Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium

Enrichment of cell cycle pathways in progesterone-treated endometrial organoids of infertile women compared to fertile women

PURPOSE

To investigate whether the transcriptome profile differs between progesterone-treated infertile and fertile endometrial organoids.

METHODS

Endometrial biopsies were obtained from 14 infertile and seven fertile women, after which organoids were generated from isolated epithelial cells. To mimic the secretory phase, organoids were sequentially treated with 17β-estradiol (E2) and progesterone (P4) and subjected to RNA sequencing. Differentially expressed genes (DEGs) were identified using DESeq2 (lfcThreshold = 0, log2 Fold Change ≥ 1.0 or ≤ -1.0), and a principal component analysis (PCA) plot was generated. Functional enrichment analysis was performed by overrepresentation analysis and Gene Set Enrichment Analysis (GSEA). To functionally assess proliferation, OrganoSeg surface measurements were performed before (T0) and after (T1) differentiation of organoids, and T1/T0 ratios were calculated to determine the proliferation rate.

RESULTS

Although the PCA plot did not show clear clustering of the fertile and infertile samples, 363 significant DEGs (129 upregulated and 234 downregulated) were detected in infertile compared to fertile organoids. Mainly cell cycle processes were highly enriched in infertile organoids. Thus, we hypothesised that proliferative activity during differentiation may be higher in infertile organoids compared to fertile organoids. However, this could not be validated by cell surface measurements.

CONCLUSIONS

This study revealed that cell cycle processes were enriched in E2/P4-treated infertile endometrial organoids as compared to fertile organoids. This could reflect persistently higher proliferative activity of the endometrial epithelial cells in differentiated infertile organoids compared to fertile organoids. To confirm this hypothesis, further studies are warranted.

The endometrial transcriptome of infertile women with and without implantation failure

INTRODUCTION

Implantation failure after transferring morphologically "good-quality" embryos in in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) may be explained by impaired endometrial receptivity. Analyzing the endometrial transcriptome analysis may reveal the underlying processes and could help in guiding prognosis and using targeted interventions for infertility. This exploratory study investigated whether the endometrial transcriptome profile was associated with short-term or long-term implantation outcomes (ie success or failure).

MATERIAL AND METHODS

Mid-luteal phase endometrial biopsies of 107 infertile women with one full failed IVF/ICSI cycle, obtained within an endometrial scratching trial, were subjected to RNA-sequencing and differentially expressed genes analysis with covariate adjustment (age, body mass index, luteinizing hormone [LH]-day). Endometrial transcriptomes were compared between implantation failure and success groups in the short term (after the second fresh IVF/ICSI cycle) and long term (including all fresh and frozen cycles within 12 months). The short-term analysis included 85/107 women (33 ongoing pregnancy vs 52 no pregnancy), excluding 22/107 women. The long-term analysis included 46/107 women (23 'fertile' group, ie infertile women with a live birth after ≤3 embryos transferred vs 23 recurrent implantation failure group, ie no live birth after ≥3 good quality embryos transferred), excluding 61/107 women not fitting these categories. As both analyses drew from the same pool of 107 samples, there was some sample overlap. Additionally, cell type enrichment scores and endometrial receptivity were analyzed, and an endometrial development pseudo-timeline was constructed to estimate transcriptomic deviations from the optimum receptivity day (LH + 7), denoted as ΔWOI (window of implantation).

RESULTS

There were no significantly differentially expressed genes between implantation failure and success groups in either the short-term or long-term analyses. Principal component analysis initially showed two clusters in the long-term analysis, unrelated to clinical phenotype and no longer distinct following covariate adjustment. Cell type enrichment scores did not differ significantly between groups in both analyses. However, endometrial receptivity analysis demonstrated a potentially significant displacement of the WOI in the non-pregnant group compared with the ongoing pregnant group in the short-term analysis.

CONCLUSIONS

No distinct endometrial transcriptome profile was associated with either implantation failure or success in infertile women. However, there may be differences in the extent to which the WOI is displaced.

The Known, the Unknown and the Future of the Pathophysiology of Endometriosis

Endometriosis is one of the most common causes of chronic pelvic pain and infertility, affecting 10% of women of reproductive age. A delay of up to 9 years is estimated between the onset of symptoms and the diagnosis of endometriosis. Endometriosis is currently defined as the presence of endometrial epithelial and stromal cells at ectopic sites; however, advances in research on endometriosis have some authors believing that endometriosis should be re-defined as "a fibrotic condition in which endometrial stroma and epithelium can be identified". There are several theories on the etiology of the disease, but the origin of endometriosis remains unclear. This review addresses the role of microRNAs (miRNAs), which are naturally occurring post-transcriptional regulatory molecules, in endometriotic lesion development, the inflammatory environment within the peritoneal cavity, including the role that cytokines play during the development of the disease, and how animal models have helped in our understanding of the pathology of this enigmatic disease.

Meta-analysis of endometrial transcriptome data reveals novel molecular targets for recurrent implantation failure

PURPOSE

Gene expression analysis of the endometrium has been shown to be a useful approach for identifying the molecular signatures and pathways involved in recurrent implantation failure (RIF). Nevertheless, individual studies have limitations in terms of study design, methodology and analysis to detect minor changes in expression levels or identify novel gene signatures associated with RIF.

METHOD

To overcome this, we conducted an in silico meta-analysis of nine studies, the systematic collection and integration of gene expression data, utilizing rigorous selection criteria and statistical techniques to ensure the robustness of our findings.

RESULTS

Our meta-analysis successfully unveiled a meta-signature of 49 genes closely associated with RIF. Of these genes, 38 were upregulated and 11 downregulated in RIF patients' endometrium and believed to participate in key processes like cell differentiation, communication, and adhesion. GADD45A, IGF2, and LIF, known for their roles in implantation, were identified, along with lesser-studied genes like OPRK1, PSIP1, SMCHD1, and SOD2 related to female infertility. Many of these genes are involved in MAPK and PI3K-Akt pathways, indicating their role in inflammation. We also investigated to look for key miRNAs regulating these 49 dysregulated mRNAs as potential diagnostic biomarkers. Along with this, we went to associate protein-protein interactions of 49 genes, and we could recognize one cluster consisting of 11 genes (consisted of 22 nodes and 11 edges) with the highest score (p = 0.001). Finally, we validated some of the genes by qRT-PCR in our samples.

CONCLUSION

In summary, the meta-signature genes hold promise for improving RIF patient identification and facilitating the development of personalized treatment strategies, illuminating the multifaceted nature of this complex condition.

The Contribution of Proteomics in Understanding Endometrial Protein Expression in Women with Recurrent Implantation Failure

Recurrent implantation failure (RIF) poses a significant challenge in assisted reproductive technology (ART) outcomes. The endometrium plays a crucial role in embryo implantation, and its protein expression profile is integral in determining receptivity. Proteomics has emerged as a valuable tool in unraveling the molecular intricacies underlying endometrial receptivity and RIF. The aim of the present review is to analyze the contribution of proteomics to the understanding of endometrial protein expression in women with RIF, based on the results of significant proteomic studies. Medline/Pubmed databases were searched using keywords pertaining to proteomics combined with terms related to RIF. 15 studies were included in the present review. Several proteins have been found to exbibit differential expression in endometrial biopsies and fluid samples between fertile women and women with RIF during the receptive endometrial phase. The profile of endometrial proteins varied significantly among the studies. Nevertheless, similar changes in the expression levels of annexin-6, progesterone receptor, MMP-2, and MMP-9 in the endometrium of women with RIF, were found in more than one study indicating that certain proteins could potentially be effective biomarkers of endometrial receptivity. Proteomics contributes significantly to the understanding of protein expression in the endometrium of women with RIF and the analysis of proteins in endometrial fluid are promising for improving the clinical management of RIF.

Identification of a rare copy number polymorphic gain at 3q12.2 with candidate genes for familial endometriosis

Endometriosis is a complex disease that affects 10-15% of women of reproductive age. Familial studies show that relatives of affected patients have a higher risk of developing the disease, implicating a genetic role for this disorder. Little is known about the impact of germline genomic copy number variant (CNV) polymorphisms on the heredity of the disease. In this study, we describe a rare CNV identified in two sisters with familial endometriosis, which contain genes that may increase the susceptibility and progression of this disease. We investigated the presence of CNVs from the endometrium and blood of the sisters with endometriosis and normal endometrium of five women as controls without the disease using array-CGH through the Agilent 2x400K platform. We excluded common CNVs that were present in the database of genomic variation. We identified, in both sisters, a rare CNV gain affecting 113kb at band 3q12.2 involving two candidate genes: ADGRG7 and TFG. The CNV gain was validated by qPCR. ADGRG7 is located at 3q12.2 and encodes a G protein-coupled receptor influencing the NF-kappaβ pathway. TFG participates in chromosomal translocations associated with hematologic tumor and soft tissue sarcomas, and is also involved in the NF-kappa B pathway. The CNV gain in this family provides a new candidate genetic marker for future familial endometriosis studies. Additional longitudinal studies of affected families must confirm any associations between this rare CNV gain and genes involved in the NF-kappaβ pathway in predisposition to endometriosis.

An ultrasound-based deep learning radiomic model combined with clinical data to predict clinical pregnancy after frozen embryo transfer: a pilot cohort study

RESEARCH QUESTION

Can a multi-modal fusion model based on ultrasound-based deep learning radiomics combined with clinical parameters provide personalized evaluation of endometrial receptivity and predict the occurrence of clinical pregnancy after frozen embryo transfer (FET)?

DESIGN

Prospective cohort study of women (n = 326) who underwent FET between August 2019 and December 2021. Input quantitative variables and input image data for radiomic feature extraction were collected to establish a multi-modal fusion prediction model. An additional independent dataset of 453 ultrasound endometrial images was used to establish the segmentation model to determine the endometrial region on ultrasound images for analysis. The performance of different algorithms and different input data for prediction of FET outcome were compared.

RESULTS

A total of 240 patients with complete data were included in the final cohort. The proposed multi-modal fusion model performed significantly better than the use of either image or quantitative variables alone to predict the occurrence of clinical pregnancy after FET (P ≤ 0.034). Its area under the curve, accuracy, sensitivity, specificity, positive predictive value and negative predictive value of the proposed model were 0.825, 72.5%, 96.2%, 58.3%, 72.3% and 89.5%, respectively. The Dice coefficient of the multi-task endometrial ultrasound segmentation model was 0.89. Use of endometrial segmentation features significantly improved the prediction performance of the model (P = 0.041).

