Endometrial polyps (EPs) are benign overgrowths of the endometrium causing abnormal uterine bleeding and infertility. Despite their clinical significance, the molecular mechanisms underlying their development and recurrence remain poorly understood, warranting comprehensive transcriptomic investigation. We hypothesized that transcriptomic differences, particularly at the single-cell level as revealed through cellular trajectory analysis, distinguish EPs from adjacent endometrium. To investigate this, paired EP and adjacent endometrium (adEN) samples were collected from 12 women undergoing hysteroscopic polypectomy (proliferative phase, n = 9; secretory phase, n = 3) and analyzed using bulk and single-cell RNA sequencing (scRNA-seq). Bulk RNA-seq revealed high transcriptional similarity between EPs and adENs, with only a few differentially expressed genes (FDR < 0.05) in proliferative-phase EPs, including upregulation of KMT2B and DLEC1 and downregulation of COL9A1 and RAB3C, potentially reflecting epigenetic regulation and protective mechanisms against tumorigenesis. scRNA-seq identified eight major cell clusters namely stromal, epithelial, endothelial, immune, perivascular, macrophage, B cell, and ciliated populations in both tissues. Pseudotime analysis revealed a mid-transcriptional arrest and enrichment of MECOM/EYA2-positive intermediate epithelial states in EPs, in contrast to the late, mature epithelial stage seen in the adENs. This aberrant epithelial maturation may be associated with impaired perivascular and endothelial differentiation, potentially contributing to defective vascular remodeling and polyp persistence. In conclusion, while EPs exhibit global transcriptomic similarity to adENs, single-cell and pseudotime analyses suggest subtle but significant disruptions in epithelial differentiation and vascular remodeling that might be involved in EPs development. Study limitations include scRNA-seq restricted to the proliferative phase, which may limit generalizability. Nevertheless, future functional studies using primary epithelial organoids derived from EPs may provide a physiologically relevant model to evaluate targeted therapeutic strategies including hormonal interventions with potential applications in infertility management.

The use of semaglutide (SE), a glucagon-like peptide-1 receptor agonist (GLP-1RA) with glucose-lowering and weight-loss effects, has risen rapidly, particularly among women of reproductive age. While preclinical studies suggest benefits for ovarian function via the hypothalamic-pituitary-ovarian axis, its impact on the endometrial-embryo interface remains unclear. Here, we show that GLP-1R is dynamically expressed in human endometrium, restricted to epithelial cells and markedly upregulated during the mid-secretory phase of the menstrual cycle. SE activated intracellular cAMP signalling and enhanced epithelial metabolism, driving a shift toward oxidative phosphorylation. Notably, even in the absence of steroid hormone priming, the highest SE concentration upregulates several endometrial receptivity markers, whereas under hormonal priming, the same concentration modestly reduces expression of a key receptivity marker, PAEP/glycodelin. By contrast, in stromal cells lacking detectable GLP-1R, SE disrupts decidualization, induces endoplasmic reticulum stress and suppresses cell-cycle at G2/M phase. Human embryo models, blastoids, expressed GLP-1R and underwent concordant SE-mediated transcriptional remodeling in epiblast and trophectoderm lineages, encompassing changes in metabolism and epigenetic regulation, but without shifts in lineage proportions. Notably, SE restored blastoid attachment under hormone-deprived conditions at all tested concentrations, but did not further enhance attachment when physiological hormonal priming was already present. Together, these findings reveal a compartment-specific mismatch, as SE augments epithelial and embryonic metabolic activity but compromises stromal support for implantation, with potential consequences for implantation due to stromal dysfunction. ### Competing Interest Statement The authors have declared no competing interest. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Endometrial biopsies of healthy fertile women were collected in South Estonian Hospital (Voru, Estonia) under ethical permissions No. 330/M-8 (16.10.2020) and No. 364/M-9 (16.05.2022) issued by the Research Ethics Committee of the University of Tartu. Ethical permits (454/02 and 2011/745/31-3) issued by Stockholm Region Ethical Review Authority allowed the use of embryonic stem cells to investigate human reproduction and blastoid generation. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors. Estonian Research Council, PSG1082, PRG1076 Novo Nordisk Foundation, NNF24OC0092384 Swedish Research Council, 2024-02530

INTRODUCTION:Cesarean section (CS) is the most common gynecological surgery globally, with rates increasing in many developed countries. In Estonia, the CS rate rose from 6.4% in 1992 to 20.6% in 2021. While CS can be lifesaving when medically necessary, its rising use without clear medical indication does not have benefits for the mother but is associated with a broad spectrum of long-term complications, including uterine rupture, abnormal placentation, ectopic pregnancy, abnormal uterine bleeding, and chronic pelvic pain. The Estonian Biobank (EstBB) is a population-based biobank that links genetic data with health records from national registries. Between 2007 and 2023, over 200 000 individuals were recruited, providing a valuable dataset for health and genetics research. This study examines maternal health conditions occurring both before and after childbirth, including short- and long-term outcomes associated with CS and vaginal delivery (VD). MATERIAL AND METHODS:We analyzed EstBB health data using International Statistical Classification of Diseases and Related Health Problems, 10th revision (ICD-10) codes to compare short- and long-term maternal health conditions occurring before and after childbirth between women with one or more VD (ICD-10 O80, n = 30 898) and women with one or more CS (ICD-10 O82, n = 8285). Women with a history of both VD and CS were excluded. Logistic regression assessed associations between delivery mode and health conditions, adjusting for maternal birth year and body mass index. RESULTS:As expected, the CS group had higher rates of comorbidities and pregnancy complications like gestational diabetes, hypertensive disorders, mental health issues, and possible postsurgical morbidities such as infections, incisional hernia, and chronic pain. In the VD group, conditions like perineal trauma, pelvic organ prolapse, and stress urinary incontinence were more prevalent. Interestingly, cervical inflammatory conditions and cervical dysplasia were also more common in the VD group. CONCLUSION:CS is related to more complications and health problems compared with VD, but the relationship may not be causative. CS risks should be weighed against clinical indications for its use. It is important for healthcare providers to recognize and openly discuss both the immediate and long-term risks associated with the procedure with women requiring or considering CS.

