scholarly journals Transcriptome sequencing identified the ceRNA network associated with recurrent spontaneous abortion

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yong Huang ◽  
Jiayuan Hao ◽  
Yuan Liao ◽  
Lihua Zhou ◽  
Kaiju Wang ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Spontaneous Abortion ◽  
Transcriptome Sequencing ◽  
Differentially Expressed ◽  
Recurrent Spontaneous Abortion ◽  
Common Complication ◽  
Tissue Samples ◽  
Cerna Network ◽  
Heavy Burden ◽  
The Common

Abstract Background Recurrent spontaneous abortion (RSA) is one of the common complication of pregnancy, bringing heavy burden to the patients and their families. The study aimed to explore the lncRNA-miRNA-mRNA network associated with recurrent spontaneous abortion. Methods By transcriptome sequencing, we detected differences in lncRNA, miRNA and mRNA expression in villus tissue samples collected from 3 patients with RSA and 3 normal abortion patients. Differentially expressed lncRNAs, miRNAs and genes (DELs, DEMs and DEGs, respectively) were identified, and Geno Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to determine the functions of DELs and DEGs, which were analysed by Fisher’s test. We also observed the regulatory relationships between miRNA-mRNA and lncRNA-miRNA by Cytoscape 3.6.1. Results The results showed that 1008 DELs (523 upregulated and 485 downregulated), 475 DEGs (201 upregulated and 274 downregulated) and 37 DEMs (15 upregulated and 22 downregulated) were identified. And we also constructed a novel lncRNA-related ceRNA network containing 31 lncRNAs, 1 miRNA (hsa-miR-210-5p) and 3 genes (NTNG2, GRIA1 and AQP1). Conclusions lncRNA-related ceRNA network containing 31 lncRNAs, 1 miRNA (hsa-miR-210-5p) and 3 mRNAs (NTNG2, GRIA1 and AQP1) was constructed. The results may provide a basic theory for elucidating the mechanism underlying RSA.

scholarly journals Integrated Insight into the Molecular Mechanisms of Spontaneous Abortion during Early Pregnancy in Pigs

2021 ◽  
Vol 22 (12) ◽  
pp. 6644
Author(s):  
Xupeng Zang ◽  
Ting Gu ◽  
Wenjing Wang ◽  
Chen Zhou ◽  
Yue Ding ◽  
...  
Keyword(s):  
Immune Response ◽  
Spontaneous Abortion ◽  
Molecular Mechanisms ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Gene Set ◽  
Cerna Network ◽  
Major Interest ◽  
End Stage ◽  
Insight Into

Due to the high rate of spontaneous abortion (SAB) in porcine pregnancy, there is a major interest and concern on commercial pig farming worldwide. Whereas the perturbed immune response at the maternal–fetal interface is an important mechanism associated with the spontaneous embryo loss in the early stages of implantation in porcine, data on the specific regulatory mechanism of the SAB at the end stage of the implantation remains scant. Therefore, we used high-throughput sequencing and bioinformatics tools to analyze the healthy and arresting endometrium on day 28 of pregnancy. We identified 639 differentially expressed lncRNAs (DELs) and 2357 differentially expressed genes (DEGs) at the end stage of implantation, and qRT-PCR was used to verify the sequencing data. Gene set variation analysis (GSVA), gene set enrichment analysis (GSEA), and immunohistochemistry analysis demonstrated weaker immune response activities in the arresting endometrium compared to the healthy one. Using the lasso regression analysis, we screened the DELs and constructed an immunological competitive endogenous RNA (ceRNA) network related to SAB, including 4 lncRNAs, 11 miRNAs, and 13 genes. In addition, Blast analysis showed the applicability of the constructed ceRNA network in different species, and subsequently determined HOXA-AS2 in pigs. Our study, for the first time, demonstrated that the SAB events at the end stages of implantation is associated with the regulation of immunobiological processes, and a specific molecular regulatory network was obtained. These novel findings may provide new insight into the possibility of increasing the litter size of sows, making pig breeding better and thus improving the efficiency of animal husbandry production.