CONCLUSIONS

The multi-modal fusion model based on ultrasound-based deep learning radiomics combined with clinical quantitative variables offers a favourable and rapid non-invasive approach for personalized prediction of FET outcome.

Review of Endometrial Receptivity Array: A Personalized Approach to Embryo Transfer and Its Clinical Applications

Successful outcomes of in vitro fertilization (IVF) rely on both the formation of a chromosomally normal embryo and its implantation in a receptive endometrium. Pre-implantation genetic testing for aneuploidy (PGT-A) has been widely accepted as a tool to assess the viability of an embryo. In 2011, the endometrial receptivity array (ERA) was first published as a tool to determine when the endometrium is most receptive to an embryo, commonly referred to as the "window of implantation" (WOI). The ERA uses molecular arrays to assess proliferation and differentiation in the endometrium and screens for inflammatory markers. Unlike PGT-A, there has been dissent within the field concerning the efficacy of the ERA. Many studies that contest the success of the ERA found that it did not improve pregnancy outcomes in patients with an already-good prognosis. Alternatively, studies that utilized the ERA in patients with repeated implantation failure (RIF) and transfer of known euploid embryos demonstrated improved outcomes. This review aims to describe the ERA as a novel technique, review the various settings that the ERA may be used in, such as natural frozen embryo transfer (nFET) and hormone replacement therapy frozen embryo transfer (HRT-FET), and provide a summary of the recent clinical data for embryo transfers in patients with RIF utilizing the ERA.

Uterine Transcriptome: Understanding Physiology and Disease Processes

In recent years, transcriptomics has enabled us to gain a deeper understanding of fundamental reproductive physiology, including the menstrual cycle, through a more precise molecular analysis. The endometrial mRNA transcript levels fluctuate during the normal menstrual cycle, indicating changes in the relative recruitment and abundance of inflammatory cells, as well as changes in the receptivity and remodeling of the endometrium. In addition to providing a more comprehensive understanding of the molecular underpinnings of pathological gynecological conditions such as endometriosis, leiomyomas, and adenomyosis through RNA sequencing, this has allowed researchers to create transcriptome profiles during both normal menstrual cycles and pathological gynecological conditions. Such insights could potentially lead to more targeted and personalized therapies for benign gynecological conditions. Here, we provide an overview of recent advances in transcriptome analysis of normal and pathological endometrium.

MicroRNAs, small regulatory elements with significant effects on human implantation: a review

Embryo implantation is a critical process for achieving a successful pregnancy and live birth. The proper implantation must have a synchronized interaction between blastocyst and a receptive endometrium. Many genes are involved in the modulation of precise molecular events during implantation. MicroRNAs (miRNAs) have been extensively reported as gene regulatory molecules on post-transcriptional levels involved in various biological processes such as gametogenesis, embryogenesis, and the quality of sperm, oocyte, and embryos. A plethora of evidence has demonstrated critical roles for miRNAs in regulating genes involved in the implantation process; hence, dysregulation of miRNAs could be associated with significant impairments in implantation, such as recurrent implantation failure. In addition to the indispensable role of miRNAs in the intracellular control of gene expression, they can also be secreted into extracellular fluid and circulation. Therefore, miRNAs in body fluids and blood may be exploited as non-invasive diagnostic biomarkers for different pathological and physiological conditions. Recently, several studies have focused on the discovery of miRNAs function in the implantation process by appraising miRNAs and their target genes in human embryos, endometrial tissue, and cell culture models. Moreover, it was revealed that there could be a significant association between endometrial receptivity or implantation status and the expression of miRNAs in human body fluids, reinforcing their role as non-invasive biomarkers. In the current work, we reviewed the studies concerning the role of intracellular and extracellular miRNAs in human implantation and the influence of their dysregulation on implantation disorders.

Can biomarkers identified from the uterine fluid transcriptome be used to establish a noninvasive endometrial receptivity prediction tool? A proof-of-concept study

BACKGROUND

Embryo implantation in a receptive endometrium is crucial for successful pregnancy. Endometrial receptivity (ER) prediction tools based on endometrial transcriptome biomarkers by endometrial biopsy have been used to guide successful embryo implantation in in vitro fertilization (IVF) patients. However, no reliable noninvasive ER prediction method has been established, and one is greatly needed. We aimed to identify biomarkers from uterine fluid transcriptomic sequencing data for establishing noninvasive ER prediction tool and to evaluate its clinical application potential in patients undergoing IVF.

METHODS

The non-invasive RNA-seq based endometrial receptivity test (nirsERT) was established by analyzing transcriptomic profile of 144 uterine fluid specimens (LH + 5, LH + 7, and LH + 9) at three different receptive status from 48 IVF patients with normal ER in combination with random forest algorithm. Subsequently, 22 IVF patients who underwent frozen-thaw blastocyst transfer were recruited and analyzed the correlation between the predicted results of nirsERT and pregnancy outcomes.

RESULTS

A total of 864 ER-associated differentially expressed genes (DEGs) involved in biological processes associated with endometrium-embryo crosstalk, including protein binding, signal reception and transduction, biomacromolecule transport and cell-cell adherens junctions, were selected. Subsequently, a nirsERT model consisting of 87 markers and 3 hub genes was established using a random forest algorithm. 10-fold cross-validation resulted in a mean accuracy of 93.0%. A small cohort (n = 22) retrospective observation shows that 77.8% (14/18) of IVF patients predicted with a normal WOI had successful intrauterine pregnancies, while none of the 3 patients with a displaced WOI had successful pregnancies. One patient failed due to poor sequencing data quality.

CONCLUSIONS

NirsERT based on uterine fluid transcriptome biomarkers can predict the WOI period relatively accurately and may serve as a noninvasive, reliable and same cycle test for ER in reproductive clinics.

TRIAL REGISTRATION

Chinese Clinical Trial Registry: ChiCTR-DDD-17013375. Registered 14 November 2017, http://www.chictr.org.cn/index.aspx .

iTRAQ-based Proteomic Analysis Unveils ACSL4 as a Novel Potential Regulator of Human Endometrial Receptivity

Competent endometrial receptivity is a prerequisite for successful embryo implantation. Identification of novel key molecules involved in endometrial receptivity is essential to better interpret human implantation and improve pregnancy rates in assisted reproduction treatment. Isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics was performed to profile the proteomes of the prereceptive (luteinizing hormone [LH] + 2, n = 4) and receptive (LH + 7, n = 4) endometrial tissues. A total of 173 differentially expressed proteins (DEPs) between LH + 2 and LH + 7 endometrial samples were identified. Integrated analysis of the proteomic data and published transcriptomic data was performed to identify the concordant DEPs with differential expression at both the messenger RNA and protein levels. Protein-protein interaction (PPI) network analysis was performed on concordant DEPs. We first identified 63 novel concordant DEPs and 5 hub proteins (ACSL4, ACSL5, COL1A1, PTGS1, and PLA2G4F) between LH + 2 and LH + 7 endometrial samples. ACSL4 was predominantly expressed in endometrial epithelial cells and its expression was significantly upregulated by progesterone in the LH + 7 endometrium and significantly downregulated in repeated implantation failure patients. Knockdown of ACSL4 in endometrial epithelial cells induced the downregulation of endometrial receptivity markers (HOXA10, COX2, and LIF) and the significant decrease of implantation rate during in vitro implantation analysis. This study provides the first gel-independent quantitative proteomes of the LH + 2 and LH + 7 human endometrium using iTRAQ technology. The identified concordant DEPs and hub proteins open a new avenue for future studies aimed at elucidating the underlying mechanisms governing endometrial receptivity. ACSL4 was identified as a novel regulatory molecule in the establishment of endometrial receptivity and might play important roles during implantation.

Endometrial whole metabolome profile at the receptive phase: influence of Mediterranean Diet and infertility

Introduction

Several metabolite classes have been identified in human endometrium, including lipids, nucleotides, amino acids, organic acids, and sugars. The first studies suggest the importance of metabolites in endometrial functions, as imbalance in uterine metabolites has been associated with low implantation rate and endometriosis. Nevertheless, most of studies have put emphasis on specific metabolite classes, and we lack the knowledge of the whole metabolome composition in human uterus. Further, a healthy dietary pattern has been shown to potentially protect against different endometrial dysfunctions and is a potential modulator of metabolomic composition and, consequently, the intrauterine microenvironment. The Mediterranean Diet (MD), characterized by a high intake of fruits, vegetables, cereals, nuts, legumes, fish, and olive oil, and a low consumption of meat, dairy products, and processed foods, has been associated with a wide range of benefits for health. Indeed, the MD pattern has displayed a beneficial role in endometriosis management and fertility; however, the relationship between the MD and the endometrial metabolome is still unknown. In our study, we set out to analyze receptive-phase endometrial metabolome profiles among women with infertility and their associations with MD.

Methods

The study included women with male factor infertility (n=8), unexplained infertility (n=10), recurrent implantation failure (n=14), and endometriosis (n=13). The endometrial metabolome was analyzed with ultrahigh-performance liquid chromatography-tandem mass spectroscopy (UPLC-MS/MS). The MD adherence of the participants was assessed using the 14-point MEDAS questionnaire of adherence to the MD.

Results

We provide the whole metabolome profile of the endometrium, where 925 different metabolites were identified. Among these metabolites, lipids comprised the largest part, where polyunsaturated fatty acids (PUFAs) prevailed. Women with endometriosis and recurrent implantation failure were found to have lower levels of PUFAs compared to women with male factor and unexplained infertility (i.e., no clear endometrial alterations), identifying a metabolome profile associated with infertility diagnoses where altered endometrial functions are suspected. Moreover, MD adherence seemed to be associated with the endometrial metabolomic profile in a manner dependent on the health status of the uterus.

Conclusion

The study findings provide insight into the molecular background of female infertility and lead to identification of potential molecular biomarkers and possibilities for modulating the endometrial microenvironment and, thereby, endometrial functions involved in embryo implantation and infertility.

