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

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 SAF201787526-R; Programa Operativo FEDER Andalucia (B-CTS-500-UGR18; A-CTS-614-UGR20); the Junta de Andalucia [BIO-302; and PAIDI P20_00158]; the University of Jaen [PAIUJA-EI_CTS02_2017]; the University of Granada, Plan Propio de Investigacion 2016, Excellence actions: Units of Excellence; Unit of Excellence on Exercise and Health (UCEES), and by the Junta de Andalucia, Consejeria de Conocimiento, Investigacio n 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).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 metaanalysed, 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.Spanish Government FPU15/01193European Commission RYC-2016-21199 ENDORE SAF201787526-RPrograma Operativo FEDER Andalucia B-CTS-500-UGR18 A-CTS-614-UGR20Junta de Andalucia BIO-302 PAIDI P20_00158University of Jaen PAIUJA-EI_CTS02_2017University of Granada, Plan Propio de Investigacion 2016, Excellence actions: Units of Excellence; Unit of Excellence on Exercise and Health (UCEES)Junta de AndaluciaEuropean Commission SOMM17/6107/UGREstonian Research Council PRG1076Horizon 2020 innovation (ERIN) of the European Commission EU952516Enterprise Estonia EU48695Margarita Salas program for the Requalification of the Spanish University system UJAR01M

Human endometrial cell-type-specific RNA sequencing provides new insights into the embryo–endometrium interplay

STUDY QUESTION: Which genes regulate receptivity in the epithelial and stromal cellular compartments of the human endometrium, and which molecules are interacting in the implantation process between the blastocyst and the endometrial cells? SUMMARY ANSWER: A set of receptivity-specific genes in the endometrial epithelial and stromal cells was identified, and the role of galectins (LGALS1 and LGALS3), integrin b1 (ITGB1), basigin (BSG) and osteopontin (SPP1) in embryo–endometrium dialogue among many other protein–protein interactions were highlighted. WHAT IS KNOWN ALREADY: The molecular dialogue taking place between the human embryo and the endometrium is poorly understood due to ethical and technical reasons, leaving human embryo implantation mostly uncharted. STUDY DESIGN, SIZE, DURATION: Paired pre-receptive and receptive phase endometrial tissue samples from 16 healthy women were used for RNA sequencing. Trophectoderm RNA sequences were from blastocysts. PARTICIPANTS/MATERIALS, SETTING, METHODS: Cell-type-specific RNA-seq analysis of freshly isolated endometrial epithelial and stromal cells using fluorescence-activated cell sorting (FACS) from 16 paired pre-receptive and receptive tissue samples was performed. Endometrial transcriptome data were further combined in silico with trophectodermal gene expression data from 466 single cells originating from 17 blastocysts to characterize the first steps of embryo implantation. We constructed a protein–protein interaction network between endometrial epithelial and embryonal trophectodermal cells, and between endometrial stromal and trophectodermal cells, thereby focusing on the very first phases of embryo implantation, and highlighting the molecules likely to be involved in the embryo apposition, attachment and invasion. MAIN RESULTS AND THE ROLE OF CHANCE: In total, 499 epithelial and 581 stromal genes were up-regulated in the receptive phase endometria when compared to pre-receptive samples. The constructed protein–protein interactions identified a complex network of 558 prioritized protein–protein interactions between trophectodermal, epithelial and stromal cells, which were grouped into clusters based on the function of the involved molecules. The role of galectins (LGALS1 and LGALS3), integrin b1 (ITGB1), basigin (BSG) and osteopontin (SPP1) in the embryo implantation process were highlighted. LARGE SCALE DATA: RNA-seq data are available at www.ncbi.nlm.nih.gov/geo under accession number GSE97929. LIMITATIONS, REASONS FOR CAUTION: Providing a static snap-shot of a dynamic process and the nature of prediction analysis is limited to the known interactions available in databases. Furthermore, the cell sorting technique used separated enriched epithelial cells and stromal cells but did not separate luminal from glandular epithelium. Also, the use of biopsies taken from non-pregnant women and using spare IVF embryos (due to ethical considerations) might miss some of the critical interactions characteristic of natural conception only. WIDER IMPLICATIONS OF THE FINDINGS: The findings of our study provide new insights into the molecular embryo–endometrium interplay in the first steps of implantation process in humans. Knowledge about the endometrial cell-type-specific molecules that coordinate successful implantation is vital for understanding human reproduction and the underlying causes of implantation failure and infertility. Our study results provide a useful resource for future reproductive research, allowing the exploration of unknown mechanisms of implantation. We envision that those studies will help to improve the understanding of the complex embryo implantation process, and hopefully generate new prognostic and diagnostic biomarkers and therapeutic approaches to target both infertility and fertility, in the form of new contraceptives.Estonian Research Council PRG1076Horizon 2020 innovation grant (ERIN) EU952516Enterprise Estonia EU48695EU-FP7 Marie Curie Industry-Academia Partnerships and Pathways (IAPP) EU324509Spanish GovernmentEuropean Commission RYC-2016-21199 ENDORE SAF2017-87526-R PID2021-127280OB-100Programa Operativo FEDER Andalucia B-CTS-500-UGR18 A-CTS-614-UGR20Junta de Andalucia PAIDI P20_00158Margarita Salas program for the Requalification of the Spanish University system UJAR01MSKnut & Alice Wallenberg Foundation KAW 2015.0096Swedish Research CouncilEuropean Commission 2012-2844Sigrid Juselius FoundationAcademy of FinlandSpanish Government PRE2018-08544