Expression of C-type lectin receptors and Toll-like receptors in decidua of patients with unexplained recurrent spontaneous abortion

2017 ◽  
Vol 29 (8) ◽  
pp. 1613 ◽  
Author(s):  
Liang Xu ◽  
Tian Qiu ◽  
Yudong Wang ◽  
Yan Chen ◽  
Weiwei Cheng
Keyword(s):  
Mrna Expression ◽  
Spontaneous Abortion ◽  
Transforming Growth Factor ◽  
Recurrent Spontaneous Abortion ◽  
Intercellular Adhesion Molecule ◽  
Control Group ◽  
Toll Like Receptors ◽  
Lectin Receptors ◽  
Unexplained Recurrent Spontaneous Abortion ◽  
Normal Controls

In the present study, the mechanisms underlying the pathogenesis of unexplained recurrent spontaneous abortion (URSA) were explored. The protein and mRNA expression of two C-type lectin-like receptors (CLRs), namely dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN) and mannose receptor (MR), and two Toll-like receptors (TLRs), namely TLR2 and TLR4, in the decidua and dendritic cells (DCs) was compared between URSA patients and normal controls. URSA patients had significantly lower protein and mRNA expression of DC-SIGN and significantly higher expression of TLR2 and TLR4 in decidual tissues compared with normal controls. In addition, URSA patients had significantly higher levels of the T helper (Th) 1 cytokines interleukin (IL)-2 and interferon-γ, and significantly lower levels of the Th2 cytokines IL-10 and transforming growth factor β1 in decidual tissues compared with the control group. The TLR2 agonist synthetic triacylated lipoprotein (Pam3CSK4) and the TLR4 agonist lipopolysaccharide were used to demonstrate that TLR2 and TLR4 modulate Th1/Th2 cytokine imbalance in DC–T cell cocultures. The results suggest that the balance between CLRs and TLRs was tilted towards a TLR-dominant response in URSA patients, which may disrupt maternal–fetal immune tolerance, resulting in spontaneous abortion.

scholarly journals iTRAQ and PRM-based quantitative proteomics in early recurrent spontaneous abortion: biomarkers discovery

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Ying Cui ◽  
Ling He ◽  
Chun-Yan Yang ◽  
Qian Ye
Keyword(s):  
Spontaneous Abortion ◽  
Early Stage ◽  
Pregnancy Termination ◽  
Diagnostic Value ◽  
Differentially Expressed ◽  
Recurrent Spontaneous Abortion ◽  
Control Group ◽  
Case Group ◽  
Differentially Expressed Proteins ◽  
History Of

Abstract Background Early recurrent spontaneous abortion (ERSA) is a common condition in pregnant women. To prevent ERSA is necessary to look for abortion indicators, such as hormones and proteins, in an early stage. Methods Thirty patients with ERSA were enrolled in the case group. In the control group, we recruited 30 healthy women without a history of miscarriage undergoing voluntary pregnancy termination. The differentially expressed proteins in the serum were identified between the two groups using PRM and iTRAQ. Results Seventy-eight differentially expressed proteins were identified. Using GO functional annotation and KEGG pathway analysis, we detected that the most significant changes occurred in the pathway of Fc gamma R-mediated phagocytosis. Meanwhile, using PRM, we identified three proteins that were closely related to abortion, B4DTF1 (highly similar to PSG1), P11464 (PSG1), and B4DF70 (highly similar to Prdx-2). The levels of B4DTF1 and P11464 were down-regulated, while the level of B4DF70 was up-regulated. Conclusions CD45, PSG1, and Prdx-2, were significantly dysregulated in the samples of ERSA and could become important biomarkers for the prediction and diagnosis of ERSA. Larger‑scale studies are required to confirm the diagnostic value of these biomarkers.

scholarly journals Integrated Analysis of lncRNA-miRNA-mRNA ceRNA Network in Human Diarrhea Irritable Bowel Syndrome

