Integrative analysis of transcriptomic and metabolomic profiles reveals abnormal phosphatidylinositol metabolism in follicles from endometriosis‐associated infertility patients

Unraveling the complexity of follicular fluid: insights into its composition, function, and clinical implications

Follicular fluid (FF) plays a vital role in the bidirectional communication between oocytes and granulosa cells (GCs), regulating and promoting oocyte growth and development. This fluid constitutes a complex microenvironment, rich in various molecules including hormones, growth factors, cytokines, lipids, proteins, and extracellular vesicles. Understanding the composition and metabolic profile of follicular fluid is important for investigating ovarian pathologies such as polycystic ovary syndrome (PCOS) and endometriosis. Additionally, analyzing follicular fluid can offer valuable insights into oocyte quality, aiding in optimal oocyte selection for in vitro fertilization (IVF). This review provides an overview of follicular fluid composition, classification of its components and discusses the influential components of oocyte development. It also highlights the role of follicular fluid in the pathogenesis and diagnosis of ovarian diseases, along with potential follicular fluid biomarkers for assessing oocyte quality. By understanding the intricate relationship between follicular fluid and oocyte development, we can advance fertility research and improve clinical outcomes for infertility patients.

Multi-omics approach to reveal follicular metabolic changes and their effects on oocyte competence in PCOS patients

Background

Polycystic ovary syndrome (PCOS) is a common heterogeneous disorder linked with endocrine and metabolic disturbances. The underlying mechanism of PCOS, especially its effect on oocyte competence, remains unclear. The study aimed to identify abnormal follicular metabolic changes using a multi-omics approach in follicular fluid from PCOS patients and to determine their effects on oocyte competence.

Methods

A total of 36 women with PCOS and 35 women without PCOS who underwent in vitro fertilization and embryo transfer were included in the study. Cumulus cells and follicular fluid samples were collected. Follicular fluid samples underwent metabolomic analysis, while cumulus cell clusters from the same patients were assessed using transcriptomic analysis. Clinical information of patients and assisted reproductive technology (ART) results were recorded. Transcriptomics and metabolomics were integrated to identify disrupted pathways, and receiver operation characteristics (ROC) analysis was conducted to identify potential diagnostic biomarkers for PCOS. Pearson correlation analysis was conducted to assess the relationship between metabolites in follicular fluid and oocyte competence (fertilization and early embryo development potential).

Results

Through multi-omics analysis, we identified aberrantly expressed pathways at both transcriptional and metabolic levels, such as the citrate cycle (TCA cycle), oxidative phosphorylation, the cAMP signaling pathway, the mTOR signaling pathway, and steroid hormone biosynthesis. Ten candidate metabolites were identified based on metabolic profiling data from these altered pathways. Phytic acid, succinic acid, 2'-deoxyinosine triphosphate, and 4-trimethylammoniobutanoic acid in the follicular fluid exhibited high specificity and sensitivity in distinguishing PCOS. Among these metabolites, L-arginine showed a negative correlation with the 2PN fertilization rate and cleavage rate, while estrone sulfate showed a negative correlation with the high-quality embryo rate in the in-vitro fertilization (IVF) cycle.

Conclusions

We have conducted a preliminary study of a novel metabolic signature in women with PCOS using a multi-omics approach. The alterations in key metabolic pathways may enhance our understanding of the pathogenesis of PCOS.

Unraveling the significance of AGPAT4 for the pathogenesis of endometriosis via a multi-omics approach

Endometriosis is characterized by the ectopic proliferation of endometrial cells, posing considerable diagnostic and therapeutic challenges. Our study investigates AGPAT4's involvement in endometriosis pathogenesis, aiming to unveil new therapeutic targets. Our investigation by analyzing eQTL data from GWAS for preliminary screening. Subsequently, within the GEO dataset, we utilized four machine learning algorithms to precisely identify risk-associated genes. Gene validity was confirmed through five Mendelian Randomization methods. AGPAT4 expression was measured by Single-Cell Analysis, ELISA and immunohistochemistry. We investigated AGPAT4's effect on endometrial stromal cells using RNA interference, assessing cell proliferation, invasion, and migration with CCK8, wound-healing, and transwell assays. Protein expression was analyzed by western blot, and AGPAT4 interactions were explored using AutoDock. Our investigation identified 11 genes associated with endometriosis risk, with AGPAT4 and COMT emerging as pivotal biomarkers through machine learning analysis. AGPAT4 exhibited significant upregulation in both ectopic tissues and serum samples from patients with endometriosis. Reduced expression of AGPAT4 was observed to detrimentally impact the proliferation, invasion, and migration capabilities of endometrial stromal cells, concomitant with diminished expression of key signaling molecules such as Wnt3a, β-Catenin, MMP-9, and SNAI2. Molecular docking analyses further underscored a substantive interaction between AGPAT4 and Wnt3a.Our study highlights AGPAT4's key role in endometriosis, influencing endometrial stromal cell behavior, and identifies AGPAT4 pathways as promising therapeutic targets for this condition.

