scholarly journals Systematic Analysis of Plasma Exosome MiRNA in Patients with Postmenopausal Osteoporosis

2021 ◽  
Author(s):  
Chengxin Zhu ◽  
Jingze Xu ◽  
Shu Cao ◽  
Changqing Yang ◽  
Renhu Li ◽  
...  
Keyword(s):  
Postmenopausal Women ◽  
Postmenopausal Osteoporosis ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Size Exclusion ◽  
Control Group ◽  
Carbohydrate Binding ◽  
Healthy Controls ◽  
Differentially Expressed Mirnas

Abstract Background: More and more studies have shown that exosomes are involved in many aspects of bone metabolism. As the content of exosomes, miRNA plays an important role in the early diagnosis, treatment and prognosis evaluation of osteoporosis.Objective: To determine the potential molecular markers of osteoporosis by analyzing the differences of plasma exosome miRNA expression between postmenopausal women with osteoporosis and healthy controls.Methods: Serum samples of postmenopausal osteoporosis (PMOP) patients over 65 years old (n = 12) and healthy controls (n = 12) were collected. The exosomes were separated by molecular size exclusion chromatography(SEC).The differentially expressed miRNAs were analyzed by cluster analysis. The target genes of miRNAs were predicted and annotated by relevant software.The target genes were classified by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The appropriate biomarkers were screened out.Results: The miRNA spectrum of the patients was significantly different from that of the control group. Validation studies showed that 14 up-regulated miRNAs had a high probability of prediction, which could distinguish osteoporosis patients from healthy controls. Thirty-one genes were predicted to be targets for these miRNAs. GO enrichment analysis showed that miRNAs were mainly concentrated in protein binding, carbohydrate-binding, chromatin binding and protein kinase binding. KEGG enrichment analysis showed that miRNAs were mainly concentrated in the p53 signalling pathway, mineral absorption, glycerin metabolism, insulin secretion, glycosaminoglycan biosynthesis heparin sulfate /heparin pathway. This study identified a large number of differentially expressed miRNAs in plasma samples from postmenopausal women with osteoporosis. It may help to obtain new diagnosis and treatment strategies for PMOP.Conclusion: Our study identified the characteristics of plasma miRNAs in patients with osteoporosis and identified 14 candidate miRNAs, which may be useful biomarkers of osteoporosis. We speculate that these differentially expressed miRNAs may play a key role in the process of bone marrow mesenchymal stem cells osteogenic metabolism and transformation.

scholarly journals Dysregulation of autophagy-associated microRNAs in condyloma acuminatum

2020 ◽  
Author(s):  
Shi Wu ◽  
Dan Lu ◽  
Xinkai Zheng ◽  
Jin Xu ◽  
Zhen Li ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Light Chain ◽  
Target Genes ◽  
Condyloma Acuminatum ◽  
Differentially Expressed ◽  
Control Group ◽  
Healthy Controls ◽  
Related Protein ◽  
Ki 67 ◽  
Differentially Expressed Mirnas

Abstract Objectives This study was designed to investigate the miRNAs that regulate the cell proliferation of condyloma acuminatum (CA) lesions and their targets.Methods The expression of Ki-67 in 26 CA patients compared with 10 healthy controls was assessed by immunohistochemistry. And the different miRNAs in 4 CA patients and 4 control cases were analyzed by bioinformatics. PCR was used to validate the expression of screened miRNA and its corresponding target genes.Results The expression of Ki-67 was abnormally increased in CA compared with healthy controls ( P <0.05). The comparison of the control group with the CA group revealed 81 differentially expressed miRNAs, of which 56 were downregulated and 25 were upregulated. Two of the differentially expressed miRNAs, miR-30a-5p and miR-514a-3p, are associated with cell proliferation and their target genes are autophagy-related protein (Atg) 5 and Atg12, and Atg3 and Atg12, respectively. PCR results showed that the expression levels of miR-30a-5p and miR-514a-3p were decreased in CA patients compared with healthy controls ( P <0.05), whereas the expression of Atg5, Atg12 and Atg3 was increased ( P <0.05). The expression of the autophagy proteins microtubule-associated protein 1 light chain 3 (LC3) and P62/SQSTM1 (P62) was abnormally increased in the local lesion tissue of the 26 patients with CA compared with the 10 healthy controls, as assessed by immunohistochemistry ( P <0.05).Conclusions Our results suggest that autophagy levels may be modulated by has-miRNA30a-5p and has-miRNA514a-3p in CA patients, leading to dysregulated cell proliferation.