The genetic background of many female reproductive health diagnoses remains uncharacterized, compromising our understanding of the underlying biology. Here, we map the genetic architecture across 42 female-specific health conditions using data from up to 293,618 women from two large population-based cohorts, the Estonian Biobank and the FinnGen study. Our study illustrates the utility of genetic analyses in understanding women's health better. As specific examples, we describe genetic risk factors for ovarian cysts that elucidate the genetic determinants of folliculogenesis and, by leveraging population-specific variants, uncover new candidate genes for uterine fibroids. We find that most female reproductive health diagnoses have a heritable component, with varying degrees of polygenicity and discoverability. Finally, we identify pleiotropic loci and genes that function in genital tract development (WNT4, PAX8, WT1, SALL1), hormonal regulation (FSHB, GREB1, BMPR1B, SYNE1/ESR1) and folliculogenesis (CHEK2), underlining their integral roles in female reproductive health.

What is the expression dynamic of glucagon-like peptide-1 receptor (GLP-1R) in human endometrium, and how does GLP-1R agonist (GLP-1RA-semaglutide) influence endometrial maturation and embryo development? GLP-1R was predominantly expressed during the mid-secretory phase. Semaglutide induced dynamic, dose-dependent transcriptomic changes in endometrial epithelial organoids (EEOs), primary stromal cells (ESCs), and blastoids. Semaglutide, a GLP-1RA, has proven effective in improving glycaemic control and is an emerging therapeutic option for type 2 diabetes, obesity and polycystic ovarian syndrome (PCOS). Based on preclinical studies, GLP-1RA therapy has shown the potential to alleviate female infertility, primarily by restoring ovulation. However, the expression landscape of GLP-1R in the endometrium and embryo, as well as the effects of GLP-1RA therapy on embryo development, remain largely unknown. Investigating the impact of GLP-1RA on in vitro modern endometrial models and embryo-like blastoids could provide valuable insights into its potential influence on endometrial receptivity and implantation. GLP-1R expression was determined in endometrial tissues from fertile women across menstrual cycle phases (n = 20). Paired primary ESCs and EEOs were derived from endometrial biopsies (n = 4) from fertile women and were hormonally stimulated with oestradiol (E2), progesterone (P) and Cyclic adenosine monophosphate (cAMP) to achieve receptive status (6 days) and decidualization (9 days) in parallel with and without semaglutide treatment. The H9 cell line was used for blastoid generation. The expression of GLP-1R in endometrium was determined by immunohistochemistry. ESCs and EEOs were exposed to semaglutide according to pharmacokinetics (39 nM, 1.25 μM and 5 μM) and evaluated with resazurin assay for cell viability. Semaglutide-treated endometrial cells were subjected to a cAMP biosensor assay. The decidualization of ESC cells was assessed by prolactin ELISA assay from spent culture media. RNA from ESCs, EEO and blastoid was subjected to library preparation and sequencing using NextSeq1000. GLP1R was expressed in the human endometrium throughout the menstrual cycle, with the highest expression in the mid-secretory phase. We observed a significant (P < 0.05) dose-dependent decrease in the metabolic capacity of viable ESCs in response to increasing semaglutide concentration whereas in EEOs, cell viability was significantly reduced after exposure to 5μM. ESCs and EEOs (treated with E2 and E2P) showed dose-dependent cAMP production, significantly increasing at 5μM exposure (P < 0.05). In ESCs, the decidualization was confirmed by prolactin assay, and in EEO, the endometrial receptivity-associated genes were upregulated in the transcriptome profile (PAEP, LIF, SPP1). Treatment with 39 nM semaglutide did not affect the transcriptome of the endometrial cells, while 1.25 μM had 10 DEGs. Treatment with 5 μM semaglutide significantly altered the transcriptomes of EEOs and ESCs (adjusted P < 0.05). In EEOs, over 400 DEGs were identified, mainly linked to metabolic processes, mitochondrial function, and endometrial receptivity. In ESCs, semaglutide primarily affected cell cycle-related genes, notably downregulating cell proliferation (adjusted P < 0.05). The blastoid transcriptome in all concentrations revealed upregulation of genes associated with regulation of pluripotent stem cells and endoderm differentiation (EPAS1, PBX1, TDGF1, PRDM14, SOX2) while it downregulated metabolic processes. This in vitro study provides important insights into the impact of semaglutide on underlying mechanisms of endometrial maturation and embryo development. Further evaluation of the semaglutide effect in obese and PCOS women is required for translational relevance. The study does not claim clinical safety and efficacy for therapeutic use. The study underscores the fundamental mechanistic effects of semaglutide on EEOs, ESCs, and blastoids which could be used to explore its impact on female fertility mediating endometrium-embryo interactions. On confirming the safety of GLP-1RAs and lack of teratogenic potential, its use could revolutionize the personalized treatment of female infertility. No

