High-throughput transcriptome-Seq and small RNA-Seq reveal novel functional genes and microRNAs for early embryonic arrest in humans

High-throughput sequencing reveals hub genes for human early embryonic development arrest in vitro fertilization: a pilot study

Many clinical studies have shown that embryos of in vitro fertilization (IVF) are often prone to developmental arrest, which leads to recurrent failure of IVF treatment. Early embryonic arrest has always been an urgent clinical problem in assisted reproduction centers. However, the molecular mechanisms underlying early embryonic development arrest remain largely unknown. The objective of this study is to investigate potential candidate hub genes and key signaling pathways involved in early stages of embryonic development. RNA-seq analysis was performed on normal and arrest embryos to study the changes of gene expression during early embryonic development. A total of 520 genes exhibiting differential expression were identified, with 174 genes being upregulated and 346 genes being downregulated. Upregulated genes show enrichment in biosynthesis, cellular proliferation and differentiation, and epigenetic regulation. While downregulated genes exhibit enrichment in transcriptional activity, epigenetic regulation, cell cycle progression, cellular proliferation and ubiquitination. The STRING (search tool for the retravel of interacting genes/proteins) database was utilized to analyze protein-protein interactions among these genes, aiming to enhance comprehension of the potential role of these differentially expressed genes (DEGs). A total of 22 hub genes (highly connected genes) were identified among the DEGs using Cytoscape software. Of these, ERBB2 and VEGFA were upregulated, while the remaining 20 genes (CCNB1, CCNA2, DICER1, NOTCH1, UBE2B, UBE2N, PRMT5, UBE2D1, MAPK3, SOX9, UBE2C, UB2D2, EGF, ACTB, UBA52, SHH, KRAS, UBE2E1, ADAM17 and BRCA2) were downregulated. These hub genes are associated with crucial biological processes such as ubiquitination, cellular senescence, cell proliferation and differentiation, and cell cycle. Among these hub genes, CCNA2 and CCNB1 may be involved in controlling cell cycle, which are critical process in early embryonic development.

lncRNA CLRN1-AS1 reduces adhesion ability of human trophoblasts via CXCL10/CXCL11

INTRODUCTION

Trophoblast cells play an important role in embryo recognition and localization, as well as placental development during embryo implantation. Dysfunction of trophoblastic cells causes pathological changes that lead to insufficient recognition, positioning, and adhesion during embryo implantation, ultimately leading to embryo development has stopped.

METHODS

High-throughput sequencing was used to identify differentially expressed the mRNA and lncRNA in the villi tissue of pregnant women diagnosed with embryo cessation. In vitro implantation cell models, characteristic analysis, and bio information analysis confirmed that CLRN1-AS1 affected the adhesion function of trophoblast cells by influencing the chemokines CXCL10/CXCL11.

RESULTS

High throughput sequencing technology was used to identify 438 differentially expressed mRNAs and 41 lncRNAs. The three lncRNAs, namely CLRN1-AS1, USP27X-AS1, and AC104809.4, were screened by the mRNA-lncRNA network. In vitro implantation model suggested that all three lncRNAs could affect the adhesion between trophoblast cells, among which CLRN1-AS1 had the most significant effect. Characteristic analysis and correlation analysis showed that CLRN1-AS1 was closely related to the expression of six adhesion-related genes, LAMA1, FGL2, ITGB2, FBN1, EMP2, and PODN. Cell experiments and re-sequencing confirmed that CLRN1-AS1 could affect the adhesion ability of trophoblast cells to the extracellular matrix, and its process was related to the chemokine CXCL10/CXCL11.

DISCUSSION

These results constructed the network of mRNA-lncRNA and enrichment when embryonic development has stopped and found CLRN1-AS1 highly correlated to failure of embryo implantation, and revealed that CLRN1-AS1 modulates the adhesion ability of trophoblast cells to the extracellular matrix via the chemokines CXCL10/CXCL11 during the early stage of embryo implantation.

Application of thromboelastography in diagnosing normal pregnancies and pregnancies with complications

Background

This observational study aimed to compare the potential application of thromboelastography (TEG) in diagnosing women with normal pregnancy (NP) and women with threatened abortion (TA), missed abortion (MA), embryo arrest (EA), fetal death (FD), history of abnormal pregnancy (HAP), and antiphospholipid antibody syndrome (AA).