scholarly journals miR-98-5p as a Novel Biomarker Suppress Liver Fibrosis by Targeting TGFβ Receptor 1

2021 ◽  
Author(s):  
Yanhua Ma ◽  
xiaoxue yuan ◽  
Ming Han ◽  
Kai Han ◽  
Pu Liang ◽  
...  
Keyword(s):  
Liver Fibrosis ◽  
Signaling Pathway ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Hbv Infection ◽  
Differentially Expressed ◽  
Control Group ◽  
Chronic Hbv Infection ◽  
Differentially Expressed Mirnas ◽  
Chronic Hbv

Abstract Hepatic fibrosis is the repair reaction of excessive deposition and abnormal distribution of extracellular matrix after various liver injuries, especially chronic HBV infection, which is a key step in the development of various chronic liver diseases to cirrhosis. Recent studies show that microRNAs (miRNA) can regulate a series of liver fibrosis-related gene express and play an important role in the development of liver fibrosis. To detect the miRNAs expression profiling and to screen the differentially expressed miRNAs in patients with HBV-related liver fibrosis, the whole blood was collected from the HBV-related liver fibrosis patients (F2/3, n=10) based on Scheuer’s staging criteria. In addition, healthy volunteers (n=8) served as the control group. The expression of plasma miRNAs was detected by IlluminaHiSeq sequencing. Cluster analysis and target genes prediction of differentially expressed miRNAs were carried out. Gene ontology (GO) enrichment analysis and KEGG pathway enrichment analysis of differentially expressed miRNAs target genes were performed. Compared with the healthy control group 104 miRNAs were screened out from the liver fibrosis group, among which 72 miRNAs were up-regulated and 32 were down-regulated. Pathway annotations for the target genes of the miRNAs identified were found that it participated in many signal pathways including MAPK signaling pathway, TNF signaling pathway, Notch signaling pathway, phosphatidylinositol signal system and so on. According to the bioinformatic analysis，miR-98-5p were selected for function research among the differentially expressed miRNAs.MiR-98-5p prevents liver fibrosis by targeting TGFβR1 and blocking TGFβ1/Smad3 signaling pathway. In addition, serum miR-98-5p levels were measured from a total of 70 recruited patients with chronic HBV infection and 29 healthy individuals as controls. We found that serum miR-98-5p level was significantly lower in patients with live fibrosis than in healthy controls and HBV carriers (P<0.05). Those results suggest that miR-98-5p could be a potential therapeutic target for liver fibrosis .

scholarly journals miR-98-5p as a Novel Biomarker Suppress Liver Fibrosis by Targeting TGFβ Receptor 1

2021 ◽  
Author(s):  
Yanhua Ma ◽  
xiaoxue yuan ◽  
Ming Han ◽  
Kai Han ◽  
Pu Liang ◽  
...  
Keyword(s):  
Liver Fibrosis ◽  
Signaling Pathway ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Hbv Infection ◽  
Differentially Expressed ◽  
Control Group ◽  
Chronic Hbv Infection ◽  
Differentially Expressed Mirnas ◽  
Chronic Hbv

Abstract Hepatic fibrosis is the repair reaction of excessive deposition and abnormal distribution of extracellular matrix after various liver injuries, especially chronic HBV infection, which is a key step in the development of various chronic liver diseases to cirrhosis. Recent studies show that microRNAs (miRNAs) can regulate a series of liver fibrosis-related gene express and play an important role in the development of liver fibrosis. To detect the miRNAs expression profiling and to screen the differentially expressed miRNAs in patients with HBV-related liver fibrosis, the whole blood was collected from the HBV-related liver fibrosis patients (S2/3, n=8) based on Scheuer’s staging criteria. In addition, healthy volunteers(n=7) served as the control group. The expression of plasma miRNAs was detected by IlluminaHiSeq sequencing. Cluster analysis and target genes prediction of differentially expressed miRNAs were performed. Gene ontology (GO) enrichment analysis and KEGG pathway enrichment analysis of differentially expressed miRNAs target genes were performed. Compared with the healthy control group 77 miRNAs were screened out from the liver fibrosis group, among which 51 miRNAs were up-regulated and 26 miRNAs were down-regulated. Pathway annotations for the target genes of the miRNAs identified were found that it participated in many signal pathways including MAPK signaling pathway, TNF signaling pathway, Notch signaling pathway, phosphatidylinositol signal system and so on. According to the bioinformatic analysis, miR-98-5p were selected for function research among the differentially expressed miRNAs.MiR-98-5p prevents liver fibrosis by targeting TGFβR1 and blocking TGF β1/Smad3 signaling pathway. In addition, serum miR-98-5p levels were measured from a total of 70 recruited patients with chronic HBV infection and 29 healthy individuals as controls. We found that serum miR-98-5p level was significantly lower in patients with live fibrosis than in healthy controls and HBV carriers (P<0.05). Those results suggest that miR-98-5p could be a potential therapeutic target for liver fibrosis.

