scholarly journals ARHGEF3 Associated with Invasion, Metastasis, and Proliferation in Human Osteosarcoma

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Jie Gong ◽  
Wei Tang ◽  
Bin Lv ◽  
Shushu Zhang ◽  
Tingjuan Fan ◽  
...  
Keyword(s):  
Target Genes ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Qrt Pcr ◽  
Human Osteosarcoma ◽  
Gene Profiles ◽  
Kaplan Meier ◽  
Differentially Expressed Mirnas ◽  
Kaplan Meier Plotter ◽  
Geo Database

Background. Osteosarcoma is a malignant bone tumor composed of mesenchymal cells producing osteoid and immature bone. This study is aimed at developing novel potential prognostic biomarkers and constructing a miRNA-mRNA network for progression in osteosarcoma. Method. GSE70367 and GSE70414 were obtained in the Gene Expression Omnibus (GEO) database. GEO software and the GEO2R calculation method were used to analyze two gene profiles. The coexpression of differentially expressed miRNAs (DEMs) and genes (DEGs) was identified and searched for in the FunRich database for pathway and ontology analysis. Cytoscape was utilized to construct the mRNA-miRNA network. Survival analysis of identified miRNAs and mRNAs was performed by utilizing the Kaplan-Meier Plotter. Besides, expression levels of DEMs and target mRNAs were verified by performing quantitative real-time PCR (qRT-PCR) and Western blot (WB). Results. Six differentially expressed microRNAs (DEMs) were identified, and 8 target genes were selected after screening. By using the KM Plotter software, miRNA-124 and ARHGEF3 were obviously associated with the overall survival of patients with osteosarcoma. Furthermore, ARHGEF3 was found downregulated in osteosarcoma cells by performing qRT-PCR and WB experiments. Results also showed that downregulated ARHGEF3 may associate with invasion, metastasis, and proliferation. Conclusions. By using microarray and bioinformatics analysis, DEMs were selected, and a complete miRNA-mRNA network was constructed. ARHGEF3 may act as a therapeutic and prognostic target of osteosarcoma.

scholarly journals Identification of key miRNA and hub genes in lung adenocarcinoma by bioinformatics and functional analysis

2020 ◽  
Author(s):  
Jiayao Zhu ◽  
Yan Zhang ◽  
Jingjing Lu ◽  
Le Wang ◽  
Xiaoren Zhu ◽  
...  
Keyword(s):  
Survival Analysis ◽  
Lung Adenocarcinoma ◽  
Target Gene ◽  
Target Genes ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Kaplan Meier ◽  
Differentially Expressed Mirnas

Abstract Background: lung adenocarcinoma is the main subtype of lung cancer and the most fatal malignant disease in the world. However, the pathogenesis of lung adenocarcinoma has not been fully elucidated.Methods: Three LUAD-associated datesets (GSE118370, GSE43767 and GSE74190) were downloaded from the Gene Expression Omnibus (GEO) datebase and the differentially expressed miRNAs (DEMs) and genes (DEGs) were screened by GEO2R. The prediction of target gene of differentially expressed miRNA were used miRWALK. Metascape was used to enrich the overlapped genes of DEGs and target genes. Then, the protein-protein interaction(PPI) and DEMs-DEGs regulatory network were created via String datebase and Cytoscape. Finally, overall survival analysis was established via the Kaplan–Meier curve and look for the possible prognostic biomarkers.Result: In this study, 433 differential genes were identified. There were 267 genes overlapped with the target gene of Dems, and eight hub genes (CDH1, CDH5, CAV1, MMP9, PECAM1, CD24, ENG, MME) were screened out. There were 85 different miRNAs in total, among which 16 miRNA target genes intersect with DEGs, 12 miRNAs with the highest interaction were screened out, and survival analysis of miRNA and hub genes was carried out.Conclusion: we found that miRNA-940, miRNA-125a-3p, miRNA-140-3p, miRNA-542-5p, CDH1, CDH5, CAV1, MMP9, PECAM1 may be related to the development of LUAD.