Methods

According to the relevant clinical criteria, patients were divided into groups, and their blood samples were subjected to TEG. Next, the parameters R, K, α‐angle, MA, LY‐30, G, and coagulation index (CI) were analyzed. Partial correlation analysis was used to analyze correlation between groups of data. LSD‐t test and Dunnett's T3 test were used to analyze continuous variables. Ordinal categorical variables were compared using ordinal logistic regression analysis and estimate odds ratio of risk factors. A receiver operating characteristic (ROC) curve was constructed to detect the ability of TEG to recognize various parameters, and areas under the curve were compared using Delong's test for diagnosing pregnancy‐related diseases.

Results

MA had a negative effect on the MA parameter in TEG; EA had a negative effect on the MA and G parameters; HAP had a negative effect on the CI parameter and a positive effect on the R parameter; AA had a negative effect on the CI parameter. Compared with that of the NP group, the G of the EA (p = 0.014) group and the CI of the TA (p = 0.036) MA (p = 0.08) EA (p = 0.026) HAP (p = 0.000004) and AA (p = 0.002) groups were reduced. In the ordinal logistic regression analysis, compared with that of the NP group, the high R value of the HAP group accounted for more than that of the NP group (OR = 48.76, p = 0.001); the high K value of the AA group accounted for more than that of the NP group (OR = 17.00, p = 0.023); the angle value distributions of the TA and AA groups were different from that of the NP group (OR = 3.30, p = 0.039; OR = 0.14, p = 0.029); the low MA value of the MA, EA, and HAP groups accounted for more than that of the NP group (OR = 0.16, p = 0.03; OR = 0.26, p = 0.005; OR = 0.11, p = 0.008); and the low CI value of the HAP group accounted for more than that of the NP group (OR = 0.09, p = 0.005). In the ROC analysis, there were no significant differences in the TEG parameters of pregnant women belonging to the NP and TA, NP and MA, NP and EA, NP and FD, NP and HAP, and NP and AA groups (p > 0.05).

hsa-miR-518-5p/hsa-miR-3135b Regulates the REL/SOD2 Pathway in Ischemic Cerebral Infarction

Objectives

Ischemic cerebral infarction (ICI) is a fatal neurovascular disorder. A bioinformatics approach based on single-cell and bulk RNA-seq analyses was applied to investigate the pathways and genes involved in ICI and study the expression profile of these genes.

Methods

First, the aberrantly regulated “small-molecule ribonucleic acids” [microRNA (miRNAs)] and messenger RNAs (mRNAs) were analyzed using transcriptome data from the ischemic brain infarction dataset of the Gene Expression Omnibus (GEO) database. In mouse cerebrovascular monocytes, the single-cell regulatory network inference and clustering (SCENIC) workflow was used to identify key transcription factors (TFs). Then, the two miRNA-TF-mRNA interaction networks were constructed. Moreover, the molecular complex detection (MCODE) extracted the core sub-networks and identified the important TFs within these sub-networks. Finally, whole blood samples were collected for validation of the expression of critical molecules in ICI.

Results

We identified four cell types and 266 regulons in mouse cerebrovascular monocytes using SCENIC analysis. Moreover, 112 differently expressed miRNAs and 3,780 differentially expressed mRNAs were identified. We discovered potential biomarkers in ICI by building a miRNA-TF-mRNA interaction network. The hsa-miR-518-5p/hsa-miR-3135b/REL/SOD2 was found to play a potential role in ICI progression. The expression of REL and superoxide dismutase 2 (SOD2) was significantly elevated in the ICI group in the clinical cohort (P < 0.05). Furthermore, a REL expression was elevated in endothelial cells and fibroblasts at the single-cell level, indicating that REL is a cell-specific regulon. Functional enrichment analyses revealed that REL is primarily engaged in neurotransmitter activity and oxidative phosphorylation.

Conclusions

Our research uncovered novel biomarkers for ICI of neurovascular disease. The hsa-miR-518-5p/hsa-miR-3135b may regulate the REL/SOD2 pathway in ICI progression.

EGR1 Overexpression Inhibits the Occurrence of Preeclampsia by Binding to MicroRNA-574 Promoter and Upregulating GAB1

Early growth response protein 1 (EGR1) is potent in modulating placental trophoblast cell growth and shows a differential expression in preeclampsia (PE). We aimed to identify the downstream mechanism of EGR1 in PE. RT-qPCR showed EGR1 was significantly decreased in PE placenta. Overexpression of EGR1 facilitated the proliferation and invasion of HTR-8/Svneo cells, and reduced the concentration of human chorionic gonadotrophin (HCG) in the supernatant. Bioinformatics prediction, ChIP, and luciferase reporter experiments revealed that EGR1 inhibited miR-574 expression by binding to miR-574 promoter and that miR-574 targeted GAB1. Furthermore, overexpression of miR-574 inhibited the proliferation and invasion of HTR-8/Svneo cells. GAB1 was downregulated in placenta of PE patients, which was positively correlated with EGR1 and negatively correlated with miR-574. Inhibition of GAB1 attenuated the effect of EGR1 overexpression on the proliferation and invasion of HTR-8/Svneo cells. All in all, EGR1 upregulated GAB1 by inhibiting miR-574, thus contributing to trophoblast cell proliferation and invasion.