Bioinformatics Analysis Reveals Functions of MicroRNAs in Rice Under the Drought Stress

2021 ◽  
Vol 15 (8) ◽  
pp. 927-936 ◽  
Author(s):  
Yan Peng ◽  
Yuewu Liu ◽  
Xinbo Chen
Keyword(s):  
Drought Stress ◽  
Target Genes ◽  
Hot Spot ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Protein Protein Interaction ◽  
Promising Tool ◽  
Differentially Expressed Mirnas ◽  
Aba Biosynthesis

Background: Drought is one of the most damaging and widespread abiotic stresses that can severely limit the rice production. MicroRNAs (miRNAs) act as a promising tool for improving the drought tolerance of rice and have become a hot spot in recent years. Objective: In order to further extend the understanding of miRNAs, the functions of miRNAs in rice under drought stress are analyzed by bioinformatics. Method: In this study, we integrated miRNAs and genes transcriptome data of rice under the drought stress. Some bioinformatics methods were used to reveal the functions of miRNAs in rice under drought stress. These methods included target genes identification, differentially expressed miRNAs screening, enrichment analysis of DEGs, network constructions for miRNA-target and target-target proteins interaction. Results: (1) A total of 229 miRNAs with differential expression in rice under the drought stress, corresponding to 73 rice miRNAs families, were identified. (2) 1035 differentially expressed genes (DEGs) were identified, which included 357 up-regulated genes, 542 down-regulated genes and 136 up/down-regulated genes. (3) The network of regulatory relationships between 73 rice miRNAs families and 1035 DEGs was constructed. (4) 25 UP_KEYWORDS terms of DEGs, 125 GO terms and 7 pathways were obtained. (5) The protein-protein interaction network of 1035 DEGs was constructed. Conclusion: (1) MiRNA-regulated targets in rice might mainly involve in a series of basic biological processes and pathways under drought conditions. (2) MiRNAs in rice might play critical roles in Lignin degradation and ABA biosynthesis. (3) MiRNAs in rice might play an important role in drought signal perceiving and transduction.

scholarly journals MicroRNA expression profiling involved in Borax-induced anti-tumor effect using gene-chip analysis

2020 ◽  
Author(s):  
Lun Wu ◽  
Ying Wei ◽  
Wen-Bo Zhou ◽  
Jiao Zhou ◽  
Li-Hua Yang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Hepg2 Cells ◽  
Enrichment Analysis ◽  
Gene Chip ◽  
Differentially Expressed ◽  
Control Group ◽  
Pathway Enrichment Analysis ◽  
Ras Signaling ◽  
Therapeutic Benefits ◽  
Differentially Expressed Mirnas

Abstract Background Borax, a boron compound, which is becoming widely recognized for its biological effects, including antioxidant activity, cytotoxicity, and potential therapeutic benefits. However, the specific molecular mechanisms underlying borax-induced anti-tumor effect still remain to be to further elucidated. MicroRNAs (miRNAs) may play key roles in cellular processes including tumor progression, cell apoptosis and cytotoxicity. Thus, this study aimed to investigate, whether miRNAs were involved in the borax-mediated anti-tumor effect using miRNA profiling of a human liver cancer cell line (HepG2) using gene-chip analysis.Methods Total RNA was extracted and purified from HepG2 cells that were treated with 4 mM borax for either 2 or 24 h. The samples underwent microarray analysis using an Agilent Human miRNA Array. Differentially expressed miRNAs were analysed by volcano plot and heatmap, and were validated using real-time fluorescent quantitative PCR (qPCR).ResultsAmong this, 2- or 24-h exposure to borax significantly altered the expression level of miRNAs in HepG2 cells, 4 or 14 were upregulated and 3 were downregulated compared with the control group, respectively (≥2-fold; P<0.05). GO enrichment analysis and KEGG pathway enrichment analysis revealed that target genes of differentially expressed miRNAs in HepG2 cells predominantly participated in MAPK signaling pathway, TGF-beta signaling pathway, NF-kappa B signaling pathway, etc; in 2-h borax treatment group, while Ras signaling pathway, FoxO signaling pathway, Cellular senescence, etc; involved in 24-h treatment group.Conclusions Result indicates that borax-induced anti-tumor effect may be associated with alterations in miRNAs.

