Analysis of long non-coding RNA expression profiles using RNA sequencing in ovarian endometriosis

Long noncoding RNA BMPR1B-AS1 stability regulated by IGF2BP2 affects the decidualization in endometriosis patients through the SMAD1/5/9 pathway

Endometriosis (EMs)-related infertility commonly has decreased endometrial receptivity and normal decidualization is the basis for establishing and maintaining endometrial receptivity. However, the potential molecular regulatory mechanisms of impaired endometrial decidualization in patients with EMs have not been fully clarified. We confirmed the existence of reduced endometrial receptivity in patients with EMs by scanning electron microscopy and quantitative real-time PCR. Here we identified an lncRNA, named BMPR1B-AS1, which is significantly downregulated in eutopic endometrium in EMs patients and plays an essential role in decidual formation. Furthermore, RNA pull-down, mass spectrometry, RNA immunoprecipitation, and rescue analyses revealed that BMPR1B-AS1 positively regulates decidual formation through interaction with the RNA-binding protein insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2). Downregulation of IGF2BP2 led to a decreased stability of BMPR1B-AS1 and inhibition of activation of the SMAD1/5/9 pathway, an inhibitory effect which diminished decidualization in human endometrial stromal cells (hESCs) decidualization. In conclusion, our identified a novel regulatory mechanism in which the IGF2BP2-BMPR1B-AS1-SMAD1/5/9 axis plays a key role in the regulation of decidualization, providing insights into the potential link between abnormal decidualization and infertility in patients with EMs, which will be of clinical significance for the management and treatment of infertility in patients with EMs.

Downregulation of lncRNA LINC01465 predicts ovarian endometriosis and its prognosis

The well-known impact of ovarian endometriosis on female quality of life and the established role of lncRNA LINC01465 in ovarian cancer pathogenesis have been extensively documented; however, the relationship between LINC01465 and ovarian endometriosis is still not clear. This study seeks to explore the potential involvement of LINC01465 in the disease. The study analyzed a sample of 80 endometriosis patients and 80 healthy women. The expression of LINC01465 was measured in ectopic and eutopic endometrial tissues through RT-qPCR. The diagnostic potential of serum LINC01465 levels was evaluated using ROC curve analysis, and the patients were followed up for 3 years after treatment to monitor recurrence. The results revealed that the expression of LINC01465 was significantly lower in ectopic endometrial tissues in comparison to paired eutopic tissues for most of the patients. No correlation was found between the patient's age or lifestyle and serum LINC01465 levels. After treatment, the serum LINC01465 level increased, and patients who experienced recurrence had significantly lower levels compared to those who did not. In conclusion, the study findings suggest that the downregulation of LINC01465 plays a role in the pathogenesis of ovarian endometriosis and may serve as a diagnostic and prognostic biomarker for the disease.

Long non-coding RNAs and female infertility: What do we know?

Ten percent of people who are of reproductive age experience infertility. Sometimes the most effective therapies, including technology for assisted reproduction, may lead to unsuccessful implantation. Because of the anticipated epigenetic alterations of in vitro as well as in vitro fertilization growth of embryos, these fertility techniques have also been linked to unfavorable pregnancy outcomes linked to infertility. In this regard, a variety of non-coding RNAs such as long noncoding RNAs (lncRNAs) act as epigenetic regulators in the various physiological and pathophysiological events such as infertility. LncRNAs have been made up of cytoplasmic and nuclear nucleotides; RNA polymerase II transcribes these, which are lengthier than 200 nt. LncRNAs perform critical roles in a number of biological procedures like nuclear transport, X chromosome inactivation, apoptosis, stem cell pluripotency, as well as genomic imprinting. A significant amount of lncRNAs were linked into a variety of biological procedures as high throughput sequencing technology advances, including the development of the testes, preserving spermatogonial stem cells' capacity for differentiation along with self-renewal, and controlling spermatocyte meiosis. All of them point to possible utility of lncRNAs to be biomarkers and treatment aims for female infertility. Herein, we summarize various lncRNAs that are involved in female infertility.