Point-of-Care Diagnosis of Endometrial Cancer Using the Surgical Intelligent Knife (iKnife)-A Prospective Pilot Study of Diagnostic Accuracy

Introduction: Delays in the diagnosis and treatment of endometrial cancer negatively impact patient survival. The aim of this study was to establish whether rapid evaporative ionisation mass spectrometry using the iKnife can accurately distinguish between normal and malignant endometrial biopsy tissue samples in real time, enabling point-of-care (POC) diagnoses. Methods: Pipelle biopsy samples were obtained from consecutive women needing biopsies for clinical reasons. A Waters G2-XS Xevo Q-Tof mass spectrometer was used in conjunction with a modified handheld diathermy (collectively called the 'iKnife'). Each tissue sample was processed with diathermy, and the resultant surgical aerosol containing ionic lipid species was then analysed, producing spectra. Principal component analyses and linear discriminant analyses were performed to determine variance in spectral signatures. Leave-one-patient-out cross-validation was used to test the diagnostic accuracy. Results: One hundred and fifty patients provided Pipelle biopsy samples (85 normal, 59 malignant, 4 hyperplasia and 2 insufficient), yielding 453 spectra. The iKnife differentiated between normal and malignant endometrial tissues on the basis of differential phospholipid spectra. Cross-validation revealed a diagnostic accuracy of 89% with sensitivity, specificity, positive predictive value and negative predictive value of 85%, 93%, 94% and 85%, respectively. Conclusions: This study is the first to use the iKnife to identify cancer in endometrial Pipelle biopsy samples. These results are highly encouraging and suggest that the iKnife could be used in the clinic to provide a POC diagnosis.

Obesity-induced follicular phase endometrial proteome dysregulation in a well-phenotyped population

OBJECTIVE

Despite obesity's significant impact on reproduction, its influence on the physiology of the human endometrium is largely understudied. We hypothesized that endometrial proteomic differences exist between obese (OW; body mass index [BMI] ≥30 kg/m²) and normal-weight women (NWW; BMI, 18.5-24.9 kg/m²).

DESIGN

Clinical cross-sectional study.

SETTING

Academic Medical Center.

PATIENT(S)

Healthy, normally-cycling, 18 to 40-year-old women (n = 6 OW and n = 6 NWW).

MAIN OUTCOME MEASURE(S)

Participants underwent screening and midfollicular phase visits. Demographic and anthropometric characteristics, blood samples, ultrasounds, and follicular phase endometrial biopsies were collected. Proteomic analyses of endometrial samples (liquid chromatography-mass spectrometry) were performed. Proteins with ≥2-fold difference and a false discovery rate of <0.1 were considered statistically significant (Benjamini-Hochberg adjustment).

RESULT(S)

Reproductive hormone levels did not differ between the two groups. Mean BMI, serum leptin concentration, and bioelectrical impedance analysis indices of adiposity were higher in OW than in NWW. Histological examination of the endometrial samples confirmed normal-appearing endometrium in both OW and NWW. A total of 2,930 proteins were detected across all samples, with an average number of proteins per sample of 2,059 ± 482 in NWW and 2,437 ± 187 in OW. A total of 17 proteins were differentially expressed in OW vs. NWW; 2 were more abundant, whereas 15 were underexpressed in OW, including the progesterone receptor.

CONCLUSION(S)

In this well-phenotyped population of healthy women, obesity was associated with significant endometrial proliferative phase proteomic differences affecting the hormonal and immunologic pathways. These could contribute to an increased risk of menstrual bleeding abnormalities and create an altered environment for future luteinization.

Lipid metabolism-related genes as biomarkers and therapeutic targets reveal endometrial receptivity and immune microenvironment in women with reproductive dysfunction

BACKGROUND

In recent years, alterations in lipid metabolism are currently considered a hallmark feature of many diseases. However, the role in women with reproductive dysfunction (WRD) remains to be fully elucidated. Here, this study aimed to explore the effect of lipid metabolism-related genes (LMRGs) on endometrial receptivity of WRD.

METHODS

This study retrospectively analyzed endometrial receptivity array (ERA) in GEO database. The differential expression genes (DEGs) were obtained by limma differential analysis, and the core genes and corresponding predicted microRNA were obtained through protein-protein interaction (PPI) analysis and TargetScan database, so as to predict the chemical targets of drug therapy. Through the intersection of DEGs and LMRGs, the target gene expression profile was obtained for subsequent consensus clustering analysis and immune analysis. In addition, the immune cell infiltration was assessed by applying the ESTIMATE and MCPcounter algorithm and potential drug targets were obtained from the HERB website.

RESULTS

1473 genes showed differential expression between the groups of WRD and fertile women, and then a large number of lipid metabolism-related pathways and immune-related pathways were enriched. Twelve core genes and corresponding predicted miR-134-3p were obtained; most importantly, we found that these 12 genes were all LMRGs. Through drug target prediction, we obtained three drugs that regulate lipid metabolism and improve blood circulation, namely lovastatin, estrogen, and quercetin. EHHADH (AUC = 0.85) and PTEN (AUC = 0.82) have the best diagnostic performance. UMAP and heatmap revealed large differences between three clusters. LMRGs revealed specific manifestations of WRD in endometrial receptivity and immune microenvironment.

CONCLUSIONS

Our study explored the expression pattern of LMRGs in endometrium of WRD, screened the corresponding biomarkers, and proposed the combination of traditional Chinese and Western medicine to improve the endometrial receptivity.

The Impact of Suppressing Estradiol During Ovarian Stimulation on the Unsupported Luteal Phase: A Randomized Controlled Trial

CONTEXT

Supraphysiological sex steroid levels at the follicular-luteal phase transition are implicated as the primary cause of luteal insufficiency after ovarian stimulation (OS) for in vitro fertilization.

OBJECTIVE

We aimed to determine the impact of suppressing estradiol levels during OS of multiple dominant follicles on the unsupported luteal phase and markers of endometrial maturation.

METHODS

At 2 university hospitals, 25 eligible egg donors were randomized to undergo OS using exogenous gonadotropins with or without adjuvant letrozole 5 mg/day. Final oocyte maturation was triggered with a GnRH agonist. No luteal support was provided. The primary outcome was the duration of the luteal phase. Secondary outcomes were luteal phase hormone profiles and the endometrial transcriptomic signature 5 days after oocyte pick up (OPU + 5).

RESULTS

The median (interquartile range [IQR]) luteal phase duration was 8.0 (6.8-11.5) days compared with 5.0 (5.0-6.8) days in the intervention and control group, respectively (P < 0.001). Estradiol levels were effectively suppressed in the letrozole group with a median of 0.86 (0.23-1.24) nmol/L at OPU compared to 2.82 (1.34-3.44) nmol/L in the control group. Median (IQR) progesterone levels at OPU + 5 were 67.05 (15.67-101.75) nmol/L in the letrozole group vs 2.27 (1.05-10.70) nmol/L in the control group (P < 0.001). In the letrozole group, 75% of participants revealed endometrial transcriptomic signatures interpreted as post-receptive. In the control group, 40% were post-receptive and 50% noninformative.

CONCLUSION

Suppressing estradiol levels in the follicular phase with adjuvant letrozole significantly reduces the disruption of the unsupported luteal phase after OS.

Metabolomic Analysis Points to Bioactive Lipid Species and Acireductone Dioxygenase 1 (ADI1) as Potential Therapeutic Targets in Poor Prognosis Endometrial Cancer

Simple Summary

Uterine serous carcinoma is considered a rare and aggressive variant of endometrial cancer that accounts for 10% of all endometrial cancers diagnosed but is responsible for 40% of endometrial cancer-related deaths. Unfortunately, current treatments for serous endometrial carcinoma are ineffective. Therefore, there is a need to find new therapeutic targets. The aim of this study was to analyse the metabolic profile of serous cancer in order to identify new molecules and thereby define potential therapeutic targets. We observed that most of the differential metabolites are lipid species (suggesting the important role of the lipid metabolism). In addition, we found an increase in 2-Oxo-4-methylthiobutanoic acid (synthesised by the ADI1 enzyme) in serous carcinomas. Using public database analysis and immunohistochemistry, we established a correlation between elevated ADI1 levels and serous carcinoma. Furthermore, the ectopic modification of ADI1 expression in vitro revealed the ability of ADI1 to induce pathological cell migration and invasion capabilities.

Abstract

Metabolomic profiling analysis has the potential to highlight new molecules and cellular pathways that may serve as potential therapeutic targets for disease treatment. In this study, we used an LC-MS/MS platform to define, for the first time, the specific metabolomic signature of uterine serous carcinoma (SC), a relatively rare and aggressive variant of endometrial cancer (EC) responsible for 40% of all endometrial cancer-related deaths. A metabolomic analysis of 31 ECs (20 endometrial endometrioid carcinomas (EECs) and 11 SCs) was performed. Following multivariate statistical analysis, we identified 232 statistically different metabolites among the SC and EEC patient samples. Notably, most of the metabolites identified (89.2%) were lipid species and showed lower levels in SCs when compared to EECs. In addition to lipids, we also documented metabolites belonging to amino acids and purine nucleotides (such as 2-Oxo-4-methylthiobutanoic acid, synthesised by acireductone dioxygenase 1 (ADI1) enzyme), which showed higher levels in SCs. To further investigate the role of ADI1 in SC, we analysed the expression protein levels of ADI1 in 96 ECs (67 EECs and 29 SCs), proving that the levels of ADI1 were higher in SCs compared to EECs. We also found that ADI1 mRNA levels were higher in p53 abnormal ECs compared to p53 wild type tumours. Furthermore, elevated ADI1 mRNA levels showed a statistically significant negative correlation with overall survival and progression-free survival among EEC patients. Finally, we tested the ability of ADI1 to induce migration and invasion capabilities in EC cell lines. Altogether, these results suggest that ADI1 could be a potential therapeutic target in poor-prognosis SCs and other Ecs with abnormal p53 expression.