STUDY QUESTION Does the molecular composition of uterine fluid extracellular vesicles (UF-EVs) reflect endometrial tissue changes across the menstrual cycle? SUMMARY ANSWER Concordance between endometrial tissue and UF-EVs exists on miRNA and mRNA levels along the menstrual cycle phases and UF-EV surface proteomic signatures suggest EVs originate from several major endometrial cell populations. WHAT IS KNOWN ALREADY The clinical value of endometrial receptivity testing is restricted by invasiveness and the use of only one omics level of input. There is promising evidence that UF-EVs can reflect changes in mid-secretory endometrium, highlighting the potential to establish endometrial receptivity testing right before embryo transfer. However, the dynamic changes of UF-EVs molecular cargo have not been directly compared to endometrial tissue on multiple omics levels. STUDY DESIGN, SIZE, DURATION This cross-sectional study included fertile women from four menstrual cycle phases: proliferative and early-, mid-, and late-secretory phases. In total, 26 paired samples of UF and endometrial tissue were collected. mRNA and miRNA were sequenced, and differential analysis was performed on consecutive phases. UF-EVs were profiled for various protein surface markers associated with different cell types. EVs from epithelial endometrial organoid-conditioned culture media were used as a reference of pure epithelial endometrial EVs. PARTICIPANTS/MATERIALS, SETTING, METHODS Paired UF and endometrial tissue samples were collected from 26 fertile, reproductive-age women. EV isolation from UF was validated using electron microscopy and western blotting, and particle numbers were measured by nanoparticle tracking analysis. The transcriptome and miRNome of UF-EVs and endometrial tissue were sequenced, and differential expression analysis was conducted on consecutive phases of the menstrual cycle. Bead-based EV flow cytometry targeting 37 surface protein markers was used to characterize EVs from UF and endometrial organoids. MAIN RESULTS AND THE ROLE OF CHANCE Surface proteome analysis revealed that UF-EVs from the mid-secretory phase had significantly increased expression of natural killer cell marker CD56 (P < 0.005), pan-leukocyte marker CD45 (P < 0.005), pan-T-cell marker CD3 (P < 0.005), and coagulation-related protein CD142 (P < 0.005) compared to those from the proliferative phase, whereas markers associated with endometrial epithelial cells (CD29, CD133, and CD326) did not significantly change across the menstrual cycle. Transcriptomic analysis highlighted differential expression of histone and metallothionein genes that correlated between paired UF-EVs and endometrial tissues in each tested menstrual cycle phase. Principal component analysis of miRNomes of paired UF-EVs and endometrial tissue samples resulted in similar clustering patterns, where mid- and late-secretory samples clustered closely, and proliferative and early-secretory phase samples clustered separately. Half of the differentially expressed miRNAs in each phase in UF-EVs were also differentially expressed in the endometrium. Importantly, nine mid-secretory phase UF-EV DE miRNAs were identified, five of which were common between UF-EVs and endometrial biopsies, including hsa-miR-30d-5p and hsa-miR-200b-3p, both of which were previously implicated in implantation. Notably, three of the nine miRNAs, hsa-miR-200b-3p, hsa-miR-141-3p, and hsa-miR-200a-3p, were predicted to regulate mRNAs in the endometrial tissue and the pre-implantation embryo trophectoderm. LARGE SCALE DATA N/A LIMITATIONS, REASONS FOR CAUTION The clinical dating of the menstrual cycle phase is based on the first day of menstruation and the time of the LH peak, which does not exclude the possibility that the expected endometrial phase was not reached. The wider limitation of our study is the lack of standardized procedures for collecting UF samples in gynaecological practice, which could challenge the replication of our findings. WIDER IMPLICATIONS OF THE FINDINGS Evidence that UF-EVs reflect endometrial phases of menstrual cycle supports the use of UF-EVs in endometrial receptivity testing. Additionally, further studies of UF-EVs in endometrial pathologies could be beneficial for diagnostics, considering that more invasive tissue biopsies only reflect the biopsy site and not the full endometrium. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by the European Regional Development Fund Enterprise Estonia's Applied Research Program under the grant agreement number 2014-2020.4.02.21-0398 (EVREM), the Estonian Research Council (grant nos. PRG1076 and PSG1082), the Horizon Europe NESTOR grant (grant no. 101120075) of the European Commission, the Swedish Research Council (grant no. 2024-02530), the Novo Nordisk Fonden (grant no. NNF24OC0092384), and the National Recovery and Resilience Plan of the Republic of Bulgaria, project number BG-RRP-2.004-0001-C01. A.S.L. received funding from the Becas Fundacion Ramon Areces para Estudios Postdoctorales. All the authors declare no conflict of interest.

STUDY QUESTION Can a large-scale genome-wide association study (GWAS) meta-analysis identify genomic risk loci and likely involved genes for female genital tract (FGT) polyps, provide insights into the biological mechanism underlying their development, and inform of potential overlap with other traits, including endometrial cancer? SUMMARY ANSWER GWAS meta-analysis of FGT polyps highlights potentially shared mechanisms between polyp development and cancerous processes. WHAT IS KNOWN ALREADY Small-scale candidate gene studies have focused on biological processes such as oestrogen stimulation and inflammation to clarify the biology behind FGT polyps. However, the exact mechanism for the development of polyps is still elusive. At the same time, a genome-wide approach, which has become the gold standard in complex disease genetics, has never been used to uncover the genetics of the FGT polyps. STUDY DESIGN, SIZE, DURATION We performed a GWAS meta-analysis including a total of 36 984 women with FGT polyps (International Classification of Diseases (ICD-10) diagnosis code N84) and 420 993 female controls (without N84 code) of European ancestry from the FinnGen study (11 092 cases and 94 394 controls), Estonian Biobank (EstBB, 14 008 cases and 112 799 controls), and the Pan-UKBB study (11 884 cases and 213 800 controls). PARTICIPANTS/MATERIALS, SETTING, METHODS GWAS meta-analysis and functional annotation of GWAS signals were performed to identify genetic risk loci and prioritize genes in associated loci. To explore associations with other traits, we performed a look-up of associated variants across multiple traits and health conditions, genetic correlation analysis, and phenome-wide association study (PheWAS) with ICD-10 diagnosis codes. MAIN RESULTS AND THE ROLE OF CHANCE Our GWAS meta-analysis revealed 16 significant (P < 5 x 10-8) genomic risk loci. Based on exonic variants in GWAS signals, we prioritized EEFSEC, ODF3, PRIM1, PLCE1, LRRC34/MYNN, EXO1, and CHEK2 which are involved in DNA repair, cell proliferation, and cell growth. Several of the identified genomic loci have previously been linked to endometrial cancer and/or uterine fibroids, highlighting the potentially shared mechanisms underlying tissue overgrowth and cancerous processes. Genetic correlation analysis revealed a positive correlation with body mass index and reproductive traits, that can be classified as symptoms or risk factors of endometrial polyps (EPs), whereas a negative correlation was observed between FGT polyps and both menopause (genetic correlation estimate (rg) = -0.29, SE = 0.08, P = 8.8x10-4) and sex hormone-binding globulin (SHBG) (rg = -0.22, SE = 0.04, P = 2.4x10-8). On the phenotypic level, the strongest associations were observed with endometriosis, uterine fibroids, and excessive, frequent, and irregular menstruation. LARGE SCALE DATA The complete GWAS summary statistics will be made available after publication through the GWAS Catalog (https://www.ebi.ac.uk/gwas/). LIMITATIONS, REASONS FOR CAUTION In this study, we focused broadly on FGT polyps and did not differentiate between the polyp subtypes. Considering the prevalence of FGT polyp subtypes, we assumed that most women included in the study had EPs. Further research on the expression profile of FGT polyps could complement the GWAS study to substantiate the functional importance of the identified variants. WIDER IMPLICATIONS OF THE FINDINGS The study findings have the potential to significantly enhance our understanding of the genetic mechanisms involved, paving the way for future functional follow-up, which in turn could improve the diagnosis, risk assessment, and targeted treatment options, since surgery is the only line of treatment available for diagnosed polyps. STUDY FUNDING/COMPETING INTEREST(S) This study was funded by European Union through the European Regional Development Fund Project No. 2014-2020.4.01.15-0012 GENTRANSMED. Computations were performed in the High-Performance Computing Center of the University of Tartu. The study was also supported by the Estonian Research Council (grant no. PRG1076 and MOBJD1056) and Horizon 2020 innovation grant (ERIN, grant no. EU952516). All the authors declared no conflict of interest.