scholarly journals Identification of microRNAs and genes as biomarkers of atrial fibrillation using a bioinformatics approach

2019 ◽  
Vol 47 (8) ◽  
pp. 3580-3589 ◽  
Author(s):  
Yingyuan Li ◽  
Wulin Tan ◽  
Fang Ye ◽  
Faling Xue ◽  
Shaowei Gao ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Control Groups ◽  
Protein Protein Interaction ◽  
Differentially Expressed Mirnas ◽  
Software Modules ◽  
And Control

Objective We aimed to explore potential microRNAs (miRNAs) and target genes related to atrial fibrillation (AF). Methods Data for microarrays GSE70887 and GSE68475, both of which include AF and control groups, were downloaded from the Gene Expression Omnibus database. Differentially expressed miRNAs between AF and control groups were identified within each microarray, and the intersection of these two sets was obtained. These miRNAs were mapped to target genes in the miRNet database. Functional annotation and enrichment analysis of these target genes was performed in the DAVID database. The protein-protein interaction (PPI) network from the STRING database and the miRNA-target-gene network were merged into a PPI-miRNA network using Cytoscape software. Modules of this network containing miRNAs were detected and further analyzed. Results Ten differentially expressed miRNAs and 1520 target genes were identified. Three PPI-miRNA modules were constructed, which contained miR-424, miR-15a, miR-542-3p, and miR-421 as well as their target genes, CDK1, CDK6, and CCND3. Conclusion The identified miRNAs and genes may be related to the pathogenesis of AF. Thus, they may be potential biomarkers for diagnosis and targets for treatment of AF.

scholarly journals System Analysis of MIRNAs in Maize Internode Elongation

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 417
Author(s):  
Chuanxi Peng ◽  
Xing Wang ◽  
Tianyu Feng ◽  
Rui He ◽  
Mingcai Zhang ◽  
...  
Keyword(s):  
Target Genes ◽  
System Analysis ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Internode Elongation ◽  
Differentially Expressed Mirnas ◽  
Post Transcriptional Regulation

MicroRNAs (miRNAs), the post-transcriptional gene regulators, are known to play an important role in plant development. The identification of differentially expressed miRNAs could better help us understand the post-transcriptional regulation that occurs during maize internode elongation. Accordingly, we compared the expression of MIRNAs between fixed internode and elongation internode samples and classified six differentially expressed MIRNAs as internode elongation-responsive miRNAs including zma-MIR160c, zma-MIR164b, zma-MIR164c, zma-MIR168a, zma-MIR396f, and zma-MIR398b, which target mRNAs supported by transcriptome sequencing. Functional enrichment analysis for predictive target genes showed that these miRNAs were involved in the development of internode elongation by regulating the genes respond to hormone signaling. To further reveal how miRNA affects internode elongation by affecting target genes, the miRNA–mRNA–PPI (protein and protein interaction) network was constructed to summarize the interaction of miRNAs and these target genes. Our results indicate that miRNAs regulate internode elongation in maize by targeting genes related to cell expansion, cell wall synthesis, transcription, and regulatory factors.

scholarly journals Identification and characterization of heat-responsive microRNAs at the booting stage in two rice varieties 9311 and Nagina 22

Genome ◽  
2021 ◽  
Author(s):  
Ying Luo ◽  
Tao Wang ◽  
Dan Yang ◽  
Biao Luo ◽  
Weiping Wang ◽  
...  
Keyword(s):  
Stress Responses ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Elevated Temperatures ◽  
Differentially Expressed ◽  
Control Group ◽  
Microrna Target ◽  
Rice Varieties ◽  
Booting Stage ◽  
Differentially Expressed Mirnas