Guide to Metabolomics Analysis: A Bioinformatics Workflow

Metabolomics is an emerging field that quantifies numerous metabolites systematically. The key purpose of metabolomics is to identify the metabolites corresponding to each biological phenotype, and then provide an analysis of the mechanisms involved. Although metabolomics is important to understand the involved biological phenomena, the approach's ability to obtain an exhaustive description of the processes is limited. Thus, an analysis-integrated metabolomics, transcriptomics, proteomics, and other omics approach is recommended. Such integration of different omics data requires specialized statistical and bioinformatics software. This review focuses on the steps involved in metabolomics research and summarizes several main tools for metabolomics analyses. We also outline the most abnormal metabolic pathways in several cancers and diseases, and discuss the importance of multi-omics integration algorithms. Overall, our goal is to summarize the current metabolomics analysis workflow and its main analysis software to provide useful insights for researchers to establish a preferable pipeline of metabolomics or multi-omics analysis.

The mid-secretory endometrial transcriptomic landscape in endometriosis: a meta-analysis

STUDY QUESTION

Do women with endometriosis have a different endometrial gene expression profile at the time of embryo implantation than women without endometriosis?

SUMMARY ANSWER

The endometrial gene expression profile of women with endometriosis differs from that of women without endometriosis at the mid-secretory phase, although the differences are small.

WHAT IS KNOWN ALREADY

About 50% of women with endometriosis suffer infertility. Several molecular studies have suggested impaired endometrial receptivity in women with endometriosis, while others have detected no dysregulation of endometrial receptivity. Nevertheless, the previous endometrial transcriptome studies comparing women with and without endometriosis have been performed in small sample size with limited statistical power. We set out to systematically search and compile data of endometrial gene expression signatures at the receptive phase in women with endometriosis versus control women. Based on the obtained data, we conducted a meta-analysis of differentially expressed genes in order to raise the power of the analysis for identifying the molecular profiles of receptive phase endometria in endometriosis.

STUDY DESIGN, SIZE, DURATION

A systematic literature search was conducted up to February 2022 following PRISMA criteria and included PubMed, Cochrane and Web of Science databases. For the systematic search, the term ‘endometriosis’ was paired with the terms ‘transcriptomics’, ‘transcriptome’, ‘gene expression’, ‘RNA-seq’, ‘sequencing’ and ‘array’, by using the Boolean operator ‘AND’ to connect them. Articles written in English were screened and interrogated for data extraction.

PARTICIPANTS/MATERIALS, SETTING, METHODS

A meta-analysis was performed on the selected studies to extract the differentially expressed genes described at the mid-secretory phase in women with endometriosis versus women without endometriosis in natural cycles, using the robust rank aggregation method. In total, transcriptome data of 125 women (78 patients and 47 controls) were meta-analysed, with a special focus on endometrial receptivity-specific genes based on commercial endometrial receptivity tests.

MAIN RESULTS AND THE ROLE OF CHANCE

In total, 8 studies were eligible for the quantitative meta-analysis, gathering transcriptome data from the mid-secretory phase endometria of 125 women. A total of 7779 differentially expressed transcripts between the study groups were retrieved (3496 up-regulated and 4283 down-regulated) and were meta-analysed. After stringent multiple correction, there was no differential expression of any single molecule in the endometrium of women with endometriosis versus controls, while enrichment analysis detected that the pathways of chemotaxis and locomotion are dysregulated in endometriosis. Further analysis of endometrial receptivity-specific genes highlighted dysregulation of C4BPA, MAOA and PAEP and enrichment of immune and defence pathways in women with endometriosis.

LIMITATIONS, REASONS FOR CAUTION

Most of the studies included into the meta-analysis were relatively small and had different study designs, which might have contributed to a bias.

WIDER IMPLICATIONS OF THE FINDINGS

The current meta-analysis supports the hypothesis that endometrial receptivity is altered in women with endometriosis, although the changes are small. The molecules and pathways identified could serve as future biomarkers and therapeutical targets in detecting and treating endometriosis-associated infertility.

STUDY FUNDING/COMPETING INTEREST(S)

The authors declare no competing interests. This work was supported by the Spanish Ministry of Education, Culture and Sport [grant FPU15/01193] and the Margarita Salas program for the Requalification of the Spanish University system [grant UJAR01MS]; Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and European Regional Development Fund (FEDER): grants RYC-2016-21199 and ENDORE SAF2017-87526-R; Programa Operativo FEDER Andalucía (B-CTS-500-UGR18; A-CTS-614-UGR20); the Junta de Andalucía [BIO-302; and PAIDI P20_00158]; the University of Jaén [PAIUJA-EI_CTS02_2017]; the University of Granada, Plan Propio de Investigación 2016, Excellence actions: Units of Excellence; Unit of Excellence on Exercise and Health (UCEES), and by the Junta de Andalucía, Consejería de Conocimiento, Investigación y Universidades and European Regional Development Fund (ERDF), ref. SOMM17/6107/UGR; the Estonian Research Council (grant PRG1076); Horizon 2020 innovation (ERIN, grant no. EU952516) of the European Commission and Enterprise Estonia (grant EU48695).

TRIAL REGISTRATION NUMBER

The systematic review was registered at PROSPERO (identifier: CRD42020122054).

Use of 'omics for endometrial timing: the cycle moves on

For some years, the prospect of precise and personalized timing of the endometrial cycle for optimal embryo replacement has been held out as a potential solution to low implantation rates. It is envisaged that a receptive state can be defined and reached at a predictable time, and embryo replacement performed in synchrony. In the last century, morphological changes characteristic of the mid secretory phase were defined in precisely timed cycles in women of proven fertility, but when deviations from this standardized schedule occur, their significance for implantation has remained uncertain. ‘Omics technologies have been widely advocated for staging the endometrial cycle and defining a set of biochemical requirements for implantation, but after two decades of research, improvements to pregnancy rates have not followed, and there is a striking lack of agreement regarding the molecular characterization of the receptive state. Some of the rationale underlying these problems is now emerging with the application of higher-level computational and biological methodology. Here, we consider the challenges of defining an endometrial phenotype that can support implantation and continuing pregnancy. Receptivity may be an emergent trait depending on contributions from multiple proteins that have low pathway connectivity. We recommend that authors choose language which rigorously avoids the implication that protocols for molecular staging of the mid secretory phase inherently identify a state of receptivity to the implanting blastocyst.

Comparative Proteomic Analysis Reveals Metformin Improves the Expression of Biomarkers of Endometrial Receptivity in Infertile Women with Minimal/Mild Endometriosis

The prevalence of endometriosis is approximately 10% in women of reproductive age, and 30-50% of women with endometriosis are infertile. Metformin has been reported to inhibit the growth of ectopic lesions in endometriosis. However, its effect on the eutopic endometrium of endometriosis is unknown. This study aimed to identify whether metformin affects endometrial receptivity in infertile women with minimal/mild endometriosis. We enrolled 10 infertile women who were diagnosed with minimal/mild endometriosis through laparoscopy. Paired endometrial tissues of the secretory phase from participants were collected during surgery and after 2 months of metformin treatment (n = 5) or no medical treatment (n = 5). Protein expression profiles of the paired endometrium were detected by proteomics and compared using the self-control method (2 months later vs. in surgery). Proteomics data revealed six proteins associated with endometrial receptivity among the significantly upregulated proteins after metformin treatment (fold change > 1.5, P < 0.05). Insulin-like growth factor binding protein 7 (IGFBP-7) showed the most robust increase in these six endometrial receptivity-related proteins (fold change: 8.668, P < 0.05), while there was no significant change in the controls (fold change: 1.906, P > 0.05). The upregulation of IGFBP-7 has been validated through target proteomics, immunohistochemistry, and further demonstrated in endometriosis mouse models induced by autotransplantation. This study revealed that metformin upregulated the expression of IGFBP-7 in the endometrium of human and mouse models of endometriosis. Metformin potentially affects endometrial receptivity of minimal/mild endometriosis by improving the expression of the endometrial receptivity marker IGFBP-7.

Transcriptional and Epigenetic Response to Sedentary Behavior and Physical Activity in Children and Adolescents: A Systematic Review

BACKGROUND

The links of sedentary behavior and physical activity with health outcomes in children and adolescents is well known. However, the molecular mechanisms involved are poorly understood. We aimed to synthesize the current knowledge of the association of sedentary behavior and physical activity (acute and chronic effects) with gene expression and epigenetic modifications in children and adolescents.

METHODS

PubMed, Web of Science, and Scopus databases were systematically searched until April 2022. A total of 15 articles were eligible for this review. The risk of bias assessment was performed using the Joanna Briggs Institute Critical Appraisal Tool for Systematic Reviews and/or a modified version of the Downs and Black checklist.

RESULTS

Thirteen studies used candidate gene approach, while only 2 studies performed high-throughput analyses. The candidate genes significantly linked to sedentary behavior or physical activity were: FOXP3, HSD11B2, IL-10, TNF-α, ADRB2, VEGF, HSP70, SOX, and GPX. Non-coding Ribonucleic acids (RNAs) regulated by sedentary behavior or physical activity were: miRNA-222, miRNA-146^a, miRNA-16, miRNA-126, miR-320^a, and long non-coding RNA MALAT1. These molecules are involved in inflammation, immune function, angiogenic process, and cardiovascular disease. Transcriptomics analyses detected thousands of genes that were altered following an acute bout of physical activity and are linked to gene pathways related to immune function, apoptosis, and metabolic diseases.

CONCLUSION

The evidence found to date is rather limited. Multidisciplinary studies are essential to characterize the molecular mechanisms in response to sedentary behavior and physical activity in the pediatric population. Larger cohorts and randomized controlled trials, in combination with multi-omics analyses, may provide the necessary data to bring the field forward.

SYSTEMATIC REVIEW REGISTRATION

[www.ClinicalTrials.gov], identifier [CRD42021235431].

circFAM120A participates in repeated implantation failure by regulating decidualization via the miR-29/ABHD5 axis

Repeated implantation failure (RIF) is a major problem that limits the pregnancy rate associated with assisted reproductive technology. However, the pathogenesis of RIF is still unknown. Recently, the expression levels of circular RNAs (circRNAs) were profiled in the endometrial tissues of patients with RIF. However, the exact role of circRNAs in RIF remains unclear. In our study, we found that circFAM120A levels were significantly down-regulated in the endometrium at the window of implantation in RIF patients compared with non-RIF controls. The suppression of circFAM120A expression inhibited decidualization in human endometrial stromal cells (hESCs). Furthermore, RNA-seq analysis after circFAM120A knockdown revealed ABHD5 as a potential downstream target gene of circFAM120A. As expected, down-regulating ABHD5 in hESCs also inhibited decidualization. Using the starBase and TargetScan databases, we predicted that miR-29 may interact with ABHD5, based on nucleotide sequence matching. Luciferase reporter assay showed that miR-29 bound to the 3' UTR of ABHD5 at the predicted complementary sites. Moreover, miR-29 mimics efficiently reduced ABHD5 expression levels and suppressed the decidualization process, whereas a miR-29 inhibitor partly rescued ABHD5 mRNA expression level and decidualization reduced by the knockdown of circFAM120A. Therefore, circFAM120A modulated decidualization in RIF through the miR-29/ABHD5 axis.