Endometrial polyps (EPs) are localized overgrowths of endometrial glands and stroma, common in reproductive-age and postmenopausal women, and can cause abnormal uterine bleeding and infertility. Here, we investigated the cellular heterogeneity and molecular mechanisms of EPs by integrating bulk and single-cell RNA sequencing (scRNA-seq) of EPs and adjacent endometrial tissues (adENs) from 12 women. Bulk RNA-seq revealed high transcriptional similarity, with few differentially expressed genes including upregulated KMT2B and DLEC1 and downregulated COL9A1 and RAB3C . ScRNA-seq identified eight major cell clusters, such as stromal, epithelial, endothelial, immune, perivascular, macrophage, B, and ciliated cells. Pseudotime analysis showed aberrant stromal-to-epithelial transitions in EPs, marked by MECOM and EYA2 intermediate clusters, indicating incomplete epithelial maturation. These altered differentiation trajectories may disrupt perivascular and endothelial cell development, contributing to abnormal vascular remodeling in EPs, despite minimal overall transcriptomic changes compared with adENs. ### Competing Interest Statement The authors have declared no competing interest. Estonian Research Council, https://ror.org/00jjeja18, PRG1076, PSG1082 Horizon Europe, NESTOR -101120075 Swedish Research Council, https://ror.org/03zttf063, 2024-02530 Novo Nordisk Fonden, NNF24OC0092384

BackgroundEndometriosis is characterized by the ectopic growth of endometrial-like cells, causing chronic pelvic pain, adhesions and impaired fertility in women of reproductive age. Usually, these lesions grow in the peritoneal cavity in a hypoxic environment. Hypoxia is known to affect gene expression and protein kinase (PK) activity. We aimed to explore the changes in the transcriptome and PK activity characteristic of eutopic and ectopic endometrium in endometriosis under hypoxia.MethodsEutopic (EuESCs) and ectopic (EcESCs) endometrial stromal cells were exposed to hypoxia (1% O2) or normoxia (20% O2) for 48 hours. We assessed PK activity and examined transcriptome using mRNA-seq in cells cultured under hypoxic or normoxic conditions. Enzyme-linked immunosorbent assay, quantitative reverse transcription-PCR and immunohistochemistry were performed for the downstream analysis of Transforming Growth Factor Beta Induced (TGFBI) expression.ResultsThe kinase assay revealed a minor decrease in cAMP-dependent PK (PKAc) and Akt activity and a trend towards an increase in Rho-dependent PK (ROCK) activity in response to exposure to hypoxic conditions in EcESCs. A wider examination of the hypoxia-mediated changes in transcriptomes of cultured cells revealed that the genes related to aerobic glycolysis and cellular metabolism were upregulated in EuESCs exposed to hypoxia. In contrast, EcESCs had a single differentially expressed gene (TGFBI) upregulated under hypoxic conditions. This gene was also found to be overexpressed in EuESCs exposed to hypoxia vs normoxia, and in EcESCs vs EuESCs in normoxia. The level of secreted TGFBI in the spent culture media was accordingly high in the EcESC cultures and in the EuESC culture exposed to hypoxia. In the eutopic endometrial tissue biopsies, TGFBI mRNA and protein expression depended on the menstrual cycle phase, with higher levels observed in the proliferative phase. TGFBI staining showed the protein localized to the stroma and around the blood vessels. In the secretory phase, TGFBI protein expression was stronger in ectopic endometrium compared to paired eutopic endometrium.ConclusionsWithin this study, we showed hypoxia-mediated transcriptome changes characteristic of EuESCs and EcESCs and identified TGFBI as a potential therapeutic target for endometriosis due to its role in fibrosis and angiogenesis.