Differential expression analysis of sugar accumulation-related genes during chestnut nut development

The chestnuts of Castanea mollissima Bl. are an important food crop in China, and have high nutritional content. To understand the pattern of sugar accumulation during chestnut nut development, the related enzyme gene regulatory pathways, and the molecular regulatory mechanisms of chestnut sugar biosynthesis metabolism, two chestnut varieties with different sugar content, namely Chengbu Youzhu (hereinafter referred to as CBYZ) and AnYou No. 1 (hereinafter referred to as AY01), were selected for investigation. Total sugar and starch content, and the activity of enzymes related to sugar accumulation, were measured in the nuts of the two chestnut varieties 10 days after flowering (DAF), 20 DAF, 30 DAF, 40 DAF, 50 DAF, 60 DAF, 70 DAF, 80 DAF, and 90 DAF. Changes in starch, straight-chain starch, and branched-chain starch content, and sucrose-phosphate synthase, soluble starch synthase, and granule-bound starch synthase enzyme activities were consistent with one-another. A total of 24 differentially expressed genes between the two varieties were associated with sugar biosynthesis and metabolism at three key stages (30, 60, and 90 DAF) of sugar accumulation. Further analysis showing upregulation of the expression of starch-related genes, such as β-amylase, GYS, and INV indicated that these genes were not actively expressed in AY01, resulting in slow accumulation of starch and reduced sugar content. By contrast, the downregulation of the expression of genes, such as PGK and MDH1, indicated that these genes were actively expressed in low-sugar chestnuts, resulting in the rapid fermentation of sugars. A link between gene up- or down-regulation during different developmental stages of chestnut and the effect of their expression on sugar content were established by KEGG pathway enrichment analysis. These findings provide further insights into the mechanism of sugar biosynthesis in chestnuts.

Expression of long noncoding RNAs in the ovarian granulosa cells of women with diminished ovarian reserve using high-throughput sequencing

Background

Infertility is a global reproductive-health problem, and diminished ovarian reserve (DOR) is one of the common causes of female infertility. Long noncoding RNAs (lncRNAs) are crucial regulators of numerous physiological and pathological processes in humans. However, whether lncRNAs are involved in the development of DOR remains to be elucidated.

Methods

Ovarian granulosa cells (OGCs) extracted from infertile women with DOR and from women with normal ovarian reserve (NOR) were subjected to high-throughput sequencing. Comprehensive bioinformatics analysis was conducted to identify the differential expression of messenger RNAs (mRNAs) and lncRNAs. Sequencing results were validated by the selection of lncRNAs and mRNAs using real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR).

Results

Compared with the NOR group, a total of 244 lncRNAs were upregulated (53 known and 191 novel), and 222 lncRNAs were downregulated (36 known and 186 novel) in the DOR group. Similarly, 457 mRNAs had differential expression between the two groups. Of these, 169 were upregulated and 288 were downregulated. Bioinformatics analysis revealed that the differentially expressed genes of mRNA and lncRNAs were considerably enriched in “cell adhesion and apoptosis”, “steroid biosynthesis”, and “immune system”. A co-expression network comprising lncRNAs and their predicted target genes revealed the possible involvement of the “thyroid hormone signaling pathway” and “protein binding, digestion and absorption” in DOR pathogenesis. The expression of SLC16A10 was positively regulated by multiple lncRNAs. After RT-qPCR validation of seven differentially expressed lncRNAs and mRNAs, respectively, the expression of lncRNA NEAT1, GNG12, ZEB2-AS1, and mRNA FN1, HAS3, RGS4, SUOX were in accordance with RNA-sequencing.

Conclusions

We presented the first data showing that the expression profiles of lncRNA and mRNA in OGCs between NOR and DOR patients using RNA sequencing. The lncRNAs and mRNAs that we identified may serve as novel diagnostic biomarkers for patients with DOR.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13048-022-01053-6.

