Recognition of the Possible miRNA-mRNA Controlling Network in Stroke by Bioinformatics Examination

Background. Based on the latest research of WHO, it has been revealed that more than 15 million people suffer from stroke every year worldwide. Of these 15 million people, 6 million succumb to death, and 5 million get permanently disabled. This is the prime reason for the substantial economic burden on all parts of the world. Methods. These data have been obtained from the GEO database, and the GEO2R tool was used to find out the differentially expressed miRNAs (DEMs) between the stroke and normal patients’ blood. FunRich and miRNet were considered to find potential upstream transcription factors and downstream target genes of candidate EMRs. Next, we use GO annotation and KEGG pathway enrichment. Target genes were analyzed with the help of the R software. Then, the STRING database and Cytoscape software were used to conduct PPI and DEM-hub gene networks. Finally, GSE58294 was used to estimate the hub gene expressions. Results. Six DEMs in total were selected out from GSE95204 and GSE117064 datasets. 663 DEMs’ target genes were predicted, and NRF1, EGR1, MYC, YY1, E2F1, SP4, and SP1 were predicted as an upstream transcription factor for DEMs’ target genes. Target genes of DEMs were primarily augmented in the PI3K-Akt signaling pathway and p53 signaling pathway. The network construction of DEM hygiene is potentially modulated by hsa-miR-3591-5p, hsa-miR-548as-3p, hsa-miR-206, and hsa-miR-4503 hub genes which were found among the top 10 of the hub genes. Among the top 10 hub genes, justification of CTNNB1, PTEN, ESR1, CCND1, KRAS, AKT1, CCND2, CDKN1B, and MYCN was constant with that in the GSE58294 dataset. Conclusion. In summary, our research first constructs the miRNA-mRNA network in stroke, which probably renders an awakening purview into the pathogenesis and cure of stroke.

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Mathematical analysis of the effect of portal vein cells on biliary epithelial cell differentiation through the Delta-Notch signaling pathway

BMC Research Notes ◽

10.1186/s13104-021-05656-y ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Masaharu Yoshihara ◽

Teppei Nishino ◽

Manoj Kumar Yadav ◽

Akihiro Kuno ◽

Takeshi Nagata ◽

...

Keyword(s):

Portal Vein ◽

Notch Signaling ◽

Signaling Pathway ◽

Target Genes ◽

Notch Signaling Pathway ◽

Epithelial Differentiation ◽

Production Rates ◽

Fine Grained ◽

Downstream Target ◽

Notch Receptors

Abstract Objective The Delta-Notch signaling pathway induces fine-grained patterns of differentiation from initially homogeneous progenitor cells in many biological contexts, including Drosophila bristle formation, where mathematical modeling reportedly suggests the importance of production rate of the components of this signaling pathway. In contrast, the epithelial differentiation of bile ducts in the developing liver is unique in that it occurs around the portal vein cells, which express extremely high amounts of Delta ligands and act as a disturbance for the amount of Delta ligands in the field by affecting the expression levels of downstream target genes in the cells nearby. In the present study, we mathematically examined the dynamics of the Delta-Notch signaling pathway components in disturbance-driven biliary differentiation, using the model for fine-grained patterns of differentiation. Results A portal vein cell induced a high Notch signal in its neighboring cells, which corresponded to epithelial differentiation, depending on the production rates of Delta ligands and Notch receptors. In addition, this epithelial differentiation tended to occur in conditions where fine-grained patterning was reported to be lacking. These results highlighted the potential importance of the stability towards homogeneity determined by the production rates in Delta ligands and Notch receptors, in a disturbance-dependent epithelial differentiation.