Endometriosis is a chronic hormone-dependent disease characterized by the spread of endometrial cells outside the uterus, which form endometriotic lesions and disrupt the functions of the affected organs. The etiopathogenesis of endometriosis is still unclear, and thus it is important to examine the genes that may contribute to the establishment of endometriotic lesions. The aim of this study was to investigate the expression of new potential candidate gene latexin (LXN), an inhibitor of carboxypeptidases, in endometrium and endometriotic lesions to elucidate its possible role in endometriosis development. LXN expression in tissues was assessed using quantitative reverse transcription PCR (qRT–PCR) analysis and immunohistochemical staining (IHC). The functions of LXN were examined using Transwell and MTT assays. qRT–PCR analysis revealed that LXN expression in endometrium was menstrual cycle-dependent, being lowest in the early-secretory phase and highest in the late-secretory phase and was significantly upregulated in endometriotic lesions. IHC confirmed LXN expression in endometrial stromal cells, and in vitro assays demonstrated that knockdown of LXN effectively reduced the migratory capacity of endometrial stromal cells while promoting cell viability. In conclusion, our results showed that LXN can be involved in the pathogenesis of endometriosis by regulating the proliferation and migration activity of endometriotic stromal cells.

Current therapeutics of endometriosis focus on hormonal disruption of endometriotic lesions (ectopic endometrium, EcE). Recent findings show higher glycolysis utilization in EcE, suggesting non-hormonal strategy for disease treatment that addresses cellular metabolism. Identifying metabolically altered cell types in EcE is important for targeted metabolic drug therapy without affecting eutopic endometrium (EuE). Here, using single-cell RNA-sequencing, we examine twelve metabolic pathways in paired samples of EuE and EcE from women with confirmed endometriosis. We detect nine major cell types in both EuE and EcE. Metabolic pathways are most differentially regulated in perivascular, stromal, and endothelial cells, with the highest changes in AMPK signaling, HIF-1 signaling, glutathione metabolism, oxidative phosphorylation, and glycolysis. We identify transcriptomic co-activation of glycolytic and oxidative metabolism in perivascular and stromal cells of EcE, indicating a critical role of metabolic reprogramming in maintaining endometriotic lesion growth. Perivascular cells, involved in endometrial stroma repair and angiogenesis, may be potential targets for non-hormonal treatment of endometriosis.

STUDY QUESTION What changes occur in the endometrium during aging, and do they impact fertility? SUMMARY ANSWER Both the transcriptome and cellular composition of endometrial samples from women of advanced maternal age (AMA) are significantly different from that of samples from young women, suggesting specific changes in epithelial cells that may affect endometrial receptivity. WHAT IS KNOWN ALREADY Aging is associated with the accumulation of senescent cells in aging tissues. Reproductive aging is mostly attributed to the decline in ovarian reserve and oocyte quality, whereas the endometrium is a unique complex tissue that is monthly renewed under hormonal regulation. Several clinical studies have reported lower implantation and pregnancy rates in oocyte recipients of AMA during IVF. Molecular studies have indicated the presence of specific mutations within the epithelial cells of AMA endometrium, along with altered gene expression of bulk endometrial tissue. STUDY DESIGN, SIZE, DURATION Endometrial transcriptome profiling was performed for 44 women undergoing HRT during the assessment of endometrial receptivity before IVF. Patients younger than 28 years were considered as the young maternal age (YMA) group (age 23-27 years) and women older than 45 years were considered as the AMA group (age 47-50 years). Endometrial biopsies were obtained on Day 5 of progesterone treatment and RNA was extracted. All endometrial samples were evaluated as being receptive based on the expression of 68 common endometrial receptivity markers. Endometrial samples from another 24 women classified into four age groups (YMA, intermediate age group 1 (IMA1, age 29-35), intermediate age group 2 (IMA2, age 36-44), and AMA) were obtained in the mid-secretory stage of a natural cycle (NC) and used for validation studies across the reproductive lifespan. PARTICIPANTS/MATERIALS, SETTING, METHODS A total of 24 HRT samples (12 YMA and 12 AMA) were subject to RNA sequencing (RNA-seq) and differential gene expression analysis, 20 samples (10 YMA and 10 AMA) were used for qPCR validation, and 24 NC samples (6 YMA, 6 IMA1, 6 IMA2 and 6AMA) were used for RNA-seq validation of AMA genes across the woman's reproductive lifespan. Immunohistochemistry (IHC) was used to confirm some expression changes at the protein level. Computational deconvolution using six endometrial cell type-specific transcriptomic profiles was conducted to compare the cellular composition between the groups. MAIN RESULTS AND THE ROLE OF CHANCE Comparisons between YMA and AMA samples identified a lower proportion of receptive endometria in the AMA group (P = 0.007). Gene expression profiling identified 491 differentially expressed age-sensitive genes (P adj < 0.05) that revealed the effects of age on endometrial epithelial growth and receptivity, likely contributing to decreased reproductive performance. Our results indicate that changes in the expression of the cellular senescence marker p16INK4a and genes associated with metabolism, inflammation, and hormone response are involved in endometrial aging. Importantly, we demonstrate that the proportion of multi-ciliated cells, as discovered based on RNA-seq data deconvolution and tissue IHC results, is affected by endometrial aging, and propose a putative onset of age-related changes. Furthermore, we propose that aging has an impact on the transcriptomic profile of endometrial tissue in the context of endometrial receptivity. LARGE SCALE DATA The raw sequencing data reported in this article are deposited at the Gene Expression Omnibus under accession code GSE236128. LIMITATIONS, REASONS FOR CAUTION This retrospective study identified changes in the endometrium of patients undergoing hormonal replacement and validated these changes using samples obtained during a NC. However, future studies must clarify the importance of these findings on the clinical outcomes of assisted reproduction. WIDER IMPLICATIONS OF THE FINDINGS The findings reported in this study have important implications for devising future strategies aimed at improving fertility management in women of advanced reproductive age. STUDY FUNDING/COMPETING INTEREST(S) This research was funded by the Estonian Research Council (grant no. PRG1076), Horizon 2020 innovation grant (ERIN, grant no. EU952516), Enterprise Estonia (grant no. EU48695), MSCA-RISE-2020 project TRENDO (grant no. 101008193), EU 874867 project HUTER, the Horizon Europe NESTOR grant (grant no. 101120075) of the European Commission, the EVA specialty program (grant no. KP111513) of the Maastricht University Medical Center (MUMC+), MICIU/AEI/10.13039/501100011033 and FEDER, EU projects Endo-Map (grant no. PID2021-12728OB-100), ROSY (grant no. CNS2022-135999), and the National Science Fund of Bulgaria (grant no. KII-06 H31/2). The authors declare no competing interests.