The Critical Roles of Circular RNAs in Basic Research and Clinical Application of Female Reproductive-Related Diseases

Circular RNAs (circRNAs), produced by precursor mRNAs, are a type of covalently closed circular molecule without 5' caps and 3' polyadenylated tails. Recently, advances in high-throughput sequencing, transcriptomics and bioinformatics, have revealed that circRNAs with specific traits in tissue or cells play emerging roles in both physiological and panthological contexts instead of as simple by-products of transcription. However, bringing circRNAs to the forefront of clinical practice is still a long way off. In this review, we highlight the progress in the formation and function of circRNAs, and how circRNAs work in female reproductive-related diseases, such as recurrent spontaneous abortion, preeclampsia, and endometriosis. We also discussed the clinical potential of circRNAs as biomarkers, and therapeutic agents in female reproductive diseases as well as research controversies, technical issues, and biological knowledge gaps that need to be addressed. This review may instruct future basic research and clinical applications on circRNAs, especially in female reproduction.

Long Noncoding RNA Mediated Regulation in Human Embryogenesis, Pluripotency, and Reproduction

Long noncoding RNAs (lncRNAs), a class of noncoding RNAs with more than 200 bp in length, are produced by pervasive transcription in mammalian genomes and regulate gene expression through various action mechanisms. Accumulating data indicate that lncRNAs mediate essential biological functions in human development, including early embryogenesis, induction of pluripotency, and germ cell development. Comprehensive analysis of sequencing data highlights that lncRNAs are expressed in a stage-specific and human/primate-specific pattern during early human development. They contribute to cell fate determination through interacting with almost all classes of cellular biomolecules, including proteins, DNA, mRNAs, and microRNAs. Furthermore, the expression of a few of lncRNAs is highly associated with the pathogenesis and progression of many reproductive diseases, suggesting that they could serve as candidate biomarkers for diagnosis or novel targets for treatment. Here, we review research on lncRNAs and their roles in embryogenesis, pluripotency, and reproduction. We aim to identify the underlying molecular mechanisms essential for human development and provide novel insight into the causes and treatments of human reproductive diseases.

Molecular Signatures Correlated With Poor IVF Outcomes: Insights From the mRNA and lncRNA Expression of Endometriotic Granulosa Cells

The outcomes of in vitro fertilization (IVF) for endometriotic women are significantly worse than for patients without ovarian endometriosis (OEM), as shown by fewer retrieved oocytes. However, the exact pathophysiological mechanism is still unknown. Thus, we conducted a prospective study that analyzed mRNA and lncRNA transcriptome between granulosa cells (GCs) from patients with fewer retrieved oocytes due to OEM and GCs from controls with male factor (MF) infertility using an RNA sequencing approach. We found a group of significantly differentially expressed genes (DEGs), including NR5A2, MAP3K5, PGRMC2, PRKAR2A, DEPTOR, ITGAV, KPNB1, GPC6, EIF3A, and SMC5, which were validated to be upregulated and negatively correlated with retrieved oocyte numbers in GCs of patients with OEM, while DUSP1 demonstrated the opposite. The molecular functions of these DEGs were mainly enriched in pathways involving mitogen-activated protein kinase (MAPK) signaling, Wnt signaling, steroid hormone response, apoptosis, and cell junction. Furthermore, we performed lncRNA analysis and identified a group of differentially expressed known/novel lncRNAs that were co-expressed with the validated DEGs and correlated with retrieved oocyte numbers. Co-expression networks were constructed between the DEGs and known/novel lncRNAs. These distinctive molecular signatures uncovered in this study are involved in the pathological regulation of ovarian reserve dysfunction in OEM patients.