Cardiorespiratory fitness in children with overweight/obesity: Insights into the molecular mechanisms

Spanish Ministry of Economy and Competitiveness, Grant/Award Number: DEP2013--47540, DEP2016-79512--R and DEP2017--91544--EXP; Spanish Ministry of Economy, Industry and Competitiveness (MINECO); European Regional Development Fund (FEDER), Grant/Award Number: RYC--2016--21199 and ENDORE SAF2017--87526--R; Junta de Andalucia, Grant/Award Number: BIO--302 and US--1254251; University of Jaen, Grant/Award Number: PAIUJA--EI_CTS02; Spanish Ministry of Education, Culture and Sport, Grant/Award Number: FPU 16/02760; NIH, Grant/Award Number:UO1 TR002004; PERC Systems Biology Fund; Unit of Excellence on EXERNET Research Network on Exercise and Health in Special Populations; Alicia Koplowitz Foundation; Henning Och Johan Throne--Holsts Stiftelse Grant; University of Granada, Plan Propio de Investigacion 2016, Excellence actions: Units of Excellence; Unit of Excellence on Exercise and Health (UCEES); Junta de Andalucia, Consejeria de Conocimiento, Investigacion y Universidades and European Regional Development Fund (ERDF), Grant/Award Number: SOMM17/6107/UGR; European Regional Development Funds, Grant/Award Number: B--CTS-355--UGR18 and B--CTS--500--UGR18; Funding for open access charge: Universidad de Granada/CBUAObjectives: High cardiorespiratory fitness (CRF) levels reduce the risk of developing cardiovascular disease (CVD) during adulthood. However, little is known about the molecular mechanisms underlying the health benefits of high CRF levels at the early stage of life. This study aimed to analyze the whole-blood transcriptome profile of fit children with overweight/obesity (OW/OB) compared to unfit children with OW/OB. Design: 27 children with OW/OB (10.14 ± 1.3 years, 59% boys) from the ActiveBrains project were evaluated. VO2peak was assessed using a gas analyzer, and participants were categorized into fit or unfit according to the CVD risk-related cut-points. Whole-blood transcriptome profile (RNA sequencing) was analyzed. Differential gene expression analysis was performed using the limma R/Bioconductor software package (analyses adjusted by sex and maturational status), and pathways’ enrichment analysis was performed with DAVID. In addition, in silico validation data mining was performed using the PHENOPEDIA database. Results: 256 genes were differentially expressed in fit children with OW/OB compared to unfit children with OW/OB after adjusting by sex and maturational status (FDR < 0.05). Enriched pathway analysis identified gene pathways related to inflammation (eg, dopaminergic and GABAergic synapse pathways). Interestingly, in silico validation data mining detected a set of the differentially expressed genes to be related to CVD, metabolic syndrome, hypertension, inflammation, and asthma. Conclusion: The distinct pattern of whole-blood gene expression in fit children with OW/OB reveals genes and gene pathways that might play a role in reducing CVD risk factors later in life.Spanish Ministry of Economy and Competitiveness DEP2013-47540 DEP2016-79512-R DEP2017-91544-EXPSpanish Ministry of Economy, Industry and Competitiveness (MINECO)European Commission RYC-2016-21199ENDORE SAF2017-87526-RJunta de Andalucia BIO-302 US-1254251University of Jaen PAIUJA-EI_CTS02Spanish Ministry of Education, Culture and Sport FPU 16/02760United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA UO1 TR002004PERC Systems Biology FundUnit of Excellence on EXERNET Research Network on Exercise and Health in Special PopulationsAlicia Koplowitz FoundationHenning Och Johan Throne-Holsts Stiftelse GrantUniversity of GranadaUnit of Excellence on Exercise and Health (UCEES)Junta de Andalucia, Consejeria de Conocimiento, Investigacion y Universidades and European RegionalDevelopment Fund (ERDF) SOMM17/6107/UGR European Commission B-CTS-355-UGR18 B-CTS-500-UGR18Universidad de Granada/CBU