Analysis of serum and endometrial progesterone in determining endometrial receptivity

STUDY QUESTION

Is there a relationship between serum and endometrial progesterone (P4) levels, including P4 and metabolites (oestrone, oestradiol and 17α-hydroxyprogesterone), and endometrial receptivity?

SUMMARY ANSWER

Serum P4 levels were not correlated with endometrial P4, nor associated with endometrial receptivity as determined by the ERA® test; however, endometrial P4 and 17α-hydroxyprogesterone levels were positively correlated and related to endometrial receptivity by ERA.

WHAT IS KNOWN ALREADY

Acquisition of endometrial receptivity is governed by P4, which induces secretory transformation. A close relationship between serum P4 and pregnancy outcome is reported for hormone replacement therapy (HRT) cycles. However, the relationship between serum and uterine P4 levels has not been described, and it is unknown whether uterine receptivity depends more on serum or uterine P4 levels.

STUDY DESIGN, SIZE, DURATION

A prospective cohort study was performed during March 2018-2019 in 85 IVF patients undergoing an evaluation-only HRT cycle with oestradiol valerate (6 mg/day) and micronised vaginal progesterone (400 mg/12 h).

PARTICIPANTS/MATERIALS, SETTING, METHODS

Patients were under 50 years of age, had undergone at least one failed IVF cycle, had no uterine pathology, and had adequate endometrial thickness (> 6.5 mm). The study was conducted at IVI Valencia and IVI Foundation. An endometrial biopsy and a blood sample were collected after 5 days of P4 vaginal treatment. Measures included serum P4 levels, ERA®-based evaluation of endometrial receptivity, and endometrial P4 levels along with metabolites (oestrone, oestradiol and 17α-hydroxyprogesterone) measured by ultra-performance liquid chromatography-tandem mass spectrometry.

MAIN RESULTS AND THE ROLE OF CHANCE

Seventy-nine women were included (mean age: 39.9 ± 4.6, BMI: 24.2 ± 3.9 kg/m2, endometrial thickness: 8.2 ± 1.4 mm). The percentage of endometria indicated as receptive by ERA® was 40.5%. When comparing receptive versus non-receptive groups, no differences were observed in baseline characteristics nor in steroid hormones levels in serum or endometrium. No association between serum P4 and endometrial steroid levels or ERA result was found (P < 0.05). When the population was stratified according to metabolite concentration levels, endometrial P4 and 17α-hydroxyprogesterone were significantly associated with endometrial receptivity (P < 0.05). A higher proportion of receptive endometria by ERA was observed when endometrial P4 levels were higher than 40.07 µg/ml (relative maximum) and a lower proportion of receptive endometria was associated with endometrial 17α-hydroxyprogesterone lower than 0.35 ng/ml (first quartile). A positive correlation R2 = 0.67, P < 0.001 was observed between endometrial P4 and 17α-hydroxyprogesterone levels.

LIMITATIONS, REASONS FOR CAUTION

This study did not analyse pregnancy outcomes. Further, the findings can only be extrapolated to HRT cycles with micronised vaginal progesterone for luteal phase support.

WIDER IMPLICATIONS OF THE FINDINGS

Our findings suggest that the combined benefits of different routes of progesterone administration for luteal phase support could be leveraged to ensure an adequate concentration of progesterone both in the uterus and in the bloodstream. Further studies will confirm whether this method can optimise both endometrial receptivity and live birth rate. Additionally, targeted treatment to increase P4 endometrial levels may normalise the timing of the window of implantation without needing to modify the progesterone administration day.

STUDY FUNDING/COMPETING INTEREST(S)

This research was supported by the IVI-RMA Valencia (1706-VLC-051-EL) and Consellería d'Educació, Investigació, Cultura, i esport Generalitat Valenciana (Valencian Government, Spain, GV/2018//151). Almudena Devesa-Peiro (FPU/15/01398) and Cristina Rodriguez-Varela (FPU18/01657) were supported by the FPU program fellowship from the Ministry of Science, Innovation and Universities (Spanish Government). P.D.-G. is co-inventor on the ERA patent, with non-economic benefits. The other authors have no competing interests.

TRIAL REGISTRATION NUMBER

NCT03456375.

Screening of Variants in the Transcript Profile of Eutopic Endometrium from Infertile Women with Endometriosis during the Implantation Window

OBJECTIVE

 Abnormalities in the eutopic endometrium of women with endometriosis may be related to disease-associated infertility. Although previous RNA-sequencing analysis did not show differential expression in endometrial transcripts of endometriosis patients, other molecular alterations could impact protein synthesis and endometrial receptivity. Our aim was to screen for functional mutations in the transcripts of eutopic endometria of infertile women with endometriosis and controls during the implantation window.

METHODS

 Data from RNA-Sequencing of endometrial biopsies collected during the implantation window from 17 patients (6 infertile women with endometriosis, 6 infertile controls, 5 fertile controls) were analyzed for variant discovery and identification of functional mutations. A targeted study of the alterations found was performed to understand the data into disease's context.

RESULTS

 None of the variants identified was common to other samples within the same group, and no mutation was repeated among patients with endometriosis, infertile and fertile controls. In the endometriosis group, nine predicted deleterious mutations were identified, but only one was previously associated to a clinical condition with no endometrial impact. When crossing the mutated genes with the descriptors endometriosis and/or endometrium, the gene CMKLR1 was associated either with inflammatory response in endometriosis or with endometrial processes for pregnancy establishment.

CONCLUSION

 Despite no pattern of mutation having been found, we ponder the small sample size and the analysis on RNA-sequencing data. Considering the purpose of the study of screening and the importance of the CMKLR1 gene on endometrial modulation, it could be a candidate gene for powered further studies evaluating mutations in eutopic endometria from endometriosis patients.

Mapping the entire functionally active endometrial microbiota

STUDY QUESTION

Does endometrium harbour functionally active microorganisms and whether the microbial composition differs between proliferative and mid-secretory phases?

SUMMARY ANSWER

Endometrium harbours functionally alive microorganisms including bacteria, viruses, archaea and fungi whose composition and metabolic functions change along the menstrual cycle.

WHAT IS KNOWN ALREADY

Resident microbes in the endometrium have been detected, where microbial dysfunction has been associated with reproductive health and disease. Nevertheless, the core microorganismal composition in healthy endometrium is not determined and whether the identified bacterial DNA sequences refer to alive/functionally active microbes is not clear. Furthermore, whether there are cyclical changes in the microbial composition remains an open issue.

STUDY DESIGN, SIZE, DURATION

RNA sequencing (RNAseq) data from 14 endometrial paired samples from healthy women, 7 samples from the mid-secretory phase and 7 samples from the consecutive proliferative phase were analysed for the microbial RNA sequences.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The raw RNAseq data were converted into FASTQ format using SRA Toolkit. The unmapped reads to human sequences were aligned to the reference database Kraken2 and visualised with Krona software. Menstrual phase taxonomic differences were performed by R package metagenomeSeq. The functional analysis of endometrial microbiota was obtained with HUMANn2 and the comparison between menstrual phases was conducted by one-way ANOVA. Human RNAseq analysis was performed using miARma-Seq and the functional enrichment analysis was carried out using gene set enrichment analysis (GSEA; HumanCyc). The integration of metabolic pathways between host and microbes was investigated. The developed method of active microbiota mapping was validated in independent sample set.

MAIN RESULTS AND THE ROLE OF CHANCE

With the novel metatranscriptomic approach, we mapped the entire alive microbiota composing of >5300 microorganisms within the endometrium of healthy women. Microbes such as bacteria, fungi, viruses and archaea were identified. The validation of three independent endometrial samples from different ethnicity confirmed the findings. Significant differences in the microbial abundances in the mid-secretory vs. proliferative phases were detected with possible metabolic activity in the host-microbiota crosstalk in receptive phase endometrium, specifically in the prostanoid biosynthesis pathway and L-tryptophan metabolism.

LARGE SCALE DATA

The raw RNAseq data used in the current study are available at GEO GSE86491 and at BioProject PRJNA379542.

LIMITATIONS, REASONS FOR CAUTION

These pioneering results should be confirmed in a bigger sample size.

WIDER IMPLICATIONS OF THE FINDINGS

Our study confirms the presence of active microbes, bacteria, fungi, viruses and archaea in the healthy human endometrium with implications in receptive phase endometrial functions, meaning that microbial dysfunction could impair the metabolic pathways important for endometrial receptivity. The results of this study contribute to the better understanding of endometrial microbiota composition in healthy women and its possible role in endometrial functions. In addition, our novel methodological pipeline for analysing alive microbes with transcriptional and metabolic activities could serve to inspire new analysis approaches in reproductive medicine.

STUDY FUNDING/COMPETING INTERESTS

This work is supported by the Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and European Regional Development Fund (FEDER): grants RYC-2016-21199 and ENDORE SAF2017-87526-R; FEDER/Junta de Andalucía-Consejería de Economía y Conocimiento: MENDO (B-CTS-500-UGR18) and by the University of Granada Plan Propio de Investigación 2016 - Excellence actions: Unit of Excellence on Exercise and Health (UCEES) (SOMM17/6107/UGR). A.S.-L. and N.M.M. are funded by the Spanish Ministry of Science, Innovation and Universities (PRE2018-0854409 and FPU19/01638). S.A. has received honoraria for lectures from Merck. The funder had no role in this study.