Abstract: MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs that play important roles in abiotic stress responses in plants. but their regulatory roles in the adaptive response to heat stress at the booting stage in two rice varieties 9311 and Nagina 22, remain largely unknown. In this study, 464 known miRNAs and 123 potential novel miRNAs were identified. Of these miRNAs, a total of 90 differential expressed miRNAs were obtained with 9311 libraries as control group, of which 54 upregulated and 36 downregulated miRNAs. To gain insight into functional significance, 2773 potential target genes of these 90 differentially expressed miRNAs were predicted. GO enrichment showed that the predicted target genes of differentially expressed miRNAs including NACs, LACs, CSD, and Hsp40. KEGG pathway analysis showed that target genes of these differentially expressed miRNAs were significantly enriched in plant hormone signal transduction pathway. The expression levels of ten differentially expressed miRNAs and their target genes obtained by qRT-PCR were largely consistent with the sequencing results. This study lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in rice at elevated temperatures. Key words: rice, heat-responsive, microRNA, target gene, booting stage, high-throughput sequencing

scholarly journals Circulating miRNA Profiling in Plasma Samples of Ovarian Cancer Patients

2019 ◽  
Vol 20 (18) ◽  
pp. 4533 ◽  
Author(s):  
András Penyige ◽  
Éva Márton ◽  
Beáta Soltész ◽  
Melinda Szilágyi-Bónizs ◽  
Róbert Póka ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Cancer Patients ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Cancer Development ◽  
Plasma Samples ◽  
Circulating Mirna ◽  
Differentially Expressed Mirnas ◽  
Potential Biomarkers

Ovarian cancer is one of the most common cancer types in women characterized by a high mortality rate due to lack of early diagnosis. Circulating miRNAs besides being important regulators of cancer development could be potential biomarkers to aid diagnosis. We performed the circulating miRNA expression analysis in plasma samples obtained from ovarian cancer patients stratified into FIGO I, FIGO III, and FIGO IV stages and from healthy females using the NanoString quantitative assay. Forty-five miRNAs were differentially expressed, out of these 17 miRNAs showed significantly different expression between controls and patients, 28 were expressed only in patients, among them 19 were expressed only in FIGO I patients. Differentially expressed miRNAs were ranked by the network-based analysis to assess their importance. Target genes of the differentially expressed miRNAs were identified then functional annotation of the target genes by the GO and KEGG-based enrichment analysis was carried out. A general and an ovary-specific protein–protein interaction network was constructed from target genes. Results of our network and the functional enrichment analysis suggest that besides HSP90AA1, MYC, SP1, BRCA1, RB1, CFTR, STAT3, E2F1, ERBB2, EZH2, and MET genes, additional genes which are enriched in cell cycle regulation, FOXO, TP53, PI-3AKT, AMPK, TGFβ, ERBB signaling pathways and in the regulation of gene expression, proliferation, cellular response to hypoxia, and negative regulation of the apoptotic process, the GO terms have central importance in ovarian cancer development. The aberrantly expressed miRNAs might be considered as potential biomarkers for the diagnosis of ovarian cancer after validation of these results in a larger cohort of ovarian cancer patients.

Genome-wide analysis of microRNAs expression profiling in patients with primary IgA nephropathy

Genome ◽  
2013 ◽  
Vol 56 (3) ◽  
pp. 161-169 ◽  
Author(s):  
Kuibi Tan ◽  
Jing Chen ◽  
Wuxian Li ◽  
Yuyu Chen ◽  
Weiguo Sui ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Immunoglobulin A ◽  
Differentially Expressed ◽  
Control Group ◽  
Pathological Changes ◽  
Genome Wide ◽  
Differentially Expressed Mirnas ◽  
Specific Tissue ◽  
Mirnas Expression

The aim of this study was to investigate the differential expression characteristics and the roles of the genome-wide microRNAs (miRNAs) in immunoglobulin A nephropathy (IgAN) kidney tissues. We used Illumina high-throughput sequencing technology to evaluate the miRNAs expression of six biopsy tissues from IgAN and six normal renal cortex specimens from patients with renal cell carcinoma. We observed a total of 85 miRNAs that were differentially expressed in the six IgAN patients, of which 11 miRNAs were up-regulated and 74 miRNAs were down-regulated in patients' tissues compared with control tissues. Additionally, we identified 55 candidate novel miRNAs in our study, which comprised seven candidates who were detected in the IgAN group and 49 candidates who were detected in the control group. Only one candidate (miR-n-9) was expressed in both groups. The bioinformatics showed that the regulated target genes of differentially expressed miRNAs were associated with immune and renal pathological changes. The identification of specific tissue miRNAs in our study not only helped clarify the genetics or immunology mechanisms involved in the pathogenesis of IgAN but also helped explain the pathological changes in the kidney tissues. We hypothesize that some significant miRNAs might potentially serve as novel diagnostic biomarkers in IgAN patients.

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