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 Small RNA sequencing evaluation of renal microRNA biomarkers in dogs with X-linked hereditary nephropathy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Candice P. Chu ◽  
Shiguang Liu ◽  
Wenping Song ◽  
Ethan Y. Xu ◽  
Mary B. Nabity
Keyword(s):  
Small Rna ◽  
Target Genes ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Ckd Progression ◽  
Critical Pathways ◽  
Qrt Pcr ◽  
Hereditary Nephropathy ◽  
Differentially Expressed Mirnas

AbstractDogs with X-linked hereditary nephropathy (XLHN) are an animal model for Alport syndrome in humans and progressive chronic kidney disease (CKD). Using mRNA sequencing (mRNA-seq), we have characterized the gene expression profile affecting the progression of XLHN; however, the microRNA (miRNA, miR) expression remains unknown. With small RNA-seq and quantitative RT-PCR (qRT-PCR), we used 3 small RNA-seq analysis tools (QIAGEN OmicSoft Studio, miRDeep2, and CPSS 2.0) to profile differentially expressed renal miRNAs, top-ranked miRNA target genes, and enriched biological processes and pathways in CKD progression. Twenty-three kidney biopsies were collected from 5 dogs with XLHN and 4 age-matched, unaffected littermates at 3 clinical time points (T1: onset of proteinuria, T2: onset of azotemia, and T3: advanced azotemia). We identified up to 23 differentially expressed miRNAs at each clinical time point. Five miRNAs (miR-21, miR-146b, miR-802, miR-142, miR-147) were consistently upregulated in affected dogs. We identified miR-186 and miR-26b as effective reference miRNAs for qRT-PCR. This study applied small RNA-seq to identify differentially expressed miRNAs that might regulate critical pathways contributing to CKD progression in dogs with XLHN.

scholarly journals Effect of miR-27b-5p on apoptosis of human vascular endothelial cells induced by simulated microgravity

APOPTOSIS ◽  
2019 ◽  
Vol 25 (1-2) ◽  
pp. 73-91 ◽  
Author(s):  
Yi-Kai Pan ◽  
Cheng-Fei Li ◽  
Yuan Gao ◽  
Yong-Chun Wang ◽  
Xi-Qing Sun
Keyword(s):  
Endothelial Cells ◽  
Western Blot ◽  
Target Gene ◽  
Simulated Microgravity ◽  
Target Genes ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Luciferase Assay ◽  
Qrt Pcr ◽  
Differentially Expressed Mirnas

AbstractWeightlessness-induced cardiovascular dysfunction can lead to physiological and pathological consequences. It has been shown that spaceflight or simulated microgravity can alter expression profiles of some microRNAs (miRNAs). Here, we attempt to identify the role of miRNAs in human umbilical vein endothelial cells (HUVECs) apoptosis under simulated microgravity. RNA-sequencing and quantitative real-time PCR (qRT-PCR) assays were used to identify differentially expressed miRNAs in HUVECs under simulated microgravity. Then we obtained the target genes of these miRNAs through target analysis software. Moreover, GO and KEGG enrichment analysis were performed. The effects of these miRNAs on HUVECs apoptosis were evaluated by flow cytometry, Western blot and Hoechst staining. Furthermore, we obtained the target gene of miR-27b-5p by luciferase assay, qRT-PCR and Western blot. Finally, we investigated the relationship between this target gene and miR-27b-5p in HUVECs apoptosis under normal gravity or simulated microgravity. We found 29 differentially expressed miRNAs in HUVECs under simulated microgravity. Of them, the expressions of 3 miRNAs were validated by qRT-PCR. We demonstrated that miR-27b-5p affected HUVECs apoptosis by inhibiting zinc fingers and homeoboxes 1 (ZHX1). Our results reported here demonstrate for the first time that simulated microgravity can alter the expression of some miRNAs in HUVECs and miR-27b-5p may protect HUVECs from apoptosis under simulated microgravity by targeting ZHX1.

scholarly journals Screening and validation of differentially expressed microRNAs and target genes in hypertensive mice induced by cytomegalovirus infection

2020 ◽  
Vol 40 (12) ◽  
Author(s):  
YunZhong Shi ◽  
DongMei Xi ◽  
XiaoNi Zhang ◽  
Zhen Huang ◽  
Na Tang ◽  
...  
Keyword(s):  
Target Genes ◽  
Reporter Gene Assay ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Luciferase Reporter Gene ◽  
Mcmv Infection ◽  
Luciferase Reporter Gene Assay ◽  
Qrt Pcr ◽  
Gene Assay ◽  
Differentially Expressed Mirnas