2021 ◽  
Author(s):  
Jun-wei LIANG ◽  
Wen-jun BAI ◽  
Xiao-yan WANG ◽  
Li-li CHI
Keyword(s):  
Irritable Bowel Syndrome ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Down Regulation ◽  
Tissue Samples ◽  
Cerna Network ◽  
Irritable Bowel

Abstract Background:Many studies on long chain non-coding RNAs (lncRNAs) are published in recent years. But the roles of lncRNAs in diarrhea irritable bowel syndrome (IBS-D) are still unclear and should be further examined. The present work focused on determining the molecular mechanisms underlying lncRNAs regulation in IBS-D on the basis of the lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network.Methods:This study collected the mRNAs (GSE36701) expression data within human tissue samples with IBS-D group and normal group based on Gene Expression Omnibus (GEO) database and collected the differentially expressed lncRNAs (DELs) and differentially expressed miRNAs (DEmiRs) based on PubMed.Functional enrichment analysis of DEGs was performed on the DAVID database. Then the interaction network was constructed and visualized using STRING database and Cytoscape.Results: This study identified 3192 DEmRNAs (1437 with up-regulation and 1755 with down-regulation),29 DEmiRs (18 upregulated and 11 downregulated)and 2 DELs(one upregulated and one downregulated) between IBS-D and control samples.Furthermore,we constructed a lncRNA-miRNA-mRNA network through two DELs (lncRNA TUG1 with up-regulation and lncRNA H19 with down-regulation), four DemiRs (hsa-miR-148a-3p,hsa-miR-342-3p,hsa-miR-149-5p with up-regulation and hsa-miR-219a-5p with down-regulation)and 24 DEGs (4 with up-regulation and 20 with down-regulation) with 42 axes. Simultaneously, we conducted functional enrichment and pathway analyses on genes within the as-constructed ceRNA network. According to our PPI/ceRNA network and functional enrichment analysis results, two critical genes were found (BCL2L11 and QKI). Conclusion:In conclusion, the ceRNA interaction axis we identified is a potentially critical target for treating IBS-D.BCL2L11 axis(LncH19-hsa-miR-148a-3p-BCL2L11) may via interaction with PI3K/AKT pathways in IBS-D.Our results shed more lights on the possible pathogenic mechanism in IBS-D using a lncRNA-associated ceRNA network.

scholarly journals Construction and investigation of a circRNA-associated ceRNA regulatory network in Tetralogy of Fallot

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Haifei Yu ◽  
Xinrui Wang ◽  
Hua Cao
Keyword(s):  
Tetralogy Of Fallot ◽  
Heart Development ◽  
Expression Profiles ◽  
Screening Strategy ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Tissue Samples ◽  
Cerna Network ◽  
Positive Correlations

Abstract Background As the most frequent type of cyanotic congenital heart disease (CHD), tetralogy of Fallot (TOF) has a relatively poor prognosis without corrective surgery. Circular RNAs (circRNAs) represent a novel class of endogenous noncoding RNAs that regulate target gene expression posttranscriptionally in heart development. Here, we investigated the potential role of the ceRNA network in the pathogenesis of TOF. Methods To identify circRNA expression profiles in TOF, microarrays were used to screen the differentially expressed circRNAs between 3 TOF and 3 control human myocardial tissue samples. Then, a dysregulated circRNA-associated ceRNA network was constructed using the established multistep screening strategy. Results In summary, a total of 276 differentially expressed circRNAs were identified, including 214 upregulated and 62 downregulated circRNAs in TOF samples. By constructing the circRNA-associated ceRNA network based on bioinformatics data, a total of 19 circRNAs, 9 miRNAs, and 34 mRNAs were further screened. Moreover, by enlarging the sample size, the qPCR results validated the positive correlations between hsa_circ_0007798 and HIF1A. Conclusions The findings in this study provide a comprehensive understanding of the ceRNA network involved in TOF biology, such as the hsa_circ_0007798/miR-199b-5p/HIF1A signalling axis, and may offer candidate diagnostic biomarkers or potential therapeutic targets for TOF. In addition, we propose that the ceRNA network regulates TOF progression.