Metabolomic and Transcriptomic Analyses Reveal the Potential Mechanisms of Dynamic Ovarian Development in Goats during Sexual Maturation

The ovary is a crucial reproductive organ in mammals, and its development directly influences an individual's sexual maturity and reproductive capacity. To comprehensively describe ovarian sexual maturation in goats, we integrated phenotypic, hormonal, metabolomic, and transcriptomic data from four specific time points: after birth (D1), at 2 months old (M2), at 4 months old (M4), and at 6 month old (M6). The study showed that during the early stage (D1-M2), ovarian growth was the most rapid, with weight and morphology increasing by 284% and 65%, respectively, and hormone levels rose significantly, with estradiol increasing by 57%. Metabolomic analysis identified 1231 metabolites, primarily lipids, lipid molecules, and organic acids, which can support hormone balance and follicle development by providing energy and participating in signaling transduction. Transcriptomic analysis identified 543 stage-specific differentially expressed genes, mainly enriched in steroid biosynthesis, amino acid metabolism, and the PI3K/AKT pathway, which are key factors influencing ovarian cell proliferation, apoptosis, hormone secretion, and metabolism. The integrated analysis revealed the key processes in the ovarian steroid hormone biosynthesis pathway and gene/metabolite networks associated with ovarian phenotypes and hormone levels, ultimately highlighting scavenger receptor class B type 1 (SCARB1), Cytochrome P450 Family 1 Subfamily A Member 1 (CYP11A1), 3beta-hydroxysteroid dehydrogenase (3BHSD), progesterone, estradiol, and L-phenylalanine as key regulators of ovarian morphological and functional changes at different developmental stages. This study is the first to reveal the metabolic changes and molecular regulatory mechanisms during ovarian sexual maturation in goats, providing valuable insights for understanding reproductive system development and optimizing reproductive performance and breeding efficiency.

Oxidative Imbalance in Endometriosis-Related Infertility-The Therapeutic Role of Antioxidants

Endometriosis in half of affected women is closely related to problems with fertility. Endometriosis-associated infertility is caused by a wide range of abnormalities affecting the female reproductive tract, from oocyte quality impairment to disturbances in the eutopic endometrium or mechanical abnormalities resulting from disease progression. Since supportive antioxidant therapies, in addition to surgical treatment or assisted reproductive techniques (ARTs), have overall been proven to be effective tools in endometriosis management, the objective of our review was to analyze the role of antioxidant substances, including vitamins, micronutrients, N-acetylcysteine (NAC), curcumin, melatonin, and resveratrol, in endometriosis-related infertility. Most of these substances have been proven to alleviate the systemic oxidant predominance, which has been expressed through decreased oxidative stress (OS) markers and enhanced antioxidative defense. In addition, we demonstrated that the predominant effect of the aforementioned substances is the inhibition of the development of endometriotic lesions as well as the suppression of pro-inflammatory molecules. Although we can undoubtedly conclude that antioxidants are beneficial in fertility support, further studies explaining the detailed pathways of their action are needed.

Research progress in rodent models of endometriosis

Endometriosis is a common and frequent disease in gynecology; its etiology and pathogenesis are partially understood and still not clear. The construction of suitable animal models is beneficial for basic research related to the disease. Currently, rodents have the advantages of low cost, fast reproduction, easy rearing, and a similar endometrial structure to humans. Depending on the purpose of the experiment, different molding methods have their advantages. In this paper, we describe the traditional methods of constructing endometriosis rodent models, compare their advantages and disadvantages, and introduce newly developed rodent models, such as cell line injection models, pain models, genetically engineered mouse models, fluorescent tracer models, iron overload models, chemical induction models, and methods of constructing rodent models of different subtypes of endometriosis. Fertility and treatment of endometriosis rodent models are also described. This study provides a reference for researchers in the selection of animal models for pathogenesis and drug treatment studies.