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Microarray analysis identification of key pathways and interaction network of differential gene expressions during osteogenic differentiation

Human Genomics ◽

10.1186/s40246-020-00293-1 ◽

2020 ◽

Vol 14 (1) ◽

Author(s):

Fatemeh Khodabandehloo ◽

Sara Taleahmad ◽

Reza Aflatoonian ◽

Farzad Rajaei ◽

Zahra Zandieh ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Signaling Pathway ◽

Expression Profiles ◽

Wnt Signaling Pathway ◽

Hub Genes ◽

Gene Expressions ◽

Cell Based Therapy ◽

Wnt Pathways ◽

Key Pathways

Abstract Background Adult bone marrow-derived mesenchymal stem cells (BM-MSCs) are multipotent stem cells that can differentiate into three lineages. They are suitable sources for cell-based therapy and regenerative medicine applications. This study aims to evaluate the hub genes and key pathways of differentially expressed genes (DEGs) related to osteogenesis by bioinformatics analysis in three different days. The DEGs were derived from the three different days compared with day 0. Results Gene expression profiles of GSE37558 were obtained from the Gene Expression Omnibus (GEO) database. A total of 4076 DEGs were acquired on days 8, 12, and 25. Gene ontology (GO) enrichment analysis showed that the non-canonical Wnt signaling pathway and lipopolysaccharide (LPS)-mediated signaling pathway were commonly upregulated DEGs for all 3 days. KEGG pathway analysis indicated that the PI3K-Akt and focal adhesion were also commonly upregulated DEGs for all 3 days. Ten hub genes were identified by CytoHubba on days 8, 12, and 25. Then, we focused on the association of these hub genes with the Wnt pathways that had been enriched from the protein-protein interaction (PPI) by the Cytoscape plugin MCODE. Conclusions These findings suggested further insights into the roles of the PI3K/AKT and Wnt pathways and their association with osteogenesis. In addition, the stem cell microenvironment via growth factors, extracellular matrix (ECM), IGF1, IGF2, LPS, and Wnt most likely affect osteogenesis by PI3K/AKT.

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Synthesizing artificial devices that redirect cellular information at will

eLife ◽

10.7554/elife.31936 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 5

Author(s):

Yuchen Liu ◽

Jianfa Li ◽

Zhicong Chen ◽

Weiren Huang ◽

Zhiming Cai

Keyword(s):

Cancer Cells ◽

Signaling Pathway ◽

Gene Networks ◽

Target Genes ◽

Logic Gates ◽

Feedback Loops ◽

Oncogenic Signaling ◽

Multiple Signals ◽

Translational Level ◽

At Will

Natural signaling circuits could be rewired to reprogram cells with pre-determined procedures. However, it is difficult to link cellular signals at will. Here, we describe signal-connectors—a series of RNA devices—that connect one signal to another signal at the translational level. We use them to either repress or enhance the translation of target genes in response to signals. Application of these devices allows us to construct various logic gates and to incorporate feedback loops into gene networks. They have also been used to rewire a native signaling pathway and even to create novel pathways. Furthermore, logical AND gates based on these devices and integration of multiple signals have been used successfully for identification and redirection of the state of cancer cells. Eventually, the malignant phenotypes of cancers have been reversed by rewiring the oncogenic signaling from promoting to suppressing tumorigenesis. We provide a novel platform for redirecting cellular information.

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Anticancer Activity of Sweroside Nanoparticles in Prostate Cancer Bone Metastasis in PC-3 Cells Involved in Wnt/β-Catenin Signaling Pathway

Journal of Biomedical Nanotechnology ◽

10.1166/jbn.2021.3172 ◽

2021 ◽

Vol 17 (10) ◽

pp. 1960-1971

Author(s):

Sheng Huang ◽

Changye Zou ◽

Shangyan Xie ◽

Bin Wang ◽

Xitao LingHu ◽

...