LncRNA-mRNA Expression Profiles and Functional Networks Associated with Cognitive Impairment in Folate-deficient Mice

2021 ◽  
Vol 24 ◽  
Author(s):  
Xiaojin Feng ◽  
Fenfang Zhan ◽  
Jialing Hu ◽  
Fuzhou Hua ◽  
Guohai Xu
Keyword(s):  
Gene Expression ◽  
Cognitive Impairment ◽  
Mrna Expression ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Functional Networks ◽  
Ppi Network ◽  
Hub Genes ◽  
Cerna Network ◽  
Deficient Mice

Background: Cognitive impairment is a common neurocognitive disorder that affects millions of worldwide people’s health,related tofolate deficiency. Objective: The present study aimed to investigate the lncRNA-mRNA functional networks associated with cognitive impairment in folate-deficient mice and elucidate their possible molecular mechanisms. Methods: We downloaded the gene expression profile (GSE148126) of lncRNAs and mRNAs from NCBI Gene Expression Omnibus (GEO) database. Four groups of mouse hippocampi were analyzed, including 4 months (4mo) and 18 months (18mo) of folic acid (FA) deficiency/supplementation. The differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were identified using gplots and heatmap packages. The functions of the DEmRNAs were evaluated using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The hub genes wereidentified by CytoHubba plugins of Cytoscape, and protein-protein interaction (PPI) network of deregulated mRNAs was performed using STRING database. Finally, lncRNA-mRNA co-expression and competitive endogenous RNA (ceRNA) network analyses were constructed. Results: In total, we screened 67 lncRNAs with 211 mRNAs, and 89 lncRNAs with 229 mRNAs were differentially expressed in 4mo_FAand 18mo_FA deficient mice, respectively. GO analyses indicated that DEmRNAs were highly related to terms involved in binding and biological regulation. KEGG pathway analyses demonstrated that these genes were significantly enriched for Renin secretion, Pancreatic secretion and AMPK signaling pathways in 18mo_FA deficiency group. Subsequently, the top 5 hub genes werescreened from the PPI network, which may be key genes with the progression of folate deficiency. Upon the lncRNA-mRNA co-expression network analysis, we identified the top 10 lncRNAs having the maximum number of connections with related mRNAs. Finally, a ceRNA network was constructed for DE lncRNAs and DEmRNAs, and several pivotal miRNAs were predicted. Conclusions: This study identified the lncRNA-mRNA expression profiles and functional networks associated with cognitive impairment in folate-deficient mice, which provided support for the possible mechanisms and therapy for this disease.

scholarly journals Integrated Analysis of Circular RNA Associated Cerna Network Reveals Potential CircRNA Biomarkers in Human Breast Cancer

2020 ◽  
Author(s):  
Hui Shen ◽  
Huan Pan ◽  
Jianju Lu ◽  
Jianfen Shen ◽  
Longsheng Xu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Survival Analysis ◽  
Correlation Analysis ◽  
Mrna Expression ◽  
Circular Rna ◽  
Comprehensive Analysis ◽  
Differentially Expressed ◽  
Hub Genes ◽  
Cerna Network ◽  
Competitive Endogenous Rna