Compliance to the recommended use of folic acid supplements for women in Sweden is higher among those under treatment for infertility than among fertile controls and is also related to socioeconomic status and lifestyle

Background: Folate has been discussed in relation to fertility among women, but studies on women under treatment for infertility are lacking. Objective: The objective of this study was to investigate folic acid supplement use and folate status among women under treatment for infertility (hereafter infertile) and fertile women also in regard to socioeconomic and lifestyle factors. Design: Lifestyle and dietary habits, and use of dietary supplements were assessed using a questionnaire. Blood samples were obtained for analysis of folate status. 24-hour recall interviews were also performed. Results: Highly educated, employed and infertile women were most prone to using folic acid supplements. The infertile women had a significantly better folate status than the fertile women. Folate status did not correlate with socioeconomic or lifestyle factors. The infertile women were physically more active, smoked less and were employed. Our questionnaire data had only fair agreement with the data from 24-hour recalls, but the folate status data was clearly correlated to our questionnaire results. Conclusions: Infertile women were most prone to using folic acid supplements and had better folate status than the controls. High educational and employment status were found to be key factors for high compliance to the recommended use folic acid supplements.Peer reviewe

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-a, ADRB2, VEGF, HSP70, SOX, and GPX. Non-coding Ribonucleic acids (RNAs) regulated by sedentary behavior or physical activity were: miRNA-222, miRNA-146a, miRNA-16, miRNA-126, miR-320a, 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.Spanish Government DEP2013-47540 DEP2016-79512-R DEP2017-91544-EXPEuropean Commission RYC-2016-21199 ENDORE SAF2017-87526-R 09/UPB/19 45/UPB/20 27/UPB/21 SOMM17/6107/UGRSpanish Government B-CTS-355 UGR18United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA B-CTS-500-UGR18PERC Systems Biology FundHuawei TechnologiesEXERNET Research Network on Exercise and Health A-CTS-614-UGR20 FPU 16/02760 FPU19/05561UO1 TR002004Alicia Koplowitz FoundationUniversity of GranadaJunta de Andalucia, Consejeria de Conocimiento, Investigacion y Universidades and European RegionalDevelopment Fund (ERDF) DEP2005- 00046/ACTI Junta de Andalucia PAIDI P20_0015

A speculative outlook on embryonic aneuploidy : Can molecular pathways be involved?

The journey of embryonic development starts at oocyte fertilization, which triggers a complex cascade of events and cellular pathways that guide early embryogenesis. Recent technological advances have greatly expanded our knowledge of cleavage-stage embryo development, which is characterized by an increased rate of whole-chromosome losses and gains, mixoploidy, and atypical cleavage morphokinetics. Embryonic aneuploidy significantly contributes to implantation failure, spontaneous miscarriage, stillbirth or congenital birth defects in both natural and assisted human reproduction. Essentially, early embryo development is strongly determined by maternal factors. Owing to considerable limitations associated with human oocyte and embryo research, the use of animal models is inevitable. However, cellular and molecular mechanisms driving the error-prone early stages of development are still poorly described. In this review, we describe known events that lead to aneuploidy in mammalian oocytes and preimplantation embryos. As the processes of oocyte and embryo development are rigorously regulated by multiple signal-transduction pathways, we explore the putative role of signaling pathways in genomic integrity maintenance. Based on the existing evidence from human and animal data, we investigate whether critical early developmental pathways, like Wnt, Hippo and MAPK, together with distinct DNA damage response and DNA repair pathways can be associated with embryo genomic instability, a question that has, so far, remained largely unexplored.Peer reviewe

