recently published transcriptome studies in different ethnic groups 30 , 37 , 38 , we hope to provide an up-to-date meta-signature of endometrial receptivity biomarkers. Nevertheless, we have to bear in mind that with our approach, analysing the significantly differentially expressed gene lists, we could have missed the potential biomarker genes that were below statistical significance in individual studies but could become relevant in a meta-analysis.…”

Section: Discussionmentioning

confidence: 99%

Meta-signature of human endometrial receptivity: a meta-analysis and validation study of transcriptomic biomarkers

Altmäe

Koel

Võsa

et al. 2017

Sci Rep

199

180

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Previous transcriptome studies of the human endometrium have revealed hundreds of simultaneously up- and down-regulated genes that are involved in endometrial receptivity. However, the overlap between the studies is relatively small, and we are still searching for potential diagnostic biomarkers. Here we perform a meta-analysis of endometrial-receptivity associated genes on 164 endometrial samples (76 from ‘pre-receptive’ and 88 from mid-secretory, ‘receptive’ phase endometria) using a robust rank aggregation (RRA) method, followed by enrichment analysis, and regulatory microRNA prediction. We identify a meta-signature of endometrial receptivity involving 57 mRNA genes as putative receptivity markers, where 39 of these we confirm experimentally using RNA-sequencing method in two separate datasets. The meta-signature genes highlight the importance of immune responses, the complement cascade pathway and the involvement of exosomes in mid-secretory endometrial functions. Bioinformatic prediction identifies 348 microRNAs that could regulate 30 endometrial-receptivity associated genes, and we confirm experimentally the decreased expression of 19 microRNAs with 11 corresponding up-regulated meta-signature genes in our validation experiments. The 57 identified meta-signature genes and involved pathways, together with their regulatory microRNAs could serve as promising and sought-after biomarkers of endometrial receptivity, fertility and infertility.

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Section: Discussionmentioning

confidence: 99%

Meta-signature of human endometrial receptivity: a meta-analysis and validation study of transcriptomic biomarkers

Altmäe

Koel

Võsa

et al. 2017

Sci Rep

199

180

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“…Transcriptome studies have demonstrated a myriad of changes in endometrial gene expression during the transition from pre-receptive to receptive phase 2, 3 , and a specific transcriptome signature has been detected that is now used to determine the individual WOI and aid in selecting the best day for embryo transfer in women undergoing in vitro fertilization 4 . Although the endometrial function is believed to be under epigenetic control 5 , less is known about how endometrial DNA methylation pattern changes throughout the menstrual cycle, what impact it has on gene expression, and whether aberrations in methylation pattern could lead to altered endometrial function.…”

Section: Introductionmentioning

confidence: 99%

DNA methylation changes in endometrium and correlation with gene expression during the transition from pre-receptive to receptive phase

Kukushkina

Modhukur

Suhorutšenko

et al. 2017

Sci Rep

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The inner uterine lining (endometrium) is a unique tissue going through remarkable changes each menstrual cycle. Endometrium has its characteristic DNA methylation profile, although not much is known about the endometrial methylome changes throughout the menstrual cycle. The impact of methylome changes on gene expression and thereby on the function of the tissue, including establishing receptivity to implanting embryo, is also unclear. Therefore, this study used genome-wide technologies to characterize the methylome and the correlation between DNA methylation and gene expression in endometrial biopsies collected from 17 healthy fertile-aged women from pre-receptive and receptive phase within one menstrual cycle. Our study showed that the overall methylome remains relatively stable during this stage of the menstrual cycle, with small-scale changes affecting 5% of the studied CpG sites (22,272 out of studied 437,022 CpGs, FDR < 0.05). Of differentially methylated CpG sites with the largest absolute changes in methylation level, approximately 30% correlated with gene expression measured by RNA sequencing, with negative correlations being more common in 5′ UTR and positive correlations in the gene ‘Body’ region. According to our results, extracellular matrix organization and immune response are the pathways most affected by methylation changes during the transition from pre-receptive to receptive phase.

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“…Some studies have reported modifications in gene expression profiles associated with transition of the human endometrium from a pre‐receptive to a receptive stage (Cuevas et al, ; Díaz‐Gimeno et al, ; Hu et al, ; Sigurgeirsson et al, ). However, only two genes were common to six of the seven largest studies, secreted phosphoprotein 1 (SPP1; previously known as osteopontin) (Wang & Yu, ).…”

Section: Discussionmentioning

confidence: 99%

“…Transcriptome analyses of distinct physiological stages were crucial for understanding the gene regulatory network, including the endometrium development in mammals (Wang et al, ; Zhang et al, , ). Moreover, studies on the endometrial transcriptomics have been reported using RNA‐Seq in humans (Hu et al, ), pigs (Lin et al, ; Samborski, Graf, Krebs, Kessler, & Bauersachs, ; Samborski, Graf, Krebs, Kessler, Reichenbach, et al, ; Wang et al, ), cattles (Mamo, Mehta, Forde, Mcgettigan, & Lonergan, ; Palma‐Vera, Sharbati, & Einspanier, ), and goats (Zhang et al, , ).…”

Section: Introductionmentioning

confidence: 99%

A comparative analysis of gene expression induced by the embryo in the caprine endometrium

Liu

Zhang

Han

et al. 2019

Veterinary Medicine & Sci

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Transcriptomics is an established powerful tool to identify potential mRNAs and ncRNAs (non‐coding RNAs) for endometrial receptivity. In this study, the goat endometrium at estrus day 5 (ED5) and estrus day 15 (ED15) were selected to systematically analyse the differential expressed genes (DEGs) what were induced by the embryo. There were 1,847 genes which were significantly differential expressed in endometrium induced by the embryo at ED5, and 1,346 at ED15 (p‐value < .05). Secreted phosphoprotein 1 (SPP) was the responsive genes for embryo in the goat endometrium during estrus cycle, neurotensis (NTS) and pleiotrophin (PTN) were the responsive genes for embryo in the goat endometrium at ED5, Testin (TES) and Phosphate and Tension Homology Deleted on Chromsome ten (PTEN) at ED15. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes (KEGG) analysis revealed cytoplasm and Endocytosis were indispensable for the endometrium development in dairy goat. In a word, this resulting view of the transcriptome greatly uncovered the global trends in mRNAs expression induced by the embryo in the endometrium of dairy goats.

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Transcriptomic Changes During the Pre-Receptive to Receptive Transition in Human Endometrium Detected by RNA-Seq

Cited by 106 publications

References 40 publications

Meta-signature of human endometrial receptivity: a meta-analysis and validation study of transcriptomic biomarkers

Meta-signature of human endometrial receptivity: a meta-analysis and validation study of transcriptomic biomarkers

DNA methylation changes in endometrium and correlation with gene expression during the transition from pre-receptive to receptive phase

A comparative analysis of gene expression induced by the embryo in the caprine endometrium

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