Essential Role of CRIM1 on Endometrial Receptivity in Goat

In domestic ruminants, endometrial receptivity is related to successful pregnancy and economic efficiency. Despite several molecules having been reported in the past regarding endometrial receptivity regulation, much regarding the mechanism of endometrial receptivity regulation remains unknown due to the complex nature of the trait. In this work, we demonstrated that the cysteine-rich transmembrane bone morphogenetic protein (BMP) regulator 1 (CRIM1) served as a novel regulator in the regulation of goat endometrial receptivity in vitro. Our results showed that hormones and IFN-τ increased the expression of CRIM1 in goat endometrial epithelial cells (EECs). Knockdown of CRIM1 via specific shRNA hindered cell proliferation, cell adhesion and prostaglandins (PGs) secretion and thus derailed normal endometrial receptivity. We further confirmed that receptivity defect phenotypes due to CRIM1 interference were restored by ATG7 overexpression in EECs while a loss of ATG7 further impaired receptivity phenotypes. Moreover, our results showed that changing the expression of ATG7 affected the reactive oxygen species (ROS) production. Moreover, mR-143-5p was shown to be a potential upstream factor of CRIM1-regulated endometrial receptivity in EECs. Overall, these results suggest that CRIM1, as the downstream target of miR-143-5p, has effects on ATG7-dependent autophagy, regulating cell proliferation, cell adhesion and PG secretion, and provides a new target for the diagnosis and treatment of early pregnancy failure and for improving the success rates of artificial reproduction.

The role of transcriptomic biomarkers of endometrial receptivity in personalized embryo transfer for patients with repeated implantation failure

Background

Window of implantation (WOI) displacement is one of the endometrial origins of embryo implantation failure, especially repeated implantation failure (RIF). An accurate prediction tool for endometrial receptivity (ER) is extraordinarily needed to precisely guide successful embryo implantation. We aimed to establish an RNA-Seq-based endometrial receptivity test (rsERT) tool using transcriptomic biomarkers and to evaluate the benefit of personalized embryo transfer (pET) guided by this tool in patients with RIF.

Methods

This was a two-phase strategy comprising tool establishment with retrospective data and benefit evaluation with a prospective, nonrandomized controlled trial. In the first phase, rsERT was established by sequencing and analyzing the RNA of endometrial tissues from 50 IVF patients with normal WOI timing. In the second phase, 142 patients with RIF were recruited and grouped by patient self-selection (experimental group, n = 56; control group, n = 86). pET guided by rsERT was performed in the experimental group and conventional ET in the control group.

Results

The rsERT, comprising 175 biomarker genes, showed an average accuracy of 98.4% by using tenfold cross-validation. The intrauterine pregnancy rate (IPR) of the experimental group (50.0%) was significantly improved compared to that (23.7%) of the control group (RR, 2.107; 95% CI 1.159 to 3.830; P = 0.017) when transferring day-3 embryos. Although not significantly different, the IPR of the experimental group (63.6%) was still 20 percentage points higher than that (40.7%) of the control group (RR, 1.562; 95% CI 0.898 to 2.718; P = 0.111) when transferring blastocysts.

Conclusions

The rsERT was developed to accurately predict the WOI period and significantly improve the pregnancy outcomes of patients with RIF, indicating the clinical potential of rsERT-guided pET.

Trial registration Chinese Clinical Trial Registry: ChiCTR-DDD-17013375. Registered 14 November 2017, http://www.chictr.org.cn/index.aspx

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-021-02837-y.

Omics and Artificial Intelligence to Improve In Vitro Fertilization (IVF) Success: A Proposed Protocol

The prediction of in vitro fertilization (IVF) outcome is an imperative achievement in assisted reproduction, substantially aiding infertile couples, health systems and communities. To date, the assessment of infertile couples depends on medical/reproductive history, biochemical indications and investigations of the reproductive tract, along with data obtained from previous IVF cycles, if any. Our project aims to develop a novel tool, integrating omics and artificial intelligence, to propose optimal treatment options and enhance treatment success rates. For this purpose, we will proceed with the following: (1) recording subfertile couples’ lifestyle and demographic parameters and previous IVF cycle characteristics; (2) measurement and evaluation of metabolomics, transcriptomics and biomarkers, and deep machine learning assessment of the oocyte, sperm and embryo; (3) creation of artificial neural network models to increase objectivity and accuracy in comparison to traditional techniques for the improvement of the success rates of IVF cycles following an IVF failure. Therefore, “omics” data are a valuable parameter for embryo selection optimization and promoting personalized IVF treatment. “Omics” combined with predictive models will substantially promote health management individualization; contribute to the successful treatment of infertile couples, particularly those with unexplained infertility or repeated implantation failures; and reduce multiple gestation rates.

Label-free proteomics uncovers SMC1A expression is Down-regulated in AUB-E

BACKGROUND

While heavy menstrual bleeding (HMB) is a prevalent symptom among women with abnormal uterine bleeding caused by endometrial disorder (AUB-E) seeking gynecologic care, the primary endometrial disorder remains poorly understood.

METHODS

Five human endometrial samples from women with AUB-E and the age-matched healthy women were selected, respectively. Proteins from the samples were analyzed by a linear ion trap (LTQ)-Orbitrap Elite mass spectrometer based label-free proteomic approach. The purpose protein was validated by western blot and immunohistochemistry staining.

RESULTS

A total of 2353 protein groups were quantified under highly stringent criteria with a false discovery rate of < 1% for protein groups, and 291 differentially expressed proteins were significantly changed between the two groups. The results showed that the down-regulation of structural maintenance of chromosomes protein 1A (SMC1A) in AUB-E patients. Next, this change in the glandular epithelial cells was validated by immunohistochemistry.

CONCLUSION

The results indicated a novel mechanism for the cause of AUB-E, as down-expression SMC1A potentially regulated the cell cycle progression in endometrial glandular epithelium further led to bleeding.

The Interaction Between Microorganisms, Metabolites, and Immune System in the Female Genital Tract Microenvironment

The female reproductive tract microenvironment includes microorganisms, metabolites, and immune components, and the balance of the interactions among them plays an important role in maintaining female reproductive tract homeostasis and health. When any one of the reproductive tract microorganisms, metabolites, or immunity is out of balance, it will affect the other two, leading to the occurrence and development of diseases and the appearance of corresponding symptoms and signs, such as infertility, miscarriage, premature delivery, and gynecological tumors caused by infectious diseases of the reproductive tract. Nutrients in the female reproductive tract provide symbiotic and pathogenic microorganisms with a source of nutrients for their own reproduction and utilization. At the same time, this interaction with the host forms a variety of metabolites. Changes in metabolites in the host reproductive tract are related not only to the interaction between the host and microbiota under dysbiosis but also to changes in host immunity or the environment, all of which will participate in the pathogenesis of diseases and lead to disease-related phenotypes. Microorganisms and their metabolites can also interact with host immunity, activate host immunity, and change the host immune status and are closely related to persistent genital pathogen infections, aggravation of infectious diseases, severe pregnancy outcomes, and even gynecological cancers. Therefore, studying the interaction between microorganisms, metabolites, and immunity in the reproductive tract cannot only reveal the pathogenic mechanisms that lead to inflammation of the reproductive tract, adverse pregnancy outcomes and tumorigenesis but also provide a basis for further research on the diagnosis and treatment of targets.

Identifying biomarkers for predicting successful embryo implantation: applying single to multi-OMICs to improve reproductive outcomes

BACKGROUND

Successful embryo implantation is a complex process that requires the coordination of a series of events, involving both the embryo and the maternal endometrium. Key to this process is the intricate cascade of molecular mechanisms regulated by endocrine, paracrine and autocrine modulators of embryonic and maternal origin. Despite significant progress in ART, implantation failure still affects numerous infertile couples worldwide and fewer than 10% of embryos successfully implant. Improved selection of both the viable embryos and the optimal endometrial phenotype for transfer remains crucial to enhancing implantation chances. However, both classical morphological embryo selection and new strategies incorporated into clinical practice, such as embryonic genetic analysis, morphokinetics or ultrasound endometrial dating, remain insufficient to predict successful implantation. Additionally, no techniques are widely applied to analyse molecular signals involved in the embryo-uterine interaction. More reliable biological markers to predict embryo and uterine reproductive competence are needed to improve pregnancy outcomes. Recent years have seen a trend towards 'omics' methods, which enable the assessment of complete endometrial and embryonic molecular profiles during implantation. Omics have advanced our knowledge of the implantation process, identifying potential but rarely implemented biomarkers of successful implantation.

OBJECTIVE AND RATIONALE

Differences between the findings of published omics studies, and perhaps because embryonic and endometrial molecular signatures were often not investigated jointly, have prevented firm conclusions being reached. A timely review summarizing omics studies on the molecular determinants of human implantation in both the embryo and the endometrium will help facilitate integrative and reliable omics approaches to enhance ART outcomes.

SEARCH METHODS

In order to provide a comprehensive review of the literature published up to September 2019, Medline databases were searched using keywords pertaining to omics, including 'transcriptome', 'proteome', 'secretome', 'metabolome' and 'expression profiles', combined with terms related to implantation, such as 'endometrial receptivity', 'embryo viability' and 'embryo implantation'. No language restrictions were imposed. References from articles were also used for additional literature.

OUTCOMES

Here we provide a complete summary of the major achievements in human implantation research supplied by omics approaches, highlighting their potential to improve reproductive outcomes while fully elucidating the implantation mechanism. The review highlights the existence of discrepancies among the postulated biomarkers from studies on embryo viability or endometrial receptivity, even using the same omic analysis.

WIDER IMPLICATIONS

Despite the huge amount of biomarker information provided by omics, we still do not have enough evidence to link data from all omics with an implantation outcome. However, in the foreseeable future, application of minimally or non-invasive omics tools, together with a more integrative interpretation of uniformly collected data, will help to overcome the difficulties for clinical implementation of omics tools. Omics assays of the embryo and endometrium are being proposed or already being used as diagnostic tools for personalised single-embryo transfer in the most favourable endometrial environment, avoiding the risk of multiple pregnancies and ensuring better pregnancy rates.