Abstract Introduction: Multiple studies have suggested an association between cytomegalovirus (CMV) infection and essential hypertension (EH). MicroRNAs (miRNAs) play a critical role in the development of EH by regulating the expression of specific target genes. However, little is known about the role of miRNAs in CMV-induced EH. In the present study, we compared the miRNA expression profiles of samples from normal and murine cytomegalovirus (MCMV)-infected C57BL/6 mice using high-throughput sequencing analysis. Methods: We collected the thoracic aorta, heart tissues, and peripheral blood from 20 normal mice and 20 MCMV-infected mice. We identified differentially expressed miRNAs in the peripheral blood samples and predicted their target genes using bioinformatics tools. We then experimentally validated them using quantitative reverse transcription polymerase chain reaction (qRT-PCR) and the target genes with double luciferase reporter gene assay. Results: We found 118 differentially expressed miRNAs, among which 9 miRNAs were identified as potential MCMV infection-induced hypertension regulators. We then validated the expression of two candidate miRNAs, mmu-miR-1929-3p and mcmv-miR-m01-4-5p, using qRT-PCR. Furthermore, the dual-luciferase reporter gene assay revealed that the 3′-untranslated region (UTR) of endothelin A receptor (Ednra) messenger RNA (mRNA) contained a binding site for mmu-miR-1929-3p. Collectively, our data suggest that MCMV infection can raise the blood pressure and reduce mmu-miR-1929-3p expression in C57BL/6 mice. Moreover, we found that mmu-miR-1929-3p targets the 3′-UTR of the Ednra mRNA. Conclusion: This novel regulatory axis could aid the development of new approaches for the clinical prevention and control of EH.

scholarly journals MiRNA biomarkers and potential critical genes associated with the prognosis of gastric cancer

2021 ◽  
Author(s):  
Zhou Chen ◽  
Hao Xu ◽  
Zhongtian Bai ◽  
Shi Dong ◽  
Jian Zhang ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Target Genes ◽  
Cox Model ◽  
Differential Expression Analysis ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Diagnosis And Prognosis ◽  
Kaplan Meier ◽  
Differentially Expressed Mirnas ◽  
Pathway Analyses

Abstract Background Dysregulated expression of miRNAs in gastric cancer (GC) is associated with tumor progression. MiRNA markers are important for the prognosis and therapeutic targeting of GC patients. Methods To detect differentially expressed miRNAs in GC from the TCGA database and predict their target genes. We downloaded RNA sequencing (RNA-seq), miRNA-seq and clinical data of GC from TCGA. Differential expression analysis of RNA-seq and miRNA-seq data was performed by R 3.6.1. MiRNAs associated with prognosis were evaluated with the Cox model, and differentially expressed miRNAs were assessed by Kaplan–Meier curve analysis. Risk factors were identified in the Cox model. Target genes of differentially expressed miRNAs were searched in three databases. GO enrichment and KEGG pathway analyses were used to evaluate the biological functions of these target genes.Results Five miRNAs (hsa-miR-135b-3p, hsa-miR-143-5p, hsa-miR-196b-3p, hsa-miR-942-3p, hsa-miR-9-3p) were related to survival. Eight target genes (AKAP12, AR, DZIP1, PCDHA11, PCDHA12, PI15, SH3BGRL and TMEM108) were closely correlated with patient overall survival (OS). Conclusion Differentially expressed miRNAs and their target genes have an important influence on the diagnosis and prognosis of GC and may be used as tumor biomarkers in further studies and as potential therapeutic targets.

scholarly journals High-Throughput Sequencing Reveals the Differential MicroRNA Expression Profiles of Human Gastric Cancer SGC7901 Cell Xenograft Nude Mouse Models Treated with Traditional Chinese Medicine Si Jun Zi Tang Decoction

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Junfu Guo ◽  
Xiangnan Li ◽  
Lanying Miao ◽  
Hongwei Sun ◽  
Xia Gao ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Human Gastric Cancer ◽  
Model Group ◽  
Sgc7901 Cell ◽  
Qrt Pcr ◽  
Differentially Expressed Mirnas