The Role of Long Non-Coding RNAs in Endometriosis

Endometriosis is a chronic gynecological disorder affecting the quality of life and fertility of many women around the world. Heterogeneous and non-specific symptoms may lead to a delay in diagnosis, with treatment options limited to surgery and hormonal therapy. Hence, there is a need to better understand the pathogenesis of the disease to improve diagnosis and treatment. Long non-coding RNAs (lncRNAs) have been increasingly shown to be involved in gene regulation but remain relatively under investigated in endometriosis. Mutational and transcriptomic studies have implicated lncRNAs in the pathogenesis of endometriosis. Single-nucleotide polymorphisms (SNPs) in lncRNAs or their regulatory regions have been associated with endometriosis. Genome-wide transcriptomic studies have identified lncRNAs that show deregulated expression in endometriosis, some of which have been subjected to further experiments, which support a role in endometriosis. Mechanistic studies indicate that lncRNAs may regulate genes involved in endometriosis by acting as a molecular sponge for miRNAs, by directly targeting regulatory elements via interactions with chromatin or transcription factors or by affecting signaling pathways. Future studies should concentrate on determining the role of uncharacterized lncRNAs revealed by endometriosis transcriptome studies and the relevance of lncRNAs implicated in the disease by in vitro and animal model studies.

Translational Applications of Linear and Circular Long Noncoding RNAs in Endometriosis

Endometriosis is a chronic gynecologic disease that negatively affects the quality of life of many women. Unfortunately, endometriosis does not have a cure. The current medical treatments involve hormonal manipulation with unwanted side effects and high recurrence rates after stopping the medication. Sadly, a definitive diagnosis for endometriosis requires invasive surgical procedures, with the risk of complications, additional surgeries in the future, and a high rate of recurrence. Both improved therapies and noninvasive diagnostic tests are needed. The unique molecular features of endometriosis have been studied at the coding gene level. While the molecular components of endometriosis at the small RNA level have been studied extensively, other noncoding RNAs, such as long intergenic noncoding RNAs and the more recently discovered subset of long noncoding RNAs called circular RNAs, have been studied more limitedly. This review describes the molecular formation of long noncoding and the unique circumstances of the formation of circular long noncoding RNAs, their expression and function in endometriosis, and promising preclinical studies. Continued translational research on long noncoding RNAs, including the more stable circular long noncoding RNAs, may lead to improved therapeutic and diagnostic opportunities.

A Newly Identified lncBCAS1-4_1 Associated With Vitamin D Signaling and EMT in Ovarian Cancer Cells

Long noncoding RNAs (lncRNAs) were identified rapidly due to their important role in many biological processes and human diseases including cancer. 1α,25-dihydroxyvitamin D3 [1α,25(OH)₂D₃] and its analogues are widely applied as preventative and therapeutic anticancer agents. However, the expression profile of lncRNAs regulated by 1α,25(OH)₂D₃ in ovarian cancer remains to be clarified. In the present study, we found 606 lncRNAs and 102 mRNAs that showed differential expression (DE) based on microarray data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the DE genes were mainly enriched in TGF-β, MAPK, Ras, PI3K-Akt, and Hippo signaling pathways, as well as the vitamin D-related pathway. We further assessed the potential lncRNAs that linked vitamin D signaling with EMT, and lncBCAS1-4_1 was identified in the first time. Moreover, we found that the most upregulated lncBCAS1-4_1 showed 75% same transcripts with CYP24A1 (metabolic enzyme of 1α,25(OH)₂D₃). Finally, the lncBCAS1-4_1 gain-of-function cell model was established, which demonstrated that the knockdown of lncBCAS1-4_1 inhibited the proliferation and migration of ovarian cancer cells. Furthermore, lncBCAS1-4_1 could resist the antitumor effect of 1α,25(OH)₂D₃, which was associated with upregulated ZEB1. These data provide new evidences that lncRNAs served as a target for the antitumor effect of 1α,25(OH)₂D₃.

Overexpressed MPS-1 contributes to endometrioma development through the NF-κB signaling pathway

BACKGROUND

Endometriosis is a benign gynecological disease that shares some characteristics with malignant tumors and affects approximately 10% of women of reproductive age. Endometrioma refers to endometriosis that appears in the ovary. Metallopanstimulin-1 (MPS-1) is a component of the 40S subunit of ribosomes that has extra-ribosomal functions that contribute to the development of diseases. This study aimed to explore the expression pattern and role of MPS-1 in endometrioma development.