Abstract Study question Are slow-freezing and vitrification suitable methods for cryopreserving endometrial biopsies intended for downstream research applications and organoid formation? Summary answer Both slow-frozen and vitrified endometrial biopsies resulted in successful organoid formation thus can be considered similar to fresh endometrial biopsies in preserving the cellular viability. What is known already Passive slow freezing (PSF) protocols have demonstrated efficacy for cryopreserving endometrial biopsies with subsequently viable isolated epithelial and stromal cells. Additionally, single-cell transcriptomic analyses and successful generation of endometrial organoids suggest a little impact of cryopreservation. By avoiding ice crystal formation, vitrification (VT) could potentially prevent mechanical injury and improve tissue integrity compared to slow freezing. Study design, size, duration Experimental study using endometrial biopsies collected using a Pipelle from eight healthy volunteers. Samples were retrieved at three cycle phases: proliferative (n = 2), mid-secretory (7 days post-LH surge, LH + 7, n = 2) and late-secretory phase (LH + 11, n = 4). Each biopsy was divided into fresh, slow-freezing and vitrification sub-samples for further comparison of outcomes according to microscopic histological analysis, transmission electron microscopy (TEM), gene expression profiling evaluation and generation of endometrial epithelial organoids (from 2 slow-frozen and 2 vitrified samples). Participants/materials, setting, methods PSF was performed using Mr Frosty with samples embedded in 1x DMEM, 30% FBS and 7.5% DMSO at -80ºC. Vitrification was performed using 40% ethylene glycol (EG); 30% Ficoll; 0.5 M Sucrose and 10 mg/ml HSA, and preserved in liquid nitrogen. Tissue morphology was evaluated by traditional histology, TEM and gene expression profiling. The viability of endometrial cells and the ability to form epithelial organoids were evaluated before and after two different freezing protocols. Main results and the role of chance Our analysis showed that both PSF and vitrification techniques are appropriate for cryopreservation and storage of endometrial biopsies aimed at organoid generation, as no significant differences were found between fresh and cryopreserved tissue samples. However, ultrastructural changes were observed by TEM in PSF samples indicating an impact on mitochondria of epithelial and stromal cells with increased swelling. Changes were also observed in epithelial cells in vitrified samples, with decreased nuclear granularity, clarity, and open karyoplasm. On TEM analyses changes in the chromatin status were more evident in vitrified samples compared to fresh and PSF samples. PSF treated samples showed similarly high quality of epithelial and stromal nuclear staining when compared to the fresh samples in haematoxylin and eosin-stained slides, while VT of samples resulted in a significant decrease of both epithelial and stromal nuclear clarity. However, despite these changes observed in the tissue morphology, all three groups displayed similar transcriptional profiles and endometrial organoids were generated from both slow-frozen and vitrified samples, indicating very little or no impact of the freezing method used for post-thaw tissue functionality. Limitations, reasons for caution Although our study demonstrated relatively mild damages in both freezing protocols, we cannot exclude the absence of additional changes not evaluated in this study, such as those concerning the epigenetic constitution of the cells. Therefore, more extended research with larger sample size is needed for further validation of the results. Wider implications of the findings Our findings indicate that both slow-freezing and vitrification methods applied to endometrial biopsies are effective in maintaining tissue morphology and functionality. Further optimization of cryopreservation methods of endometrium could contribute to future experimental and clinical use of cryopreserved endometrial tissue. Trial registration number not applicable

