Identification of core genes and prediction of miRNAs associated with osteoporosis using a bioinformatics approach

Chai, Yi; Tan, Feng; Ye, Sumin; Liu, Feixiang; Fan, Qing

doi:10.3892/ol.2018.9508

Cited by 10 publications

(11 citation statements)

References 55 publications

(54 reference statements)

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“…576 genes were detected as the target of this miRNA and KEGG pathway analysis has shown that these genes were mostly enriched in adrenergic signaling in cardiomyocytes and adherens junction. Some other reports in the literature that show the association of these two pathways with osteoporosis [54,55]. Furthermore, target genes of miR-133a-3p were used to establish the PPI network by using Cytoscape and six genes in the PPI network were identified as hub genes (degree≥15).…”

Section: Discussionmentioning

confidence: 99%

Differentially expressed circulating miRNAs in postmenopausal osteoporosis: a meta-analysis

Pala

Denkçeken

2019

Bioscience Reports

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MicroRNAs (miRNAs) have been proven to play a crucial role in postmenopausal osteoporosis (PMO), and studies on their diagnostic value have been increasing. In our study, we aim to identify the key miRNAs in the PMO that might be potential biomarkers. A comprehensive systematic literature search was conducted by searching PubMed, Web of Science, Embase and Cochrane Library databases. In the total of 16 independent miRNA expression studies which contained 327 PMO patients and 328 postmenopausal (PM) healthy control samples, miRNAs were evaluated by using robust rank aggregation (RRA) method. A statistically significant meta-signature of up-regulated hsa-miR-133a-3p (P = 1.38e−03) was determined. Then bioinformatics analysis to recruit putative target genes prediction of hsa-miR-133a-3p and pathway enrichment analysis to reveal what biological processes this miRNA may affect were conducted. It was indicated that pathways were commonly associated with adrenergic signaling in cardiomyocytes, adherens junction, PI3K-Akt signaling pathway and AMPK signaling pathway. Furthermore, STRING and Cytoscape tools were used to visualize the interactions between target genes of hsa-miR-133a-3p. Six genes were detected as hub genes among 576 targets which were CDC42, RHOA, EGFR, VAMP2, PIK3R2 and FN1. After Kyoto Encyclopedia of Genes and Genomes pathway analysis, it was detected that these hub genes were mostly enriched in signaling pathways and cancer. In this meta-analysis, it is stated that circulating hsa-miR-133a-3p may serve as a potential non-invasive biomarker and therapeutic target in PMO.

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Section: Discussionmentioning

confidence: 99%

Differentially expressed circulating miRNAs in postmenopausal osteoporosis: a meta-analysis

Pala

Denkçeken

2019

Bioscience Reports

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“…A microRNA profiling microarray expression dataset consisting of three pairs of parental EOC cells and their PTX-resistant sublines (GSE148251) ( 20 ) was downloaded from Gene Expression Omnibus (GEO platform). The miRNA expression levels were analyzed using GEO2R bioconductor project and provided as log2 ratios ( 21 ). We explored three mRNA target-predicting algorithms including mirSVR, Target scan and miRDB to screen the potential downstream targets of hsa-miR-105 ( 22 ).…”

Section: Methodsmentioning

confidence: 99%

Role of hsa‑miR‑105 during the pathogenesis of paclitaxel resistance and its clinical implication in ovarian cancer

Mao

Zhang

et al. 2021

Oncol Rep

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More than 70% of patients with epithelial ovarian cancer (EOC), one of the leading cause of gynecological cancer-related deaths worldwide, are diagnosed at an advanced stage of the disease. Currently, the mainstay for treatment of advanced EOC is tumor debulking surgery followed by combined platinum-and paclitaxel (PTX)-based chemotherapy. However, most patients eventually develop chemoresistance, which remains a major obstacle to successful treatment. Herein, by using clinical specimens and experimentally induced cell models, we found that the expression levels of hsa-miR-105 were significantly decreased in PTX-resistant EOC tissues and cell lines. Follow-up functional experiments demonstrated that repression of hsa-miR-105 conferred resistance to paclitaxel in EOC cells, whereas restoration of hsa-miR-105 expression in situ via intratumoral injection of hsa-miR-105 micrON™ agomir potentiated in vivo sensitivity to PTX and thereafter significantly inhibited tumor growth in a PTX-challenged xenograft model. Mechanistically, hsa-miR-105 exerted its tumor suppressor function by directly inhibiting the zinc and ring finger 2 (ZNRF2) signaling pathway. Importantly, aberrant expression of hsa-miR-105 in both tumor and circulating samples predicted a poor post-chemotherapy prognosis in EOC patients. These findings collectively suggest that hsa-miR-105 may act as a potent tumor suppressor miRNA during the progression of EOC, likely affecting cell proliferation, invasiveness and chemosensitivity to PTX, and functioning at least in part via inhibition of ZNRF2 signaling. The stability and availability and ease in measurement of circulating hsa-miR-105 make it a valuable diagnostic/prognostic biomarker candidate for chemotherapy of EOC.