Exposure to bisphenol A affects transcriptome-wide N6-methyladenine methylation in ovarian granulosa cells

Bisphenol A (BPA) is an endocrine disruptor of potential reproductive toxicities. Increasingly research elucidated that BPA exposure to the environment would change the epigenetic modifications of transcriptome, but the mechanism by which BPA affects m6A methylation in interfering with female reproductive health remains uncertain. Therefore, this study preliminarily proposed and tested the hypothesis that BPA exposure alters the m6A modification level in transcripts in female ovarian granulosa cells. After BPA was exposed to granulosa cells for 24 h, RNA methylation related regulatory genes (such as METTL3, METTL14, ALKBH5, FTO) and the global m6A levels showed significant differences. Next, we applied MERIP-seq analysis to obtain information on the genome-wide m6A modification changes and identified 1595 differentially methylated mRNA transcripts, and 50 differentially methylated lncRNA transcripts. Further joint analysis of gene common expression showed that 33 genes were hypermethylated and up-regulated, 71 were hypermethylated and down-regulated, 49 were hypomethylated and up-regulated, and 20 were hypomethylated and down-regulated. Enriched Gene Ontology (GO) and biological pathway analysis revealed that these unique genes were mainly enriched in lipid metabolism, cell proliferation, and apoptosis related pathways. Six of these genes (mRNAs IMPA1, MCOLN1, DCTN3, BRCA2, and lncRNAs MALAT1, XIST) were validated using RT-qPCR and IGV software. Through comprehensive analysis of epitranscriptome and protein-protein interaction (PPI) data, lncRNAs MALAT1 and XIST are expected to serve as new markers for BPA interfering with the female reproductive system. In brief, these data show a novel and necessary connection between the damage of BPA exposure on female ovarian granulosa cells and RNA methylation modification.

Altered ovarian tissue level of lysophosphatidic acid and mRNA expressions of its metabolic enzymes and receptors in rats received gonadotropin-hyperstimulation

Lysophosphatidic acid (LPA), a well-studied member of the lysophospholipid family, is known to exert an important bio-effect on oocyte maturation and ovulation in mammals. We attempted to determine how follicle maturation in the rat ovary affects the levels of LPA and its precursor lysophospholipids, as well as mRNA levels of LPA-producing and -degrading enzymes and LPA receptors in rats that received gonadotropin-hyper-stimulation. Tissue levels of lysophospholipids were quantified by LC-MS/MS, and relative mRNA expression levels of LPA-producing and -degrading enzymes, and LPA receptors were measured by RT-PCR. Tissue levels of n-6 polyunsaturated LPAs and LPCs were higher in the ovaries of rats after receiving human chorionic gonadotropin, unlike the distinct profiles of n-3 polyunsaturated LPAs, which had lower levels, and LPCs which had higher levels, after the gonadotropin treatment. The effects of different levels of other polyunsaturated lysophospholipids were variable: decreased levels of lysophosphatidylglycerol, and unaltered levels of lysophosphatidylethanolamine, lysophosphatidylinositol, and lysophosphatidylserine. The results indicate that expression of mRNA levels of autotaxin and acylglycerol kinase were reduced and expression of lipid phosphate phosphatase 3 was elevated, whereas expressions of two membrane phosphatidic acid phosphatases (A1α and A1β) and lipid phosphate phosphatase 1 were essentially unaltered in rat ovary at several stages after ovary hyperstimulation. After the gonadotropin treatment, the expression levels of all LPA receptors except LPA3 were decreased at various times. These results are discussed with respect to the physiological processes of the ovarian environment and development in rats.

Trifloxystrobin induced developmental toxicity by disturbing the ABC transporters, carbohydrate and lipid metabolism in adult zebrafish