Assessing the testicular sperm microbiome: a low-biomass site with abundant contamination

We thank all men who generously donated testicular material for the purpose of this study. We also acknowledge the research support by Copan Italia S.p.A Inc., and Clearblue, SPD Swiss Precision Diagnostics GmbH. This study is part of a PhD Thesis conducted at the Official Doctoral Program in Biomedicine of the University of Granada, Spain. This work was supported by the Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and European Regional Development Fund (FEDER): grant numbers RYC-2016-21199 and ENDORE (SAF2017-87526-R); by FEDER/Junta de Andalucia-Consejeria de Economia y Conocimiento: MENDO (B-CTS-500-UGR18); by Junta de Andalucia: (PAIDI P20_00158) by the University of Granada, Plan Propio de Investigacion 2016, Excellence actions: Units of Excellence; Unit of Excellence on Exercise and Health (UCEES), and the Junta de Andalucia, Consejeria de Conocimiento, Investigacion y Universidades and European Regional Development Fund: (SOMM17/6107/UGR); by Spanish Ministry of Science, Innovation, and Universities: (PRE2018085440 and FPU19/01638); and by Spanish Ministry of Education, Culture, and Sport: (FPU15/01193). Funding for open access charge: Universidad de Granada/CBUA Sequence data of all testicular spermatozoa and negative control samples have been deposited in the National Centre for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (http://www.ncbi.nlm.nih.gov/sra) under the BioProject ID PRJNA643898. The preliminary results of this study were presented as a poster communication at the 35th Annual ESHRE Meeting (Vienna, 2019).Research question: The semen harbours a diverse range of microorganisms. The origin of the seminal microbes, however, has not yet been established. Do testicular spermatozoa harbour microbes and could they potentially contribute to the seminal microbiome composition? Design: The study included 24 samples, comprising a total of 307 testicular maturing spermatozoa. A high-throughput sequencing method targeting V3 and V4 regions of 16S rRNA gene was applied. A series of negative controls together with stringent in-silico decontamination methods were analysed. Results: Between 50 and 70% of all the detected bacterial reads accounted for contamination in the testicular sperm samples. After stringent decontamination, Blautia (P = 0.04), Cellulosibacter (P = 0.02), Clostridium XIVa (P = 0.01), Clostridium XIVb (P = 0.04), Clostridium XVIII (P = 0.02), Collinsella (P = 0.005), Prevotella (P = 0.04), Prolixibacter (P = 0.02), Robinsoniella (P = 0.04), and Wandonia (P = 0.04) genera demonstrated statistically significant abundance among immature spermatozoa. Conclusions: Our results indicate that the human testicle harbours potential bacterial signature, though in a low-biomass, and could contribute to the seminal microbiome composition. Further, applying stringent decontamination methods is crucial for analysing microbiome in low-biomass site.Copan Italia S.p.A Inc.ClearblueSPD Swiss Precision Diagnostics GmbHSpanish GovernmentEuropean Commission RYC-2016-21199 SAF2017-87526-RFEDER/Junta de Andalucia-Consejeria de Economia y Conocimiento: MENDO B-CTS-500-UGR18 Junta de Andalucia PAIDI P20_00158University of Granada, Plan Propio de Investigacion 2016, Excellence actions: Units of ExcellenceUnit of Excellence on Exercise and Health (UCEES)Junta de Andalucia Consejeria de Conocimiento, Investigacion y UniversidadesEuropean Commission SOMM17/6107/UGRSpanish Government PRE2018085440 FPU19/01638 FPU15/01193Universidad de Granada/CBUA Sequence BioProject PRJNA64389

Maternal Pre-Pregnancy Obesity Is Associated with Altered Placental Transcriptome

<p><b>(A)</b> Principal component analysis (PCA) of term placental gene expression profiles in obese (Ob_ N°) and normal weight women (N_N°). <b>(B)</b> Cluster analysis of dysregulated genes in term placentas from obese (Ob_ N°) <i>vs</i>. normal weight women (N_N°). Red represents genes with high expression levels and green represents genes with low expression levels.</p

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

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