METHODS

Quantitative real time polymerase chain reaction, western blotting, immunohistochemistry, and enzyme-linked immunosorbent assay were used to determine the expression of MPS-1 in patients with endometrioma. Following the successful knockdown of MPS-1 by siRNA, CCK-8 assays, flow cytometry, and transwell assays were performed to detect ectopic endometrial stromal cells (EcESCs) proliferation, the rate of apoptosis, and cell cycle, migration, and invasion, respectively. Western blotting was used to explore the effect of MPS-1 knockdown on protein levels in the NF-κB signaling pathway.

RESULTS

The expression of MPS-1 was significantly higher in endometrioma and the serum of endometrioma patients than in the patients without endometriosis. In addition, the downregulation of MPS-1 expression inhibited EcESCs proliferation, migration, and invasion. This downregulation led to the arrest of the EcESCs cycle in the G0/G1 phase and apoptosis and depressed the NF-κB signaling pathway.

CONCLUSION

MPS-1 can regulate EcESCs proliferation, motility, invasion, apoptosis, and cell cycle via the NF-κB signaling pathway in endometrioma. This may contribute to the formation or development of endometriotic foci. This study suggests the potential role of MPS-1 in the pathogenesis of endometriosis and enabled further research into the use of MPS-1 in the clinical diagnosis of endometrioma.

Endometriosis and ovarian cancer risk, an epigenetic connection

Endometriosis is a gynecological disorder that affects 176 million women worldwide and 1 in 10 females in the United States. Endometriosis most often affects women of child-bearing age, with most going undiagnosed. Endometriosis also shares many characteristics common to invasive cancer and has been known to be associated with epithelial ovarian cancer. Ovarian cancer is the 11^th most common cancer among women and over 22,000 new cases will be diagnosed within the next year. Women most commonly diagnosed with this cancer are between the ages of 55–64 years, outside the range of the age of women affected with endometriosis. While no known cause of either disease has been established, epigenetic regulation is thought to play a major role in both. This review focuses on epigenetic changes that occur within each individual disease as well as those that are similar in both, suggesting a possible etiological link between the two diseases.

Analysis and Screening of Reproductive Long Non-coding RNAs Through Genome-Wide Analyses of Goat Endometrium During the Pre-attachment Phase

Reproduction in goat is highly impeded by implantation failure. Of concern, the underlying mechanism leading to embryo implantation remains unclear. In this study, deep sequencing was employed through strand-specific Ribo-Zero RNA-Seq to characterize transcriptome changes in the endometrium during the maternal recognition of pregnancy. A total of 996 differential transcripts (115 lncRNAs and 881 mRNAs) existing between the pregnant and non-pregnant endometrium were revealed through bioinformatics analysis. The screening was performed on lncRNAs (XR_001918173.1, LNC_002760, and LNC_000599) and LNC_009053, to determine their potential role in regulating the synthesis of retinol and endometrium remolding through the proteasome pathway, respectively. The hypothesis of whether certain lncRNAs, namely, LNC_007223, LNC_005256, and LNC_010092 could play important roles in embryo implantation was tested. These novel findings are of paramount relevance to further elucidate the molecular mechanisms of embryo implantation and uncover new targets to improve goat reproduction.

Role of Non-coding RNAs in the Pathogenesis of Endometriosis

Endometriosis is a disorder characterized by the presence of endometrial glands and stroma like lesions outside of the uterus. Although several hypothesis have tried to explain the underlying cause of endometriosis, yet the main cause remained obscure. Recent studies have shown contribution of non-coding RNAs in the pathogenesis of endometriosis. Two classes of these transcripts namely long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have mostly attracted attention of researchers. Several studies have reported aberrant expression of these transcripts in affected tissues from patients as well as animal models. Modulation of important signaling pathways such as PI3K/AKT, P38-MAPK, ERK1/2-MAPK and Wnt-β catenin by miRNAs and lncRNAs have potentiated these molecules as biomarkers or therapeutic agents in endometriosis. Single nucleotide polymorphisms with miR-126, miR-143 and miR-146b have been associated with risk of endometriosis. Moreover, miRNAs and lncRNAs control inflammatory responses, cell proliferation, angiogenesis and tissue remodeling, thus understanding the role of these transcripts in endometriosis is a possible way to develop novel diagnostic tests and therapeutic targets for this disorder.