Placental miRNAs in feto-maternal communication mediated by extracellular vesicles

A complex network composed of at least 1900 microRNA (miRNA) species orchestrates the development and function of the human placenta. These molecules regulate genes and pathways operating major functional processes in trophoblast cells such as proliferation, invasion, differentiation, and metabolism. Nevertheless, the cellular localization and role of most placental miRNAs remain to be determined. The existence of eutherian- (C14MC) and primate-specific miRNA clusters (C19MC), together with human placenta-specific miRNAs, indicate the relevance of these molecules in evolution and diversification of the placenta, including the acquisition of its unique features in humans. They may be related also to diseases that are exclusively present in primates, such as preeclampsia. Changes in the miRNA expression profile have been reported in several placental pathologies. Which miRNAs are involved in the pathomechanism of these diseases or act to maintain placental homeostasis is uncertain. Placenta-derived miRNAs are packed into extracellular vesicles (EVs) and distributed through the maternal circulation to distant organs, where they contribute to adaptations required during pregnancy. Similarly, the placenta also receives molecular information from other tissues to adapt fetoplacental metabolic demands to the maternal energetic supply. These processes can be impaired in pathologic conditions. Therefore, the collection of circulating placental miRNAs constitutes potentially a minimally-invasive approach to assess the fetoplacental status and to diagnose pregnancy diseases. Future therapies may include manipulation of miRNA levels for prevention and treatment of placental complications to protect maternal health and fetal development.

Functional Genomics of Healthy and Pathological Fetal Membranes

Premature preterm rupture of membranes (PPROM), rupture of fetal membranes before 37 weeks of gestation, is the leading identifiable cause of spontaneous preterm births. Often there is no obvious cause that is identified in a patient who presents with PPROM. Identifying the upstream molecular events that lead to fetal membrane weakening presents potentially actionable mechanisms which could lead to the identification of at-risk patients and to the development of new therapeutic interventions. Functional genomic studies have transformed understanding of the role of gene regulation in diverse cells and tissues involved health and disease. Here, we review the results of those studies in the context of fetal membranes. We will highlight relevant results from major coordinated functional genomics efforts and from targeted studies focused on individual cell or tissue models. Studies comparing gene expression and DNA methylation between healthy and pathological fetal membranes have found differential regulation between labor and quiescent tissue as well as in preterm births, preeclampsia, and recurrent pregnancy loss. Whole genome and exome sequencing studies have identified common and rare fetal variants associated with preterm births. However, few fetal membrane tissue studies have modeled the response to stimuli relevant to pregnancy. Fetal membranes are readily adaptable to cell culture and relevant cellular phenotypes are readily observable. For these reasons, this is now an unrealized opportunity for genomic studies isolating the effect of cell signaling cascades and mapping the fetal membrane responses that lead to PPROM and other pregnancy complications.

Application of magnetic nanoparticles in nucleic acid detection

Nucleic acid is the main material for storing, copying, and transmitting genetic information. Gene sequencing is of great significance in DNA damage research, gene therapy, mutation analysis, bacterial infection, drug development, and clinical diagnosis. Gene detection has a wide range of applications, such as environmental, biomedical, pharmaceutical, agriculture and forensic medicine to name a few. Compared with Sanger sequencing, high-throughput sequencing technology has the advantages of larger output, high resolution, and low cost which greatly promotes the application of sequencing technology in life science research. Magnetic nanoparticles, as an important part of nanomaterials, have been widely used in various applications because of their good dispersion, high surface area, low cost, easy separation in buffer systems and signal detection. Based on the above, the application of magnetic nanoparticles in nucleic acid detection was reviewed.