The environmental risks of trifloxystrobin (TR) have drawn attention because of its multiplex toxicity on aquatic organisms, but few studies have paid close attention to its chronic toxicity at environmental concentrations. In present study, histopathology, metabolomics and transcriptomics were comprehensively performed to investigate the toxic effects and biological responses on adult zebrafish after exposure to 0.1, 1 and 10 μg/L TR for 21 d. Results demonstrated long-term exposure of TR affected zebrafish liver, ovary and heart development. Metabolomics revealed 0.1, 1 and 10 μg/L TR simultaneously decreased the carbohydrates enriched in glucose metabolism and ABC transporters pathways, such as glycogen, lactose, lactulose, maltose, maltotriose, d-trehalose, while 1 μg/L and 10 μg/L TR significantly increased many metabolites related to glycerophospholipid and sphingolipid metabolism in zebrafish liver. Transcriptomics showed TR activated the transcription of the Abcb4, Abcb5 and Abcb11 involved in ABC transporters, Pck1, Pfk, Hk, Gyg1a and Pygma related to glucose metabolism, as well as the Lpcat1, Lpcat4, Gpat2, Cers and Sgms in glycerophospholipid and sphingolipid metabolism. Results further demonstrated high concentration of TR strongly affected the DNA repair system, while low dose of TR caused pronounced effects on cardiomyocytes and oocyte regulation pathways at transcriptional levels. The results indicated the abnormal liver, gonad and heart development caused by TR might be ascribed to the disturbance of carbohydrates and lipid metabolism mediating by the Abcb4, Abcb5 and Abcb11 ABC transporters, and long-term exposure of environmental concentration of TR was sufficient to affect zebrafish normal metabolism and development.

Regulated Cell Death in Endometriosis

Regulated cell death (RCD) represents a distinct mode of cell demise, differing from accidental cell death (ACD), characterized by specific signaling cascades orchestrated by diverse biomolecules. The regular process of cell death plays a crucial role in upholding internal homeostasis, acting as a safeguard against biological or chemical damage. Nonetheless, specific programmed cell deaths have the potential to activate an immune-inflammatory response, potentially contributing to diseases by enlisting immune cells and releasing pro-inflammatory factors. Endometriosis, a prevalent gynecological ailment, remains incompletely understood despite substantial progress in unraveling associated signaling pathways. Its complexity is intricately tied to the dysregulation of inflammatory immune responses, with various RCD processes such as apoptosis, autophagic cell death, pyroptosis, and ferroptosis implicated in its development. Notably, limited research explores the association between endometriosis and specific RCD pathways like pyroptosis and cuproptosis. The exploration of regulated cell death in the context of endometriosis holds tremendous potential for further advancements. This article thoroughly reviews the molecular mechanisms governed by regulated cell death and their implications for endometriosis. A comprehensive understanding of the regulated cell death mechanism in endometriosis has the potential to catalyze the development of promising therapeutic strategies and chart the course for future research directions in the field.

Recent progress in metabolomics for analyzing common infertility conditions that affect ovarian function

Background

Numerous efforts have been undertaken to identify biomarkers associated with embryo and oocyte quality to improve the success rate of in vitro fertilization. Metabolomics has gained traction for its ability to detect dynamic biological changes in real time and provide comprehensive metabolite profiles. This review synthesizes the most recent findings on metabolomic analysis of follicular fluid (FF) in clinical conditions leading to infertility, with a focus on the dynamics of energy metabolism and oocyte quality, and discusses future research directions.

Methods

A literature search was conducted without time constraints.

Main findings

The metabolites present in FF originate from five primary pathways: glycolysis, oxidative phosphorylation, lipid metabolism and β-oxidation, nucleic acid synthesis, and ketogenesis. Metabolomic profiling can broadly categorize infertile women into two groups: those with infertility due to aging and endometriosis, and those with infertility associated with polycystic ovarian syndrome and obesity. In the former group, glycolysis and lipid metabolism are upregulated to compensate for mitochondrial dysfunction, whereas the latter group exhibits the opposite trend. Assessing the levels of glucose, pyruvate, lactate, and plasmalogens in FF may be valuable for evaluating oocyte quality.

Conclusion

Metabolomic analysis, particularly focusing on energy metabolism in FF, holds promise for predicting female reproductive outcomes.

The Pathological Role of miRNAs in Endometriosis

Association studies investigating miRNA in relation to diseases have consistently shown significant alterations in miRNA expression, particularly within inflammatory pathways, where they regulate inflammatory cytokines, transcription factors (such as NF-κB, STAT3, HIF1α), and inflammatory proteins (including COX-2 and iNOS). Given that endometriosis (EMS) is characterized as an inflammatory disease, albeit one influenced by estrogen levels, it is natural to speculate about the connection between EMS and miRNA. Recent research has indeed confirmed alterations in the expression levels of numerous microRNAs (miRNAs) in both endometriotic lesions and the eutopic endometrium of women with EMS, when compared to healthy controls. The undeniable association of miRNAs with EMS hints at the emergence of a new era in the study of miRNA in the context of EMS. This article reviews the advancements made in understanding the pathological role of miRNA in EMS and its association with EMS-associated infertility. These findings contribute to the ongoing pursuit of developing miRNA-based therapeutics and diagnostic markers for EMS.