LncRNA MEG3-210 regulates endometrial stromal cells migration, invasion and apoptosis through p38 MAPK and PKA/SERCA2 signalling via interaction with Galectin-1 in endometriosis

BACKGROUND

Endometriosis is a benign gynaecological disease with malignant characteristics that severely affects women's quality of life. Long noncoding RNA maternally expressed gene 3 (LncRNA MEG3) is a tumour suppressor that is downregulated in various cancer cells and tissues, and regulates multiple biological processes. Emerging studies have revealed that the interactions between MEG3 and proteins are involved in disease progression. Galectin-1 affects cell motility, signal transduction and vascularization, and is overexpressed in endometriosis. Our study is the first to explore the role of MEG3-210 transcript in endometriosis and to reveal the regulatory mechanism mediated by the interaction between MEG3-210 and Galectin-1.

MATERIALS AND METHODS

Endometrial tissues and sera from patients with endometriosis and controls were collected. qRT-PCR was performed to detect the expression of MEG3-210 in the endometrium and endometrial stromal cells (ESCs). The CCK-8 assay, the Transwell assay, flow cytometry and animal models were conducted to evaluate the functions of MEG3-210 in vitro and in vivo. Bioinformatic analysis, Western blot assays, RNA-pull down assays and RNA immunoprecipitation were used to explore the potential mechanism of MEG3-210 in endometriosis.

RESULTS

Our results showed that MEG3-210 expression was lower in the eutopic endometrium of women with endometriosis. MEG3-210 downregulation promoted ESCs migration, invasion, anti-apoptosis in vitro and growth of endometriotic lesions in vivo. Furthermore, MEG3-210 downregulation could activate p38 mitogen-activated protein kinase (p38 MAPK) and inhibit cAMP-dependent protein kinase A/sarcoplasmic reticulum Ca²⁺ ATPase 2 (PKA/SERCA2) signalling, which was mediated by Galectin-1. The protein levels of Galectin-1 in patients with endometriosis were elevated, and Galectin-1 siRNA could reduce the size of lesions.

CONCLUSION

MEG3-210 regulates ESCs through p38 MAPK and PKA/SERCA signalling via interaction with Galectin-1. The novel regulatory mechanism may provide new insights into drug therapy and the diagnosis of endometriosis.

Long noncoding RNAs in endometriosis: Biological functions, expressions, and mechanisms

Endometriosis refers to a benign chronic gynecological disorder, and is defined as the ectopic growth of endometrium in pelvic cavity. Endometriosis affects about 10% of reproductive-aged women. Unfortunately, the pathogenesis of endometriosis remains obscure, and the disease witnesses a lack of effective therapy approaches. Therefore, more research needs to be performed to throw light on endometriosis, its pathogenesis, and therapy. Long noncoding RNAs (lncRNAs), which are defined as functional cellular RNA longer than 200 nucleotides, have been implicated in many chronic disorders. It has been suggested that lncRNAs are closely related to the endometriosis process. Nevertheless, the molecular mechanisms by which lncRNAs associate with endometriosis should be elucidated more detailed. In our brief review, we first exhibit the aberrant lncRNAs expression in endometriosis. Then, we talk about the molecular mechanisms underlying lncRNAs in endometriosis. Finally, we also present the potential of lncRNAs as biomarkers for endometriosis.

Molecular signature of eutopic endometrium in endometriosis based on the multi-omics integrative synthesis

Purpose

To synthesise data from genome-wide studies reporting molecular signature of eutopic endometrium through the phases of the menstrual cycle in endometriosis.

Methods

Extraction of data from publications reporting genetic signatures characterising endometrium associated with endometriosis. The nomenclature of extracted differentially expressed transcripts and proteins was adopted according to the HUGO Gene Nomenclature Committee (HGNC). Loci were further sorted according to the different phases of the menstrual cycle, i.e. menstrual (M), proliferative (P), secretory (S), early-secretory (ES), mid-secretory (MS), late-secretory (LS), and not specified (N/S) if the endometrial dating was not available. Enrichment analysis was performed using the DAVID bioinformatics tool.