Keyword(s):

Prostate Cancer ◽

Stem Cell ◽

Bone Metastasis ◽

Cyclin D1 ◽

Signaling Pathway ◽

Colony Formation ◽

Target Genes ◽

Downstream Target ◽

Sphere Formation ◽

In Cells

Bone metastasis is a significant cause of morbidity and mortality in patients with prostate cancer (PCa). This study is aimed at illustrating the mechanism of sweroside-mediated regulation in bone metastasis in PCa cells. Owing to the limitations of antitumor drugs in terms of their physical and chemical properties, making them into nanomaterials can effectively improve drug stability and bioavailability. Apoptosis was assessed with flow cytometry using the annexin V/propidium iodide binding assay; proteins, including p53, P21, Bcl-2, and Bax; and induction of intracellular reactive oxygen species (ROS). Using colony formation assay, sphere formation assay, and the expression changes in CD133 and CD44, stem cell characteristics were assessed. Epithelial–mesenchymal transition (EMT) activity was accessed by levels of the expression changes of EMT-related markers, vimentin and E-cadherin. Wnt/β-catenin signaling pathway was examined to detect the levels of the expression changes of snail and β-catenin. PC-3 cells were treated with lithium chloride (LiCl), which is an agonist of Wnt/β-catenin signaling, and the levels of CD133, CD44, vimentin, E-cadherin, snail, and β-catenin were detected. T-cell factor/lymphocyte enhancer factor (TCF/LEF) activity in cells overexpressing β-catenin was used to detect the effects on β-catenin transcription, and the expression of c-myc, Cyclin D1, Survivin, and MMP-7 were used to detect Wnt downstream target genes. Our results suggest that sweroside induces apoptosis and intracellular ROS; upregulates apoptotic proteins; and suppresses proliferation, invasion, and migration, preventing stem cell characteristics, including sphere formation, colony formation, and CD133 and CD44 expressions. Furthermore, sweroside nanoparticles exerts inhibitory effects on β-catenin transcription by suppressing TTCF/LEF activity in cells overexpressing β-catenin and downregulation of the expression of Wnt downstream target genes, including c-myc, Cyclin D1, Survivin, and MMP-7. The potential therapeutic effect of sweroside nanoparticles on bone metastatis of PCa was suggested, by these findings.

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Identification and Classification of Hubs in microRNA Target Gene Networks in Human Neural Stem/Progenitor Cells following Japanese Encephalitis Virus Infection

mSphere ◽

10.1128/msphere.00588-19 ◽

2019 ◽

Vol 4 (5) ◽

Author(s):

Sriparna Mukherjee ◽

Irshad Akbar ◽

Reshma Bhagat ◽

Bibhabasu Hazra ◽

Arindam Bhattacharyya ◽

...

Keyword(s):

Progenitor Cells ◽

Gene Networks ◽

Mirna Target ◽

Target Gene ◽

Target Genes ◽

Hub Genes ◽

Protein Protein Interaction ◽

Ppi Networks ◽

Neural Stem Progenitor Cells

ABSTRACT RNA viruses are known to modulate host microRNA (miRNA) machinery for their own benefit. Japanese encephalitis virus (JEV), a neurotropic RNA virus, has been reported to manipulate several miRNAs in neurons or microglia. However, no report indicates a complete sketch of the miRNA profile of neural stem/progenitor cells (NSPCs), hence the focus of our current study. We used an miRNA array of 84 miRNAs in uninfected and JEV-infected human neuronal progenitor cells and primary neural precursor cells isolated from aborted fetuses. Severalfold downregulation of hsa-miR-9-5p, hsa-miR-22-3p, hsa-miR-124-3p, and hsa-miR-132-3p was found postinfection in both of the cell types compared to the uninfected cells. Subsequently, we screened for the target genes of these miRNAs and looked for the biological pathways that were significantly regulated by the genes. The target genes involved in two or more pathways were sorted out. Protein-protein interaction (PPI) networks of the miRNA target genes were formed based on their interaction patterns. A binary adjacency matrix for each gene network was prepared. Different modules or communities were identified in those networks by community detection algorithms. Mathematically, we identified the hub genes by analyzing their degree centrality and participation coefficient in the network. The hub genes were classified as either provincial (P < 0.4) or connector (P > 0.4) hubs. We validated the expression of hub genes in both cell line and primary cells through qRT-PCR after JEV infection and respective miR mimic transfection. Taken together, our findings highlight the importance of specific target gene networks of miRNAs affected by JEV infection in NSPCs. IMPORTANCE JEV damages the neural stem/progenitor cell population of the mammalian brain. However, JEV-induced alteration in the miRNA expression pattern of the cell population remains an open question, hence warranting our present study. In this study, we specifically address the downregulation of four miRNAs, and we prepared a protein-protein interaction network of miRNA target genes. We identified two types of hub genes in the PPI network, namely, connector hubs and provincial hubs. These two types of miRNA target hub genes critically influence the participation strength in the networks and thereby significantly impact up- and downregulation in several key biological pathways. Computational analysis of the PPI networks identifies key protein interactions and hubs in those modules, which opens up the possibility of precise identification and classification of host factors for viral infection in NSPCs.