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“…Microarray analysis, as an important tool in the field of tumor medicine, has important clinical application value in the key genes, molecular diagnosis of some diseases, molecular diagnosis, and the discovery of new drug targets. [ 2 , 3 ] There are already many disease databases, such as gene expression omnibus (GEO) [ 4 ] and the cancer genome atlas. Also, more and more researchers are using bioinformatics analysis.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive analyses of potential key genes in active tuberculosis

et al. 2021

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Background: Tuberculosis (TB) is a global health problem that brings us numerous difficulties. Diverse genetic factors play a significant role in the progress of TB disease. However, still no key genes for TB susceptibility have been reported. This study aimed to identify the key genes of TB through comprehensive bioinformatics analysis.Methods: The series microarray datasets from the gene expression omnibus (GEO) database were analyzed. We used the online tool GEO2R to filtrate differentially expressed genes (DEGs) between TB and health control. Database for annotation can complete gene ontology function analysis as well as Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Protein-protein interaction (PPI) networks of DEGs were established by STRING online tool and visualized by Cytoscape software. Molecular Complex Detection can complete the analysis of modules in the PPI networks. Finally, the significant hub genes were confirmed by plug-in Genemania of Cytoscape, and verified by the verification cohort and protein test.Results: There are a total of 143 genes were confirmed as DEGs, containing 48 up-regulated genes and 50 down-regulated genes. The gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis show that upregulated DEGs were associated with cancer and phylogenetic, whereas downregulated DEGs mainly concentrate on inflammatory immunity. PPI networks show that signal transducer and activator of transcription 1 (STAT1), guanylate binding protein 5 (GBP5), 2 0 -5 0 -oligoadenylate synthetase 1 (OAS1), catenin beta 1 (CTNNB1), and guanylate binding protein 1 (GBP1) were identified as significantly different hub genes. Conclusion:We conclude that these genes, including TAT1, GBP5, OAS1, CTNNB1, GBP1 are a candidate as potential core genes in TB and treatment of TB in the future.Abbreviations: CTNNB1 = catenin beta 1, DEG = differentially expressed gene, GBP1 = guanylate binding protein 1, GBP5 = guanylate binding protein 5, GEO = gene expression omnibus, GO = gene ontology, IFI44 = interferon-induced protein 44 like, KEGG = Kyoto Encyclopedia of Genes and Genomes, MTB = Mycobacterium tuberculosis, OAS1 = 2 0 -5 0 -oligoadenylate synthetase 1, OAS2 = 2 0 -5 0 -oligoadenylate synthetase 2, OAS3 = 2 0 -5 0 -oligoadenylate synthetase 3, PARP9 = poly(ADP-ribose) polymerase family member 9, PPI = protein-protein interaction , SOCS3 = suppressor of cytokine signaling 3, STAT1 = signal transducer and activator of transcription 1, TB = tuberculosis, XAF1 = XIAP associated factor 1.

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Identification of core genes and prediction of miRNAs associated with osteoporosis using a bioinformatics approach

Cited by 10 publications

References 55 publications

Differentially expressed circulating miRNAs in postmenopausal osteoporosis: a meta-analysis

Differentially expressed circulating miRNAs in postmenopausal osteoporosis: a meta-analysis

Role of hsa‑miR‑105 during the pathogenesis of paclitaxel resistance and its clinical implication in ovarian cancer

Comprehensive analyses of potential key genes in active tuberculosis

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