Objective. The present study aimed to investigate the potential mechanism underlying the antitumor effect of Si Jun Zi Tang (SJZT) decoction on gastric cancer. Methods. Twelve human gastric cancer SGC7901 cell xenograft nude mouse models were established. The mice were randomly divided into the Model group and SJZT group. SJZT exerted significant antitumor effects after 21 days of decoction administration. High-throughput sequencing was used to analyze the microRNA (miRNA) expression profiles of tumor tissues. Bioinformatics analysis was performed to provide further information regarding the differentially expressed miRNAs. Five representative differentially expressed miRNAs and four predicted target genes were further validated using quantitative real-time reverse transcription PCR (qRT-PCR). Results. We identified 33 miRNAs that were differentially expressed in the SJZT group compared with the Model group. Among them, 32 miRNAs were upregulated and 1 miRNA was downregulated. Bioinformatic analysis showed that most of miRNAs acted as tumor suppressors and their target genes participated in multiple signaling pathways, including the PI3K/Akt signaling pathway, microRNAs in cancer, and Wnt signaling pathway. The qRT-PCR result confirmed that miR-223-3p, miR-205-5p, miR-147b-3p, and miR-223-5p were overexpressed and their respective paired target genes FUT9, POU2F1, MUC4, and RAB14 mRNA were obviously downregulated in the SJZT group compared with those in the Model group. Network analysis revealed that miR-223-3p and miR-205-5p shared two targets POU2F1 (encoding POU class 2 homeobox 1) and FUT9 (encoding fucosyltransferase 9), suggesting they have a common role in certain pathways. Conclusion. This study provided novel insights into the anticancer mechanism of SJZT against gastric cancer, which might be partly related to the modulation of miRNA expression and their target pathways in tumors.

scholarly journals Chinese Herbal Medicine Formula Shenling Baizhu San Ameliorates High-Fat Diet-Induced NAFLD in Rats by Modulating Hepatic MicroRNA Expression Profiles

2019 ◽  
Vol 2019 ◽  
pp. 1-14
Author(s):  
Maoxing Pan ◽  
Yuanjun Deng ◽  
Chuiyang Zheng ◽  
Huan Nie ◽  
Kairui Tang ◽  
...  
Keyword(s):  
Mirna Expression ◽  
High Fat Diet ◽  
Target Genes ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
High Fat ◽  
Expression Levels ◽  
Qrt Pcr ◽  
Mirna Expression Profiles ◽  
Differentially Expressed Mirnas

Objective. The purpose of present study was to investigate the potential mechanism underlying the protective effect of Shenling Baizhu San (SLBZS) on nonalcoholic fatty liver disease (NAFLD) by microRNA (miRNA) sequencing. Methods. Thirty male Wistar rats were randomly divided into a normal control (NC) group, a high-fat diet (HFD) group, and an SLBZS group. After 12 weeks, the biochemical parameters and liver histologies of the rats were assessed. The Illumina HiSeq 2500 sequencing platform was used to analyse the hepatic miRNA expression profiles. Representative differentially expressed miRNAs were further validated by qRT-PCR. The functions of the differentially expressed miRNAs were analysed by bioinformatics. Results. Our results identified 102 miRNAs that were differentially expressed in the HFD group compared with the NC group. Among those differentially expressed miRNAs, the expression levels of 28 miRNAs were reversed by SLBZS administration, suggesting the modulation effect of SLBZS on hepatic miRNA expression profiles. The qRT-PCR results confirmed that the expression levels of miR-155-5p, miR-146b-5p, miR-132-3p, and miR-34a-5p were consistent with those detected by sequencing. Bioinformatics analyses indicated that the target genes of the differentially expressed miRNAs reversed by SLBZS were mainly related to metabolic pathways. Conclusion. This study provides novel insights into the mechanism of SLBZS in protecting against NAFLD; this mechanism may be partly related to the modulation of hepatic miRNA expression and their target pathways.