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MicroRNA expression analysis for identification of biomarkers in inflammatory bowel disease subtypes

10.21203/rs.3.rs-27227/v1 ◽

2020 ◽

Author(s):

Manisha Mandal ◽

Shyamapada Mandal

Keyword(s):

Ribosome Biogenesis ◽

Target Genes ◽

Proteasomal Degradation ◽

Differentially Expressed ◽

Hub Genes ◽

Hub Gene ◽

Protein Protein Interaction ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

Protein Protein Interaction Networks

Abstract The potential biomarkers in inflammatory bowel diseases (IBDs) were analyzed from GSE53867 dataset. Differentially expressed microRNAs (DEMs)-genes and protein-protein interaction networks were constructed, and hub genes selected using Cytoscape. Differentially expressed genes were analyzed for GO and Reactome-pathway. Seven DEMs were upregulated in Crohn's disease (CD), 4 downregulated in ulcerative colitis (UC), 8 upregulated and 2 downregulated in IBD. A 620, 2377, and 1821 target-genes were in CD, UC, and IBD, respectively. SOCS3, upregulated by miR-650, was hub gene in CD, induced by cytokines, through NFKB-signalling pathway to mediate ubiquitin-proteasomal degradation. CIRH1A, downregulated by miR-16, was hub gene of UC, acted by impairing ribosome-biogenesis. SKP2 and ASB1, up- and downregulated, by miR-142 and miR-665, respectively, were hub genes of IBD, induced cytokines through activation of TLR- and TNF-signalling pathways to mediate ubiquitin-proteasomal degradation. SOCS3, CIRH1A, SKP2 and ASB1 genes might serve as valuable biomarkers to differentiate CD, UC and IBD.

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Construction and validation of a novel prognostic signature of microRNAs in lung adenocarcinoma

PeerJ ◽

10.7717/peerj.10470 ◽

2021 ◽

Vol 9 ◽

pp. e10470

Author(s):

Wanzhen Li ◽

Shiqing Liu ◽

Shihong Su ◽

Yang Chen ◽

Gengyun Sun

Keyword(s):