Urinary Biomarkers and Their Potential for the Non-Invasive Detection of Endometrial Cancer

Endometrial cancer is the most common malignancy of the female genital tract and its incidence is rising in parallel with the mounting prevalence of obesity. Early diagnosis has great potential to improve outcomes as treatment can be curative, especially for early stage disease. Current tests and procedures for diagnosis are limited by insufficient accuracy in some and unacceptable levels of invasiveness and discomfort in others. There has, therefore, been a growing interest in the search for sensitive and specific biomarkers for endometrial cancer detection based on non-invasive sampling methodologies. Urine, the prototype non-invasive sample, is attractive for biomarker discovery as it is easily accessible and can be collected repeatedly and in quantity. Identification of urinary biomarkers for endometrial cancer detection relies on the excretion of systemic biomarkers by the kidneys or urinary contamination by biomarkers shed from the uterus. In this review, we present the current standing of the search for endometrial cancer urinary biomarkers based on cytology, genomic, transcriptomic, proteomic, and metabolomic platforms. We summarize the biomarker candidates and highlight the challenges inherent in urinary biomarker discovery. We review the various technologies with promise for biomarker detection and assess these novel approaches for endometrial cancer biomarker research.

Menstruation: science and society

Women's health concerns are generally underrepresented in basic and translational research, but reproductive health in particular has been hampered by a lack of understanding of basic uterine and menstrual physiology. Menstrual health is an integral part of overall health because between menarche and menopause, most women menstruate. Yet for tens of millions of women around the world, menstruation regularly and often catastrophically disrupts their physical, mental, and social well-being. Enhancing our understanding of the underlying phenomena involved in menstruation, abnormal uterine bleeding, and other menstruation-related disorders will move us closer to the goal of personalized care. Furthermore, a deeper mechanistic understanding of menstruation-a fast, scarless healing process in healthy individuals-will likely yield insights into a myriad of other diseases involving regulation of vascular function locally and systemically. We also recognize that many women now delay pregnancy and that there is an increasing desire for fertility and uterine preservation. In September 2018, the Gynecologic Health and Disease Branch of the Eunice Kennedy Shriver National Institute of Child Health and Human Development convened a 2-day meeting, "Menstruation: Science and Society" with an aim to "identify gaps and opportunities in menstruation science and to raise awareness of the need for more research in this field." Experts in fields ranging from the evolutionary role of menstruation to basic endometrial biology (including omic analysis of the endometrium, stem cells and tissue engineering of the endometrium, endometrial microbiome, and abnormal uterine bleeding and fibroids) and translational medicine (imaging and sampling modalities, patient-focused analysis of menstrual disorders including abnormal uterine bleeding, smart technologies or applications and mobile health platforms) to societal challenges in health literacy and dissemination frameworks across different economic and cultural landscapes shared current state-of-the-art and future vision, incorporating the patient voice at the launch of the meeting. Here, we provide an enhanced meeting report with extensive up-to-date (as of submission) context, capturing the spectrum from how the basic processes of menstruation commence in response to progesterone withdrawal, through the role of tissue-resident and circulating stem and progenitor cells in monthly regeneration-and current gaps in knowledge on how dysregulation leads to abnormal uterine bleeding and other menstruation-related disorders such as adenomyosis, endometriosis, and fibroids-to the clinical challenges in diagnostics, treatment, and patient and societal education. We conclude with an overview of how the global agenda concerning menstruation, and specifically menstrual health and hygiene, are gaining momentum, ranging from increasing investment in addressing menstruation-related barriers facing girls in schools in low- to middle-income countries to the more recent "menstrual equity" and "period poverty" movements spreading across high-income countries.

The endometrial proteomic profile around the time of embryo implantation†

Embryo implantation is an intricate process which requires competent embryo and receptive endometrium. The failure of endometrium to achieve receptivity is a recognized cause of infertility. However, due to multiplicity of events involved, the molecular mechanisms governing endometrial receptivity are still not fully understood. Traditional one-by-one approaches, including western blotting and histochemistry, are insufficient to examine the extensive changes of endometrial proteome. Although genomics and transcriptomics studies have identified several significant genes, the underlying mechanism remains to be uncovered owing to post-transcriptional and post-translational modifications. Proteomic technologies are high throughput in protein identification, and they are now intensively used to identify diagnostic and prognostic markers in the field of reproductive medicine. There is a series of studies analyzing endometrial proteomic profile, which has provided a mechanistic insight into implantation failure. These published studies mainly focused on the difference between pre-receptive and receptive stages of endometrium, as well as on the alternation of endometrial proteomics in women with reproductive failure. Here, we review recent data from proteomic analyses regarding endometrium around the time of embryo implantation and propose possible future research directions.

Endometriosis: current challenges in modeling a multifactorial disease of unknown etiology

Endometriosis is a chronic inflammatory hormone-dependent condition associated with pelvic pain and infertility, characterized by the growth of ectopic endometrium outside the uterus. Given its still unknown etiology, treatments usually aim at diminishing pain and/or achieving pregnancy. Despite some progress in defining mode-of-action for drug development, the lack of reliable animal models indicates that novel approaches are required. The difficulties inherent to modeling endometriosis are related to its multifactorial nature, a condition that hinders the recreation of its pathology and the identification of clinically relevant metrics to assess drug efficacy. In this review, we report and comment endometriosis models and how they have led to new therapies. We envision a roadmap for endometriosis research, integrating Artificial Intelligence, three-dimensional cultures and organ-on-chip models as ways to achieve better understanding of physiopathological features and better tailored effective treatments.

Endometrial receptivity and pregnancy outcome

Human implantation is a highly complex and multifactorial process. Successful implantation requires the presence of a healthy embryo, a receptive endometrium, and a synchronized molecular dialogue between the two, as well as immune tolerance/protection from the host. The endometrial receptivity refers to a hormonally limited period in which the endometrial tissue acquires a transient functional status allowing blastocyst implantation and pregnancy initiation. Global knowledge of endometrial receptivity grew up in recent years. Improvements in genetics, new biomarkers, noninvasive methods, new advanced techniques (Endometrial receptivity assay - the ERA system, proteomic analysis) offer the possibility to evaluate the endometrial status and to manage patients with infertility problems, especially women undergoing assisted reproductive treatment. This overview reports the most relevant knowledge and recent advances in the study of implantation processes from the perspective of the endometrium, often considered as being the main barrier for a successful pregnancy initiation. Endometrial receptivity is a topic of great interest and further studies are needed for the early identification of endometrial abnormalities and the discovery of new strategies for increasing the chance for the establishment of pregnancy.

Harmonization of quality metrics and power calculation in multi-omic studies

Multi-omic studies combine measurements at different molecular levels to build comprehensive models of cellular systems. The success of a multi-omic data analysis strategy depends largely on the adoption of adequate experimental designs, and on the quality of the measurements provided by the different omic platforms. However, the field lacks a comparative description of performance parameters across omic technologies and a formulation for experimental design in multi-omic data scenarios. Here, we propose a set of harmonized Figures of Merit (FoM) as quality descriptors applicable to different omic data types. Employing this information, we formulate the MultiPower method to estimate and assess the optimal sample size in a multi-omics experiment. MultiPower supports different experimental settings, data types and sample sizes, and includes graphical for experimental design decision-making. MultiPower is complemented with MultiML, an algorithm to estimate sample size for machine learning classification problems based on multi-omic data.

Conventional and modern markers of endometrial receptivity: a systematic review and meta-analysis

BACKGROUND

Early reproductive failure is the most common complication of pregnancy with only 30% of conceptions reaching live birth. Establishing a successful pregnancy depends upon implantation, a complex process involving interactions between the endometrium and the blastocyst. It is estimated that embryos account for one-third of implantation failures, while suboptimal endometrial receptivity and altered embryo-endometrial dialogue are responsible for the remaining two-thirds. Endometrial receptivity has been the focus of extensive research for over 80 years, leading to an indepth understanding of the processes associated with embryo-endometrial cross-talk and implantation. However, little progress has been achieved to translate this understanding into clinically meaningful prognostic tests and treatments for suboptimal endometrial receptivity.

OBJECTIVE AND RATIONALE

The objective of this systematic review was to examine the evidence from observational studies supporting the use of endometrial receptivity markers as prognostic factors for pregnancy outcome in women wishing to conceive, in order to aid clinicians in choosing the most useful marker in clinical practice and for informing further research.

SEARCH METHODS

The review protocol was registered with PROSPERO (CRD42017077891). MEDLINE and Embase were searched for observational studies published from inception until 26 February 2018. We included studies that measured potential markers of endometrial receptivity prior to pregnancy attempts and reported the subsequent pregnancy outcomes. We performed association and accuracy analyses using clinical pregnancy as an outcome to reflect the presence of receptive endometrium. The Newcastle-Ottawa scale for observational studies was employed to assess the quality of the included studies.

OUTCOMES

We included 163 studies (88 834 women) of moderate overall quality in the narrative synthesis, out of which 96 were included in the meta-analyses. Studies reported on various endometrial receptivity markers evaluated by ultrasound, endometrial biopsy, endometrial fluid aspirate and hysteroscopy in the context of natural conception, IUI and IVF. Associations were identified between clinical pregnancy and various endometrial receptivity markers (endometrial thickness, endometrial pattern, Doppler indices, endometrial wave-like activity and various molecules); however, their poor ability to predict clinical pregnancy prevents them from being used in clinical practice. Results from several modern molecular tests are promising and further data are awaited.

WIDER IMPLICATIONS

The post-test probabilities from our analyses may be used in clinical practice to manage couples' expectations during fertility treatments (IUI and IVF). Conventionally, endometrial receptivity is seen as a dichotomous outcome (present or absent), but we propose that various levels of endometrial receptivity exist within the window of implantation. For instance, different transcriptomic signatures could represent varying levels of endometrial receptivity, which can be linked to different pregnancy outcomes. Many studies reported the means of a particular biomarker in those who achieved a pregnancy compared with those who did not. However, extreme values of a biomarker (as opposite to the means) may have significant prognostic and diagnostic implications that are not captured in the means. Therefore, we suggest reporting the outcomes by categories of biomarker levels rather than reporting means of biomarker levels within clinical outcome groups.