Results

Altered molecular changes were reported by 21 studies, including 13 performed at the transcriptomic, 6 at proteomic, and 2 at epigenomic level. Extracted data resulted in a catalogue of total 670 genetic causes with available 591 official gene symbols, i.e. M = 3, P = 188, S = 81, ES = 82, MS = 173, LS = 36, and N/S = 28. Enriched pathways included oestrogen signalling pathway, extracellular matrix organization, and endothelial cell chemotaxis. Our study revealed that knowledge of endometrium biology in endometriosis is fragmented due to heterogeneity of published data. However, 15 genes reported as dysregulated by at least two studies within the same phase and 33 significantly enriched GO-BP terms/KEGG pathways associated with different phases of the menstrual cycle were identified.

Conclusions

A multi-omics insight into molecular patterns underlying endometriosis could contribute towards identification of endometrial pathological mechanisms that impact fertility capacities of women with endometriosis.

Electronic supplementary material

The online version of this article (10.1007/s10815-020-01833-3) contains supplementary material, which is available to authorized users.

Circulating non-coding RNAs as non-invasive diagnostic markers of endometriosis: a comprehensive meta-analysis

BACKGROUND

Circulating non-coding RNAs have great potential for diagnosing endometriosis as non-invasive markers. We have assessed the potential accuracy and utility for diagnosis of endometriosis.

METHODS

We searched many bases to identify the included literature, which included English bases, such as, Pubmed, Embase, Web of Science, Cochrane library and Chinese bases, for instance, CNKI, Wang Fang, VIP, DuXiu, ChaoXing. We also calculated the general sensitivity and specificity, negative likelihood ratio, positive likelihood ratio, diagnostic odds ratio, ROC curve plotting and so on with Stata 15. I² could test the heterogeneity of the meta-analysis, the funnel plot valuated whether meta-analysis had a publication bias. Regression analysis could explore heterogeneity in studies.

RESULT

Comprehensive reading and integrating extracted data, we included 11 published papers. The total number of people included in the case group was 453, and the control group was 362. We, respectively, calculated the general sensitivity and general specificity which were 0.81 (95% CI 0.76-0.85) and 0.77 (95% CI 0.71-0.82) by bivariate analysis. The area under the ROC curve was 0.86 (95% CI 0.83-0.89). There was significant heterogeneity in studies which is I² = 89.62% (95% CI 87.41%-91.83%). In addition, the results of meta-regression and subgroup analysis showed that the heterogeneity might come from gold standard, evaluation standard, experimental group size, experimental sample and race CONCLUSION: The circulating non-coding RNAs have great ability of diagnosing endometriosis as non-invasive markers which were performed robustly and accurately.

Circular RNA expression profiles and bioinformatics analysis in ovarian endometriosis

Background

Circular RNAs (circRNAs) with miRNA response elements (MREs) could function as competing endogenous RNA (ceRNA) in regulating gene expression, thus playing vital roles in pathogenesis and progression of many diseases. However, the function of circRNAs in endometriosis remains unknown. This study was carried to profile the expression patterns of circRNAs in ovarian endometriosis.

Methods

High throughput RNA‐Seq was performed in six paired ectopic and eutopic endometrium tissues (ecEM vs. euEM), followed by quantitative real‐time polymerase chain reaction (qRT‐PCR) in 30 paired samples. Through bioinformatics prediction, we constructed a circRNA‐miRNA ‐mRNA network and elucidated circRNAs functions by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses.

Results

A total of 146 upregulated and 148 downregulated circRNAs were identified, binding with 2,495 MREs. The qRT‐PCR validation results of four upregulated circRNAs matched the RNA‐Seq data. The ceRNA network included 48 miRNAs and 296 mRNAs. Functional analysis revealed several important pathways such as MAPK signaling pathway, and PI3K‐AKT signaling pathway, which might be associated with the pathogenesis and development of endometriosis.