Lung Adenocarcinoma ◽

Signaling Pathway ◽

Prognostic Value ◽

Target Genes ◽

Predictive Accuracy ◽

Differentially Expressed ◽

Prognostic Signature ◽

Tissue Samples ◽

Gene Set ◽

Differentially Expressed Mirnas

MicroRNA (miRNA, miR) has been reported to be highly implicated in a wide range of biological processes in lung cancer (LC), and identification of differentially expressed miRNAs between normal and LC samples has been widely used in the discovery of prognostic factors for overall survival (OS) and response to therapy. The present study was designed to develop and evaluate a miRNA-based signature with prognostic value for the OS of lung adenocarcinoma (LUAD), a common histologic subtype of LC. In brief, the miRNA expression profiles and clinicopathological factors of 499 LUAD patients were collected from The Cancer Genome Atlas (TCGA) database. Kaplan–Meier (K-M) survival analysis showed significant correlations between differentially expressed miRNAs and LUAD survival outcomes. Afterward, 1,000 resample LUAD training matrices based on the training set was applied to identify the potential prognostic miRNAs. The least absolute shrinkage and selection operator (LASSO) cox regression analysis was used to constructed a six-miRNA based prognostic signature for LUAD patients. Samples with different risk scores displayed distinct OS in K-M analysis, indicating considerable predictive accuracy of this signature in both training and validation sets. Furthermore, time-dependent receiver operating characteristic (ROC) analysis demonstrated the nomogram achieved higher predictive accuracy than any other clinical variables after incorporating the clinical information (age, sex, stage, and recurrence). In the stratification analysis, the prognostic value of this classifier in LUAD patients was validated to be independent of other clinicopathological variables, such as age, gender, tumor recurrence, and early stage. Gene set annotation analyses were also conducted through the Hallmark gene set and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, indicating target genes of the six miRNAs were positively related to various molecular pathways of cancer, such as hallmark UV response, Wnt signaling pathway and mTOR signaling pathway. In addition, fresh cancer tissue samples and matched adjacent tissue samples from 12 LUAD patients were collected to verify the expression of miR-582’s target genes in the model, further revealing the potential relationship between SOX9, RASA1, CEP55, MAP4K4 and LUAD tumorigenesis, and validating the predictive value of the model. Taken together, the present study identified a robust signature for the OS prediction of LUAD patients, which could potentially aid in the individualized selection of therapeutic approaches for LUAD patients.

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Analysis of MicroRNA Transcriptomes Insights into the miR-148a-3p Inducer of Rumen Development in Goats

10.21203/rs.3.rs-40834/v1 ◽

2020 ◽

Author(s):

Tao Zhong ◽

Cheng Wang ◽

Jiangtao Hu ◽

Xiaoyong Chen ◽

Lili Niu ◽

...

Keyword(s):

Signaling Pathway ◽

Target Genes ◽

Genetic Regulation ◽

Mapk Signaling ◽

Regulation Mechanism ◽

Ras Signaling ◽

Genome Wide ◽

A Genome ◽

Differentially Expressed Mirnas ◽

And Function

Abstract Background: Rumen is an important digestive organ of ruminant. From fetal to adult stage, the morphology, structure and function of rumen have changed significantly. But the intrinsic genetic regulation is still limited. We previously reported a genome-wide expression profile of miRNAs in prenatal goat rumens. In the present study, we rejoined analyzed the transcriptomes of rumen miRNAs during prenatal (E60 and E135) and postnatal (D30 and D150) stages.Results: A total of 66 differentially expressed miRNAs (DEMs) were identified in the rumen tissues from D30 and D150 goats. Of these, 17 DEMs were consistently highly expressed in the rumens at the preweaning stages (E60, E135 and D30), while down-regulated at D150. Noteworthy, annotation analysis revealed that the target genes regulated by the DEMs were mainly enriched in MAPK signaling pathway, Jak-STAT signaling pathway and Ras signaling pathway. Interestingly, the expression of miR-148a-3p was significantly high in the embryonic stage and down-regulated at D150. The potential binding sites between miR-148a-3p and QKI were predicted by the TargetScan and verified by the dual luciferase report assay. The co-localization of miR-148a-3p and QKI was observed not in intestinal tracts but in rumen tissues by in situ hybridization. Moreover, the expression of miR-148a-3p in the epithelium was significantly higher than that in the other layers, suggesting that miR-148a-3p involve in the development of rumen epithelial cells by targeting QKI. Subsequently, miR-148a-3p inhibitor was found to induce the proliferation of GES-1 cells.Conclusions: Taken together, these results identified the DEMs involved in the development of rumen and provided an insight into the regulation mechanism of goat rumens during development.

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ERK1/2-Egr-1 Signaling Pathway-Mediated Protective Effects of Electroacupuncture in a Mouse Model of Myocardial Ischemia-Reperfusion

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2014/253075 ◽

2014 ◽

Vol 2014 ◽

pp. 1-11 ◽

Cited By ~ 4

Author(s):

Juan Zhang ◽

Jiangang Song ◽

Jin Xu ◽

Xuemei Chen ◽

Peihao Yin ◽

...