Interleukin 1 alpha (IL1A) polymorphisms and risk of endometriosis in Iranian population: a case-control study

Endometriosis is one of the most common gynecological diseases and a major cause of pain and infertility. It is influenced by genetic, epigenetic, and environmental factors. Recently, genome-wide association studies have revealed a strong association between IL1A single nucleotide polymorphisms (SNPs) and increased risk of endometriosis in Japanese women. The aim of the present study was to evaluate the association of three IL1A SNPs, rs17561, rs1304037, and rs2856836 with the risk of endometriosis in Iranian population. Totally, 105 women with diagnosis of endometriosis and 102 healthy women as control group were included. Three SNPs of the IL1A, rs17561 G/T, rs1304037 A/G, and rs2856836 T/C, were genotyped by PCR and RFLP. The rs2856836 TC genotype was significantly higher (p = .002; OR = 3.1, 95% CI: 1.5-6.5) in the patients (28.1%) than the control group (12.7%). The rs2856836 CC genotype was significantly higher (p = .047; OR = 2.3, 95% CI: 1.0-5.3) in the patients (17.5%) than the control group (10.8%). The rs2856836 C allele was significantly higher (p = .001; OR = 2.2, 95% CI: 1.4-3.6) in the patients (31.6%) than the control group (17.2%). The IL1A rs2856836 T/C SNP was associated with susceptibility to endometriosis and the rs2856836 C allele may increase the risk of endometriosis in Iranian women.

Transcriptome sequencing of endometrium revealed alterations in mRNAs and lncRNAs after ovarian stimulation

RESEARCH QUESTION

Using RNA-sequencing analysis, we investigated the relationship between ovarian stimulation and endometrial transcriptome profiles during the window of implantation (WOI) to identify candidate predictive factors for the WOI and to optimize timing for embryo transfer.

METHODS

Twelve women with normal basal hormone levels and regular ovulation were randomly assigned into three groups based on sampling time: late-proliferate phase (P group), and receptive phase in natural cycles (LH+7, N group) and stimulated cycles (hCG+7, S group). Transcriptome profiles of mRNAs and long non-coding RNAs (lncRNAs) were then compared among the three groups. Validation was performed using real-time qPCR.

RESULTS

Comparison of transcriptome profiles between the natural and stimulated endometrium revealed 173 differentially expressed genes (DEGs), with a > 2-fold change (FC) and p < 0.05, under the influence of supraphysiological estradiol (E2) induced by ovarian stimulation. By clustering and KEGG pathway analysis, molecules and pathways associated with endometrial receptivity were identified. Of the 39 DEGs common to the three groups, eight genes were validated using real-time PCR. ESR1, MMP10, and HPSE were previously reported to be associated with endometrial receptivity. In addition, three novel genes (IL13RA2, ZCCHC12, SRARP) and two lncRNAs (LINC01060, LINC01104) were new potential endometrial receptivity-related markers.

CONCLUSION

Using mRNA and lncRNA sequencing, we found that supraphysiological E2 levels from ovarian stimulation had a marked impact upon endometrial transcriptome profiles and may result in a shift of the WOI. The precise mechanisms underlying the supraphysiological hormone-induced shift of the WOI require further research.

REGISTRATION NUMBER

ChiCTR180001453.

Is the profile of transcripts altered in the eutopic endometrium of infertile women with endometriosis during the implantation window?

STUDY QUESTION

Compared to healthy women, is the profile of transcripts altered in the eutopic endometrium of infertile women with endometriosis during the implantation window (IW)?

SUMMARY ANSWER

The eutopic endometrium of infertile women with endometriosis seems to be transcriptionally similar to the endometrium of infertile and fertile controls (FC) during the IW.

WHAT IS KNOWN ALREADY

Endometriosis is a disease related to infertility; nevertheless, little is known regarding the ethiopathogenic mechanisms underlying this association. Some studies evaluating the eutopic endometrium of endometriosis patients suggest there is an endometrial factor involved in the disease-related infertility. However, no study to date has evaluated the endometrial transcriptome (mRNA and miRNA) by next generation sequencing (NGS), comparing patients with endometriosis as the exclusive infertility factor (END) to infertile controls (IC; male and/or tubal factor) and FC.

STUDY DESIGN, SIZE, DURATION

From November 2011 to November 2015 we performed a case-control study, where 17 endometrial samples (six END, six IC, five FC) were collected during the IW.

PARTICIPANTS/MATERIALS, SETTING, METHODS

All endometrial samples had the RNA extracted. Two libraries were prepared for each one (mRNA and miRNA), which were sequenced, respectively, at HISEQ 2500 (RNA-Seq) and MiSeq System (miRNA-Seq), Illumina. The normalization and differential expression were conducted in statistical R environment using DESeq2 package. qPCR was used for data validation, which were analyzed by Kruskal–Wallis test and Dunn posttest (P &lt; 0.05).

MAIN RESULTS AND THE ROLE OF CHANCE

RNA-Seq revealed no differentially expressed genes (DEG) among END, IC and FC groups. miRNA-Seq revealed three differentially expressed miRNAs (has-27a-5p, has-miR-150-5p, has-miR-504-5p) in END group compared to FC group. However, none of the miRNAs identified in the sequencing was validated by qPCR.

LIMITATIONS, REASONS FOR CAUTION

The main limitation of this study was the small sample size evaluated as a result of the restrictive eligibility criteria adopted, limiting the generalization of the results obtained here. On the other hand, strict eligibility criteria, which eliminated factors potentially related to impaired endometrial receptivity, were required to increase the study’s internal validity.

WIDER IMPLICATIONS OF THE FINDINGS

This study brings new perspectives on the mechanisms involved in endometriosis-related infertility. The present findings suggest the eutopic endometrium of infertile women with endometriosis, without considering the disease’s stage, is transcriptionally similar to controls during the IW, possibly not affecting receptivity. Further studies are needed to evaluate endometrial alterations related to endometriosis’ stages.

STUDY FUNDING/COMPETING INTEREST(S)

This study received financial support from the Sao Paulo Research Foundation (FAPESP—Fundação de Amparo à Pesquisa do Estado de São Paulo; fellowship 2011/17614–6, MGB) and from the National Council for Scientific and Technological Development (CNPq—Conselho Nacional de Desenvolvimento Científico e Tecnológico; INCT—National Institutes of Hormones and Woman’s Health, grant 471 943/2012-6, 309 397/2016-2, PAN; fellowship 140 137/2015-7, MGB). The authors have no conflicts of interest.

TRIAL REGISTRATION NUMBER

N/A.

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

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.

Cross-disorder analysis of endometriosis and its comorbid diseases reveals shared genes and molecular pathways and proposes putative biomarkers of endometriosis

RESEARCH QUESTION

Women with endometriosis are considered to be at higher risk of several chronic diseases, such as autoimmune disorders, gynaecological cancers, asthma/atopic diseases and cardiovascular and inflammatory bowel diseases. Could the study of endometriosis-associated comorbidities help to identify potential biomarkers and target pathways of endometriosis?

DESIGN

A systematic review was performed to identify all possible endometriosis-associated comorbid conditions. Next, this list of disorders was coded into MeSH terms, and the gene expression profiles were downloaded from the Phenopedia database and subsequently analysed following a systems biology approach.

RESULTS

The results identified a group of 127 candidate genes that were recurrently expressed in endometriosis and its closest comorbidities and that were defined as 'endometriosis sibling disorders' (ESD). The enrichment analysis showed that these candidate genes are principally involved in immune and drug responses, hormone metabolism and cell proliferation, which are well-known hallmarks of endometriosis. The expression of ESD genes was then validated on independent sample cohorts (n = 207 samples), in which the involvement of 16 genes (AGTR1, BDNF, C3, CCL2, CD40, CYP17A1, ESR1, IGF1, IGF2, IL10, MMP1, MMP7, MMP9, PGR, SERPINE1 and TIMP2) in endometriosis was confirmed. Several of these genes harbour polymorphisms that associate to either endometriosis or its comorbid conditions.

CONCLUSIONS

The study results highlight the molecular processes underlying the aetiopathogenesis of endometriosis and its comorbid conditions, and identify putative endometriosis biomarkers.

Proteomic Biomarkers for the Detection of Endometrial Cancer

Endometrial cancer is the leading gynaecological malignancy in the western world and its incidence is rising in tandem with the global epidemic of obesity. Early diagnosis is key to improving survival, which at 5 years is less than 20% in advanced disease and over 90% in early-stage disease. As yet, there are no validated biological markers for its early detection. Advances in high-throughput technologies and machine learning techniques now offer unique and promising perspectives for biomarker discovery, especially through the integration of genomic, transcriptomic, proteomic, metabolomic and imaging data. Because the proteome closely mirrors the dynamic state of cells, tissues and organisms, proteomics has great potential to deliver clinically relevant biomarkers for cancer diagnosis. In this review, we present the current progress in endometrial cancer diagnostic biomarker discovery using proteomics. We describe the various mass spectrometry-based approaches and highlight the challenges inherent in biomarker discovery studies. We suggest novel strategies for endometrial cancer detection exploiting biologically important protein biomarkers and set the scene for future directions in endometrial cancer biomarker research.

MUC20 expression marks the receptive phase of the human endometrium

RESEARCH QUESTION

How does mucin MUC20 expression change during the menstrual cycle in different cell types of human endometrium?

DESIGN

Study involved examination of MUC20 expression in two previously published RNA-seq datasets in whole endometrial tissue (n = 10), sorted endometrial epithelial (n = 44) or stromal (n = 42) cell samples. RNA-Seq results were validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR) in whole tissue (n = 10), sorted epithelial (n = 17) and stromal (n = 17) cell samples. MUC20 protein localization and expression were analysed in human endometrium by immunohistochemical analysis of intact endometrial tissue (n = 6) and also Western blot of cultured stromal and epithelial cells (n = 2).

RESULTS

MUC20 is differentially expressed in the endometrium between the pre-receptive and receptive phases. We show that MUC20 is predominantly expressed by epithelial cells of the receptive endometrium, both at the mRNA (RNA-Seq, P = 0.005; qRT-PCR, P = 0.039) and protein levels (Western blot; immunohistochemistry, P = 0.029).

CONCLUSION

Our results indicate MUC20 as a novel marker of mid-secretory endometrial biology. We propose a model of MUC20 function in the hepatocyte growth factor (HGF)-activated mesenchymal-epithelial transition (MET) receptor signalling specifically in the receptive phase. Further investigations should reveal the precise function of MUC20 in human endometrium and the possible connection between MUC20 and HGF-activated MET receptor signalling. MUC20 could potentially be included in the list of endometrial receptivity markers after further clinical validation.