STUDY QUESTION Can a large-scale genome-wide association study (GWAS) meta-analysis identify the genomic risk loci and associated candidate genes for female genital tract (FGT) polyps, provide insights into the mechanism underlying their development, and inform potential overlap with other traits, including endometrial cancer? SUMMARY ANSWER GWAS meta-analysis of FGT polyps highlighted the potentially shared mechanisms between polyp development and cancerous processes. WHAT IS KNOWN ALREADY Small-scale candidate gene studies have focused on biological processes such as estrogen stimulation and inflammation to clarify the biology behind FGT polyps. However, the exact mechanism for the development of polyps is still elusive. At the same time, a genome-wide approach, which has become the gold standard in complex disease genetics, has never been used to uncover the genetics of the FGT polyps. STUDY DESIGN, SIZE, DURATION We performed a genome wide association study (GWAS) meta-analysis including a total of 25,100 women with FGT polyps (International Classification of Disease, ICD-10 diagnosis code N84) and 207,193 female controls (without N84 code) of European ancestry from the FinnGen study (11,092 cases and 94,394 controls) and the Estonian Biobank (EstBB, 14,008 cases and 112,799 controls). PARTICIPANTS/MATERIALS, SETTING, METHODS A meta-analysis and functional annotation of GWAS signals were performed to identify and prioritise genes in associated loci. To determine associations with other phenotypes, we performed a look-up of associated variants across multiple traits and health conditions, a genetic correlation analysis, and a phenome-wide association study (PheWAS) with ICD10 diagnosis codes. MAIN RESULTS AND THE ROLE OF CHANCE Our GWAS meta-analysis revealed ten significant (P < 5 x 10-8) genomic risk loci. Two signals, rs2277339 (P = 7.6 x 10-10) and rs1265005 (P = 1.1 x 10-9) (in linkage disequilibrium (LD) with rs805698 r2 = 0.75), are exonic missense variants in PRIM1 , and COL17A1 genes, respectively. Based on the literature, these genes may play a role in cellular proliferation. Several of the identified genomic loci had previously been linked to endometrial cancer and/or uterine fibroids. Thus, highlighting the potentially shared mechanisms underlying tissue overgrowth and cancerous processes, which may be relevant to the development of polyps. Genetic correlation analysis revealed a negative correlation between sex hormone-binding globulin (SHBG) and the risk of FGT polyps (rg = -0,21, se = 0.04, P = 2.9 x 10-6), and on the phenotypic level (PheWAS), the strongest associations were observed with endometriosis, leiomyoma of the uterus and excessive, frequent and irregular menstruation. LARGE SCALE DATA The complete GWAS summary statistics will be made available after publication through the GWAS Catalogue (). LIMITATIONS, REASONS FOR CAUTION In this study, we focused broadly on polyps of FGT and did not differentiate between the polyp subtypes. The prevalence of FGT polyps led us to assume that most women included in the study had endometrial polyps. Further study on the expression profile of FGT polyps could complement the GWAS study to substantiate the functional importance of the identified variants. WIDER IMPLICATIONS OF THE FINDINGS The study findings have the potential to significantly enhance our understanding of the genetic mechanisms involved, paving the way for future functional follow-up, which in turn could improve the diagnosis, risk assessment, and targeted treatment options, since surgery is the only line of treatment available for diagnosed polyps. TRIAL REGISTRATION NUMBER Not applicable ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement N.P.G. was supported by MATER Marie Sklodowska-Curie which received funding from the European Union Horizon 2020 research and innovation programme under grant agreement No. 813707. T.L. was supported by the Estonian Research Council grant PSG776. This study was funded by European Union through the European Regional Development Fund Project No. 2014-2020.4.01.15-0012 GENTRANSMED. Computations were performed in the High-Performance Computing Center of University of Tartu. The study was also supported by the Estonian Research Council (grant no. PRG1076 and MOBJD1056) and Horizon 2020 innovation grant (ERIN, grant no. EU952516). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: All Estonian Biobank (EstBB) participants have signed a broad informed consent form, and analyses were carried out under ethical approvals 1.1-12/624 and 1.1-12/2733 from the Estonian Committee on Bioethics and Human Research (Estonian Ministry of Social Affairs) and data release application 6-7/GI/630 from the EstBB. For the FinnGen study, we used only publicly available GWAS summary statistics without individual-level data and thus, a separate ethics approval was not needed. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes FinnGen cohort level summary statistics can be accessed as described here: . Protocol for accessing the Estonian Biobank data is described here: . GWAS meta-analysis summary statistics will be made available via the GWAS Catalogue (data upload pending).

(1) Background: Endometriosis is a highly prevalent gynecological disease affecting 10% of women of reproductive age worldwide. miRNAs may play a role in endometriosis, though their exact function remains unclear. This study aimed to identify differentially expressed miRNAs in endometriosis and study their functions in the disease. (2) Methods: Endometrial tissue was collected from women with endometriosis (n = 15) and non-endometriosis controls (n = 17). Dysregulated miRNAs were identified through small RNA-sequencing, and their biological significance was explored by target gene prediction and pathway analysis. Selected miRNAs were examined in paired ectopic endometriomas and eutopic endometrium (n = 10) using qRT-PCR. Their roles in cell migration and proliferation were further examined in vitro using functional assays. To identify potential target genes, we performed mRNA sequencing on transfected cells and the endometrioma cohort. (3) Results: We identified 14 dysregulated miRNAs in the eutopic endometrium of women with endometriosis compared to endometrial tissue from women without endometriosis. Pathway analysis indicated enrichment in cell migration and proliferation-associated pathways. Further ex vivo studies of miR-193b-5p and miR-374b-5p showed that both miRNAs were upregulated in endometrioma. Overexpression of these two miRNAs in vitro inhibited cell migration, and mRNA sequencing revealed several migration-related genes that are targeted by these miRNAs. (4) Conclusions: Our study identified two key endometrial miRNAs that may be involved in the pathogenesis of endometriosis by regulating cell migration.

Patient-derived endometrial biopsies serve as a crucial source for molecular studies, highlighting the necessity for tissue cryopreservation methods that preserve cell viability and tissue morphology with minimal to no impact. The passive slow freezing (PSF) protocol has demonstrated efficacy for cryopreserving endometrial biopsies, allowing for the subsequent isolation of viable epithelial and stromal cells. Vitrification (VT) enables the avoidance of ice crystal formation and could therefore potentially prevent mechanical injury to tissues. In this study, PSF and VT techniques were applied to endometrial biopsies, and the effects of cryopreservation on tissue samples were evaluated using traditional histology. In addition, transmission electron microscopy (TEM), gene expression profiling analyses, the viability of endometrial cells, and the ability to form epithelial organoids were compared between PSF and VT endometrial biopsies in a subset of samples. The histology and TEM studies demonstrated relatively mild cellular and sub-cellular damage in both cryopreservation protocols which did not affect tissue functionality and the formation of the organoids. Additionally, the cryopreservation methodology did not affect the gene expression profile of the 68 endometrial-receptivity associated genes studied. In conclusion, our findings indicate that although current cryopreservation methodologies need further improvements, they still allow us to achieve acceptable cell viability and functionality, showing promising potential for facilitating the utilization of cryopreserved endometrial tissue samples for research purposes.