Keyword(s):

Myocardial Ischemia ◽

Signaling Pathway ◽

Target Genes ◽

Troponin I ◽

Inflammatory Responses ◽

Ischemia Reperfusion ◽

Interleukin 1 ◽

Protective Effects ◽

Downstream Target ◽

Myocardial Ischemia Reperfusion

Early growth response- (Egr-) 1 is an upstream master switch in controlling inflammatory responses following myocardial ischemia-reperfusion (I/R). Activation of extracellular signal-regulated protein kinase-1 and kinase-2 (ERK1/2) signaling is known to upregulate Egr-1. ERK1/2 pathway has been previously shown to mediate the therapeutic action of electroacupucture (EA). Thus, we hypothesized that EA would reduce myocardial I/R injury and inflammatory responses through inhibiting Egr-1 expression via the ERK1/2 pathway. Mice were pretreated with EA, U0126, or combination of EA and U0126 and then underwent 1 h myocardial ischemia and 3 h reperfusion. We investigated that EA significantly attenuated the I/R-induced upregulation of both Egr-1 and phosporylated-ERK1/2 (p-ERK1/2), decreased myocardial inflammatory cytokines including tumor necrosis factor-α(TNF-α) and interleukin-1β(IL-1β), and reduced the infarct size and the release of cardiac troponin I (cTnI). U0126 treatment also exhibited the same effect as EA on Egr-1 level and subsequent cardioprotective effects. There was no additive effect of cotreatment with EA and U0126 on the expression of Egr-1 and its downstream target genes (TNF-α, IL-1β) or serum cTnI level. Collectively, these observations suggested that EA attenuates myocardial I/R injury, possibly through inhibiting the ERK1/2-Egr-1 signaling pathway and reducing the release of proinflammatory cytokines.

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Identification of Metastasis-Associated MicroRNAs in Metastatic Melanoma by miRNA Expression Profile and Experimental Validation

Frontiers in Genetics ◽

10.3389/fgene.2021.663110 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yunshu Gao ◽

Jiahua Xu ◽

Hongwei Li ◽

Yi Hu ◽

Guanzhen Yu

Keyword(s):

Metastatic Melanoma ◽

Signaling Pathway ◽

Target Genes ◽

Primary Melanoma ◽

Mirna Expression Profile ◽

Melanoma Metastasis ◽

Hippo Signaling ◽

Invasive Ability ◽

Hub Genes ◽

Proliferation And Apoptosis

It is reported that microRNAs (miRNA) have paramount functions in many cellular biological processes, development, metabolism, differentiation, survival, proliferation, and apoptosis included, some of which are involved in metastasis of tumors, such as melanoma. Here, three metastasis-associated miRNAs, miR-18a-5p (upregulated), miR-155-5p (downregulated), and miR-93-5p (upregulated), were identified from a total of 63 different expression miRNAs (DEMs) in metastatic melanoma compared with primary melanoma. We predicted 262 target genes of miR-18a-5p, 904 miR-155-5p target genes, and 1220 miR-93-5p target genes. They participated in pathways concerning melanoma, such as TNF signaling pathway, pathways in cancer, FoxO signaling pathway, cell cycle, Hippo signaling pathway, and TGF-beta signaling pathway. We identified the top 10 hub nodes whose degrees were higher for each survival-associated miRNA as hub genes through constructing the PPI network. Using the selected miRNA and the hub genes, we constructed the miRNA-hub gene network, and PTEN and CCND1 were found to be regulated by all three miRNAs. Of note, miR-155-5p was obviously downregulated in metastatic melanoma tissues, and miR-18a-5p and miR-93-5p were obviously regulated positively in metastatic melanoma tissues. In validating experiments, miR-155-5p's overexpression inhibited miR-18a-5p's and miR-93-5p's expression, which could all significantly reduce SK-MEL-28 cells' invasive ability. Finally, miR-93-5p and its potential target gene UBC were selected for further validation. We found that miR-93-5p's inhibition could reduce SK-MEL-28 cell's invasive ability through upregulated the expression of UBC, and the anti-invasive effect was reserved by downregulation of UBC. The results show that the selected three metastasis-associated miRNAs participate in the process of melanoma metastasis via regulating their target genes, providing a potential molecular mechanism for this disease.

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