Conclusion

Our data suggested that circRNAs are differentially expressed in endometriosis, which might be candidate factors for pathogenesis of this disease and be considered as promising therapeutic targets in the future.

Aberrant expression of CHL1 gene and long non-coding RNA CHL1-AS1, CHL1-AS2 in ovarian endometriosis

OBJECTIVE(S)

CHL1 (close homologue of L1 or cell adhesion molecule L1 like), also referred as CALL, is a member of the L1 gene family of neural cell adhesion molecules and belongs to immunoglobulin superfamily. This study aims to investigate the potential correlation of the CHL1 gene and the long non-coding RNAs (lncRNAs), i.e., CHL1-AS1 and CHL1-AS2, and to validate the expression patterns of CHL1 and CHL1-AS2 in ovarian endometriosis (EM).

STUDY DESIGN

Our previous microarray analyses (GSE86534) of 4 patients with ovarian EM indicated that CHL1 was the most upregulated mRNA in ectopic endometrium (EC) compared with eutopic endometrium (EU) tissues, and that its two antisense lncRNAs CHL1-AS1 and CHL1-AS2, exhibited the same expression pattern. We used a bioinformatics-based strategy to calculate the correlation among CHL1, CHL1-AS1 and CHL1-AS2. Gene set enrichment analysis (GSEA) was performed to analyze commonly enriched gene sets for CHL1-AS1 and CHL1-AS2. Using quantitative real-time polymerase chain reaction (qPCR), we examined the expression levels of CHL1 mRNA and lncRNA CHL1-AS2 in paired tissues of EC and EU from 30 EM patients and normal endometrium (NE) tissues from 27 controls using quantitative real-time polymerase chain reaction (qPCR). We also examined the expression of CHL1 protein in EC, EU and NE tissues using western blotting and immunohistochemistry (IHC).

RESULTS

CHL1, CHL1-AS1 and CHL1-AS2 were significantly correlated with each other given that the Pearson correlation values were > 0.9 using bioinformatic calculation. GSEA revealed that CHL1-AS1 and CHL1-AS2 were negatively associated with the same gene set "WAMUNYOKOLI_OVARIAN_CANCER_LMP". qPCR confirmed that the CHL1 and CHL1-AS2 expression levels were significantly higher in EC tissues than in EU and NE tissues, while they were not significantly different in EU compared with NE tissues. The relative expression levels of CHL1 and CHL1-AS2 in EC compared with EU tissues were positively significantly correlated (Pearson correlation coefficient = 0.421 and P value = 0.02). Elevated expression of CHL1 protein in EC tissues was detected by western blotting. IHC revealed that CHL1 protein expression levels enhanced in ectopic endometrial glands and stroma.

CONCLUSION(S)

Our results indicate a significant correlation among CHL1, CHL1-AS1 and CHL1-AS2, which might be involved in the development of ovarian EM and serve as novel targets for future research.

Inside the Endometrial Cell Signaling Subway: Mind the Gap(s)

Endometrial cells perceive and respond to their microenvironment forming the basis of endometrial homeostasis. Errors in endometrial cell signaling are responsible for a wide spectrum of endometrial pathologies ranging from infertility to cancer. Intensive research over the years has been decoding the sophisticated molecular means by which endometrial cells communicate to each other and with the embryo. The objective of this review is to provide the scientific community with the first overview of key endometrial cell signaling pathways operating throughout the menstrual cycle. On this basis, a comprehensive and critical assessment of the literature was performed to provide the tools for the authorship of this narrative review summarizing the pivotal components and signaling cascades operating during seven endometrial cell fate “routes”: proliferation, decidualization, implantation, migration, breakdown, regeneration, and angiogenesis. Albeit schematically presented as separate transit routes in a subway network and narrated in a distinct fashion, the majority of the time these routes overlap or occur simultaneously within endometrial cells. This review facilitates identification of novel trajectories of research in endometrial cellular communication and signaling. The meticulous study of endometrial signaling pathways potentiates both the discovery of novel therapeutic targets to tackle disease and vanguard fertility approaches.