Abstract Study question What is the role of dysregulated endometrial microRNAs (miRNAs) in the development of endometriosis? Summary answer Dysregulated miRNAs in the endometrium of women with endometriosis can also be found in endometriomas and may affect the migratory ability of endometriotic cells. What is known already The molecular mechanisms underlying the pathogenesis of endometriosis are poorly understood. One of the hypotheses is that changes in cell properties observed in endometriotic lesions could be initiated already in the endometrium. Dysregulation of miRNAs in the endometrium of women with endometriosis has been reported in previous microarray-based studies. However, little overlap has been seen between published miRNA expression data. Moreover, the potential role of dysregulated miRNAs in the endometrium of women with endometriosis and whether these changes are also present in the endometrioma are largely unknown. Study design, size, duration In this experimental case-control study miRNA gene expression in proliferative phase endometrium was compared between 15 women with laparoscopically confirmed endometriosis (stage III–IV) and 17 age-matched controls who were laparoscopically confirmed to be free of endometriosis. Selected miRNAs were further compared between paired proliferative-phase endometrium and endometrioma from a new cohort of women with endometriosis (stage III–IV) and studied in vitro to understand their effect on cell migration. Participants/materials, setting, methods Samples were collected during laparoscopic operations performed at Tartu University Hospital, Estonia. Dysregulated endometrial miRNAs were detected with small RNA sequencing and differential gene expression analysis. Target genes and biological pathways were predicted to understand their potential role in the disease. Selected miRNAs were further studied for their expression in endometriomas using qRT-PCR and in-vitro for their proliferation and migration ability using a transwell-migration assay after miRNA mimic transfection of the 12Z endometriotic cell line. Main results and the role of chance In total, we identified 9 upregulated and 5 downregulated (-2 2, FDR < 0.05) miRNAs in the endometrium of women with endometriosis compared to controls. In-silico analyses showed that predicted target genes of the dysregulated miRNAs were significantly enriched in migration-related KEGG pathways such as adherens junctions, focal adhesion, MAPK-, PI3-AKT-, and TGF-beta signaling. The most down-regulated miRNA, miR-193b-5p, and the most up-regulated miRNA, miR-374b-5p, were selected for further characterization. Validation of their expression in endometriomas showed a significant up-regulation of both miRNAs compared to paired endometrium (Fold change > 2, FDR < 0.05). Since it has been reported that altered cell migratory ability could be involved in the pathogenesis of endometriosis and our dysregulated miRNA were associated with migration-related pathways, we explored if miR-193b-5p mimic transfection affects the migration capacity of 12Z cells. A 2-fold decrease in cell migration (p-value 0.0021) was observed after 12Z cell mimic transfection. No change in proliferation was demonstrated. Limitations, reasons for caution Although our findings both in-silico and in-vitro suggest a link between dysregulated miRNAs and cell migration, further in-vitro studies in primary cells and in-vivo studies in animal models are needed to reveal the specific pathways that these miRNAs regulate to explain the observed functional changes in the context of endometriosis. Wider implications of the findings This study gives molecular insight into the pathogenesis of endometriosis, a poorly understood disease, by demonstrating changes in miRNA expression in both the endometrium and endometrioma that potentially can be linked to a changed cell migratory ability. Furthermore, identified miRNAs could be further evaluated as diagnostic biomarkers in larger studies. Trial registration number Not applicable

Endometriosis is a debilitating and difficult-to-diagnose gynecological disease. Owing to limited information and awareness, women often rely on social media platforms as a support system to engage in discussions regarding their disease-related concerns. This study aimed to apply computational techniques to social media posts to identify discussion topics about endometriosis and to identify themes that require more attention from health care professionals and researchers. We also aimed to explore whether, amid the challenging nature of the disease, there are themes within the endometriosis community that gather posts with positive sentiments. We retrospectively extracted posts from the subreddits r/Endo and r/endometriosis from January 2011 to April 2022. We analyzed 45,693 Reddit posts using sentiment analysis and topic modeling–based methods in machine learning. Since 2011, the number of posts and comments has increased steadily. The posts were categorized into 11 categories, and the highest number of posts were related to either asking for information (Question); sharing the experiences (Rant/Vent); or diagnosing and treating endometriosis, especially surgery (Surgery related). Sentiment analysis revealed that 92.09% (42,077/45,693) of posts were associated with negative sentiments, only 2.3% (1053/45,693) expressed positive feelings, and there were no categories with more positive than negative posts. Topic modeling revealed 27 major topics, and the most popular topics were Surgery, Questions/Advice, Diagnosis, and Pain. The Survey/Research topic, which brought together most research-related posts, was the last in terms of posts. Our study shows that posts on social media platforms can provide insights into the concerns of women with endometriosis symptoms. The analysis of the posts confirmed that women with endometriosis have to face negative emotions and pain daily. The large number of posts related to asking questions shows that women do not receive sufficient information from physicians and need community support to cope with the disease. Health care professionals should pay more attention to the symptoms and diagnosis of endometriosis, discuss these topics with patients to reduce their dissatisfaction with doctors, and contribute more to the overall well-being of women with endometriosis. Researchers should also become more involved in social media and share new science-based knowledge regarding endometriosis.

Endometriosis is a common condition associated with debilitating pelvic pain and infertility. A genome-wide association study meta-analysis, including 60,674 cases and 701,926 controls of European and East Asian descent, identified 42 genome-wide significant loci comprising 49 distinct association signals. Effect sizes were largest for stage 3/4 disease, driven by ovarian endometriosis. Identified signals explained up to 5.01% of disease variance and regulated expression or methylation of genes in endometrium and blood, many of which were associated with pain perception/maintenance (SRP14/BMF, GDAP1, MLLT10, BSN and NGF). We observed significant genetic correlations between endometriosis and 11 pain conditions, including migraine, back and multisite chronic pain (MCP), as well as inflammatory conditions, including asthma and osteoarthritis. Multitrait genetic analyses identified substantial sharing of variants associated with endometriosis and MCP/migraine. Targeted investigations of genetically regulated mechanisms shared between endometriosis and other pain conditions are needed to aid the development of new treatments and facilitate early symptomatic intervention. Meta-analyses of genome-wide association studies for endometriosis identify 49 distinct association signals. Fine-mapping of causal variants explores functional effects across various tissues. Genetic correlations between endometriosis and other pain conditions are also highlighted.