Generation of an enteric smooth muscle cell line from the pig ileum

Smooth muscle cells (SMCs) play an important role in physiology and production in farm animals such as pigs. Here, we report the generation of a pig SMC line. Our original objective was to establish an enteroendocrine cell line from the pig ileum epithelium through lentiviral transduction of the Simian Virus (SV) 40 large T antigen. However, an initial expression analysis of marker genes in nine cell clones revealed that none of them were enteroendocrine cells or absorptive enterocytes, goblet cells, or Paneth cells, some of the major cell types existing in the ileum epithelium. A more detailed characterization of one clone named PIC7 by RNA-seq showed that these cells expressed many of the known smooth muscle-specific or -enriched genes, including smooth muscle actin alpha 2, calponin 1, calponin 3, myosin heavy chain 11, myosin light chain kinase, smoothelin, tenascin C, transgelin, tropomyosin 1, and tropomyosin 2. Both quantitative PCR and RNA-seq analyses showed that the PIC7 cells had a high expression of mRNA for smooth muscle actin gamma 2, also known as enteric smooth muscle actin. A Western blot analysis confirmed the expression of SV40 T antigen in the PIC7 cells. An immunohistochemical analysis demonstrated the expression of smooth muscle actin alpha 2 filaments in the PIC7 cells. A collagen gel contraction assay showed that the PIC7 cells were capable of both spontaneous contraction and contraction in response to serotonin stimulation. We conclude that the PIC7 cells are derived from an enteric SMC from the pig ileum. These cells may be a useful model for studying the cellular and molecular physiology of pig enteric SMCs. Because pigs are similar to humans in anatomy and physiology, the PIC7 cells may be also used as a model for human intestinal SMCs.

microRNA-670 modulates Igf2bp1 expression to regulate RNA methylation in parthenogenetic mouse embryonic development

Aberrant epigenetic modification, including N⁶-methylation of adenosine (m6A), has been frequently reported in embryos derived from parthenogenetic activation (PA). However, the role of Igf2bp1 expression pattern in m6A modification and the mechanism through which Igf2bp1 function is regulated in PA embryos remains elusive. Therefore, in this study, using si-Igf2bp1 and betaine (N,N,N-trimethylglycine, a major methyl donor), we investigated the effect of Igf2bp1 expression in m6A modification on the development of PA embryos. The results indicated that the down-regulation of Igf2bp1 reduced the cleavage and blastula rates of PA embryos. Moreover, m6A expression level was markedly down-regulated following microinjection with si-Igf2bp1. However, the treatment with betaine could significantly restore the m6A level. Further bioinformatics analysis revealed Igf2bp1 as the putative target of microRNA 670 (miR-670). Thus, to confirm this finding, mimics and inhibitor of miR-670 were microinjected into PA embryos. The results demonstrated that miR-670 inhibitor augmented the expression of Igf2bp1 and rescued cleavage and blastula rates. In addition, the miR-670 inhibitor promoted the m6A expression level. TUNEL assay revealed a loss of expression of Igf2bp1 induced cell apoptosis in PA embryos. Taken together, these results demonstrated that miR-670-3p functions as the regulator of Igf2bp1 expression and plays a crucial role in PA development through m6A modification.

Expression profiles of candidate microRNAs in the peripheral blood leukocytes of patients with early- and late-onset preeclampsia versus normal pregnancies

OBJECTIVES

Maternal leucocytes play an important role in the pathogenesis of preeclampsia (PE). Circulating microRNAs (miRNAs) are small, noncoding RNA molecules. The purpose of this study was to investigate miR-518b, miR-155-5p, and miR-21-3p in the peripheral blood leukocytes of patients with PE, compared to controls.

STUDY DESIGN

Using real-time quantitative PCR method, the selected miRNAs which have been associated with PE were examined from early- onset PE (EOPE) (<34 weeks) (n = 48), late- onset PE (LOPE) (≥34 weeks) (n = 48), total cases of PE (n = 96), and healthy controls (n = 52).

MAIN OUTCOME MEASURES

The relative expression of the target miR in patient samples was compared to the calibrator and the results were expressed as relative quantification values.

RESULTS

Gestational age (GA) was significantly different between PE and controls. Univariate logistic regression analysis adjusted for GA at blood draw were fit to compare miR-518b, miR-155-5p, and miR-21-3p between PE and controls. The expression of miR-518b, miR-155-5p, and miR-21-3p were not significantly different in PE, compared to controls. The expression of miR-518b was upregulated in the EOPE and LOPE group, compared to controls, and the area under the receiver operating characteristic curve (AUC) of miR-518b was 0.65 and 0.62, respectively. miR-518b was positively correlated with WBC count, platelet count, serum levels of AST, ALT, LDH in EOPE. miR-21-3p expression level was negatively correlated with body mass index at blood draw and systolic blood pressure in the LOPE group.

CONCLUSIONS

Increased miR-518b expression levels were found to be associated with EOPE and LOPE.

Recent advances in nanomaterial-based electrochemical and optical sensing platforms for microRNA assays

This review describes recent efforts in the application of nanomaterials as sensing elements in electrochemical and optical miRNAs assays.