Screening miRNA and their target genes related to tetralogy of Fallot with microarray

2013 ◽  
Vol 24 (3) ◽  
pp. 442-446 ◽  
Author(s):  
Xian-min Wang ◽  
Kui Zhang ◽  
Yan Li ◽  
Kun Shi ◽  
Yi-ling Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Functional Analysis ◽  
Tetralogy Of Fallot ◽  
Gene Expression Profile ◽  
Target Genes ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Differentially Expressed Mirnas ◽  
Protein Localisation ◽  
Relationship Of

AbstractOur aim is to screen miRNAs and genes related to tetralogy of Fallot and construct a co-expression network based on integrating miRNA and gene microarrays. We downloaded the gene expression profile GSE35490 (miRNA) and GSE35776 (mRNA) of tetralogy of Fallot from the Gene Expression Omnibus database, which includes eight normal and 15 disease samples from infants, and screened differentially expressed miRNAs and genes between normal and disease samples (cut-off: p < 0.05; FDR < 0.05; and log FC > 2 or log FC < −2); in addition, we downloaded human miRNA and their targets, which were collected in the miRNA targets prediction database TargetScan, and selected ones that also appeared in our differentially expressed miRNAs and their predicted targets (score >0.9) and then made a relationship of diff_miRNAs and diff_genes of our results. Finally, we uploaded all the diff_target genes into String, constructed a co-expression network regulated by diff_miRNAs, and performed functional analysis with the software DAVID. Comparing normal and disease lesion tissue, we got 32 and 875 differentially expressed miRNAs and genes, respectively, and found hsa-miR-124 with 34 diff_target genes and hsa-miR-138 with two diff_target genes. Then we constructed a co-expression network that contains 231 pairs of genes. Genes in the network were enriched into 14 function clusters, and the most significant one is protein localisation. We screened the tetralogy of Fallot-related hsa-miR-124 and hsa-miR-138 with their direct and indirect differentially expressed target genes, and found that protein localisation is the significant cause affecting tetralogy of Fallot. Our approach may provide the groundwork for a new therapy approach to treating tetralogy of Fallot.

scholarly journals MiRNAs expression profiling of rat ovaries displaying PCOS with insulin resistance

2020 ◽  
Vol 302 (5) ◽  
pp. 1205-1213
Author(s):  
Chunren Zhang ◽  
Chuyi Yu ◽  
Zengxian Lin ◽  
Haixia Pan ◽  
Kunyin Li ◽  
...  
Keyword(s):  
Insulin Resistance ◽  
Target Genes ◽  
Kegg Pathway ◽  
Polycystic Ovary ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Real Time Quantitative Pcr ◽  
Qrt Pcr ◽  
Differentially Expressed Mirnas ◽  
Pathway Analyses

Abstract Purpose The present study established microRNA (miRNA) expression profiles for rat ovaries displaying polycystic ovary syndrome (PCOS) with insulin resistance and explored the underlying biological functions of differentially expressed miRNAs. Methods A PCOS with insulin resistance rat model was created by administering letrozole and a high-fat diet. Total RNA was extracted from the ovaries of PCOS with insulin resistance rats and normal rats. Three ovaries from each group were used to identify differentially expressed miRNAs by deep sequencing. A hierarchical clustering heatmap and volcano plot were used to display the pattern of differentially expressed miRNAs. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to explore the potential target genes of the differentially expressed miRNAs and identify their putative biological function. Nine of the differentially expressed miRNAs were selected for validation by Real-time Quantitative PCR (qRT-PCR). Results A total of 58 differentially expressed miRNAs were identified in the rat ovaries exhibiting PCOS with insulin resistance compared with control ovaries, including 23 miRNAs that were upregulated and 35 miRNAs that were downregulated. GO and KEGG pathway analyses revealed that the predicted target genes were related to metabolic processes, cellular processes, and metabolic pathways. Furthermore, qRT-PCR confirmed that miR-3585-5p and miR-30-5p were significantly upregulated and miR-146-5p was downregulated in the ovaries of PCOS with insulin resistance rats compared with the controls. Conclusion These results indicate that differentially expressed miRNAs in rat ovaries may be involved in the pathophysiology of insulin resistance in PCOS. Our study may be beneficial in establishing miRNAs as novel diagnostic and therapeutic biomarkers for insulin resistance in PCOS.

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