Abstract BackgroundThere is increasing evidence that circular RNA (circRNA) is closely related to tumorigenesis and cancer progression. circRNA has been identified as a sponge of microRNA (miRNA) in a competitive endogenous RNA (ceRNA) network and is involved in the regulation of mRNA expression. However, the roles of cancer specific circRNAs in circRNA-related ceRNA network of breast cancer (BRCA) are still unclear. This study aims to construct a ceRNA network associated with circRNA and to explore new therapeutic and prognostic targets and biomarkers for breast cancer.MethodsWe downloaded the circRNA expression profile of BRCA from Gene Expression Omnibus (GEO) microarray datasets and downloaded the miRNA and mRNA expression profiles of BRCA from The Cancer Genome Atlas (TCGA) database, these data were included in the study for comprehensive analysis. Differentially expressed mRNAs (DEmRNAs), differentially expressed miRNAs (DEmiRNAs) and differentially expressed circRNAs (DEcircRNAs) were identified and a competitive endogenous RNA (ceRNA) regulatory network was constructed based on circRNA–miRNA pairs and miRNA–mRNA pairs. Gene ontology and pathway enrichment analysis were performed on mRNAs regulated by circRNAs in ceRNA networks. Survival analysis and correlation analysis of all mRNAs and miRNAs in the ceRNA network were performed. The STRING search tool was used to predict the interaction between proteins, and the hub genes were screened by the MCODE plugin in Cytoscape.ResultsA total of 72 DEcircRNAs, 158 DEmiRNAs and 2762 DE mRNAs were identified. The constructed ceRNA network contains 60 circRNA-miRNA pairs and 140 miRNA-mRNA pairs, including 40 circRNAs, 30 miRNAs and 100 mRNAs. Functional enrichment indicated that DEmRNAs regulated by DEcircRNAs in ceRNA networks were significantly enriched in PI3K-Akt signaling pathway, MicroRNAs in cancer and Proteoglycans in cancer. Survival analysis and correlation analysis of all mRNAs and miRNAs in the ceRNA network showed that a total of 13 mRNAs and 6 miRNAs were significantly associated with overall survival, and 48 miRNA-mRNA interaction pairs had a significant negative correlation. A PPI network was established and 21 hub genes were determined from the network. After comprehensive analysis, four potential ceRNA regulatory axes were constructed based on three circRNAs, two miRNAs, and three mRNAs.ConclusionsThis study provides an effective bioinformatics basis for further understanding the molecular mechanisms and predictions of breast cancer. A better understanding of the circRNA-related ceRNA network in BRCA will help identify potential biomarkers for diagnosis and prognosis.

scholarly journals Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in human aortic dissection

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Hao Zhang ◽  
Ce Bian ◽  
Simei Tu ◽  
Fanxing Yin ◽  
Panpan Guo ◽  
...  
Keyword(s):  
Aortic Dissection ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Down Regulation ◽  
Tissue Samples ◽  
Cerna Network

Abstract Background Many studies on long chain non-coding RNAs (lncRNAs) are published in recent years. But the roles of lncRNAs in aortic dissection (AD) are still unclear and should be further examined. The present work focused on determining the molecular mechanisms underlying lncRNAs regulation in aortic dissection on the basis of the lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network. Methods This study collected the lncRNAs (GSE52093), mRNAs (GSE52093) and miRNAs (GSE92427) expression data within human tissue samples with aortic dissection group and normal group based on Gene Expression Omnibus (GEO) database. Results This study identified three differentially expressed lncRNAs (DELs), 19 differentially expressed miRNAs (DEmiRs) and 1046 differentially expressed mRNAs (DEGs) identified regarding aortic dissection. Furthermore, we constructed a lncRNA-miRNA-mRNA network through three lncRNAs (including two with up-regulation and one with down-regulation), five miRNAs (five with up-regulation), as well as 211 mRNAs (including 103 with up-regulation and 108 with down-regulation). Simultaneously, we conducted functional enrichment and pathway analyses on genes within the as-constructed ceRNA network. According to our PPI/ceRNA network and functional enrichment analysis results, four critical genes were found (E2F2, IGF1R, BDNF and PPP2R1B). In addition, E2F2 level was possibly modulated via lncRNA FAM87A-hsa-miR-31-5p/hsa-miR-7-5p or lncRNA C9orf106-hsa-miR-7-5p. The expression of IGF1R may be regulated by lncRNA FAM87A-hsa-miR-16-5p/hsa-miR-7-5p or lncRNA C9orf106-hsa-miR-7-5p. Conclusion In conclusion, the ceRNA interaction axis we identified is a potentially critical target for treating AD. Our results shed more lights on the possible pathogenic mechanism in AD using a lncRNA-associated ceRNA network.

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