Bioinformatics analysis of differentially expressed miRNA-related mRNAs and their prognostic value in breast carcinoma

Zhang, Guo-Ming; Goyal, Hemant; Song, Lixia

doi:10.3892/or.2018.6393

Cited by 10 publications

(12 citation statements)

References 37 publications

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“…COL12A1 is a protein that is a member of the fibril-associated collagens with interrupted triple helix (FACIT) collagen family, which is related to the ECM –receptor interaction, PPAR-Peroxisome proliferator-activated receptor and the MAPK-Mitogen-activated protein kinase signaling pathway ( Kim et al, 2016 ; Punetha et al, 2017 ; Zhang et al, 2018 ; Xiang et al, 2019 ). COL12A1 is associated with joint anomalies, gastric cancer, myopathies, ECM defects, and chondromyxoid fibroma.…”

Section: Discussionmentioning

confidence: 99%

Systematic Investigation of the Efficacy of Sinitang Decoction Against Ulcerative Colitis

Wang

et al. 2020

Front. Pharmacol.

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The aim of this study was to investigate the precise clinical use of Sinitang decoction (SNT) in ulcerative colitis (UC). Network pharmacology-based analysis of the drug components–targets–diseases–pathways was used to predict the possible clinical applications of SNT. Next, 2,4,6-trinitrobenzenesulfonic acid (TNBS) was used to establish a rat model of UC, and the efficacy of SNT against UC was tested, followed by a proteomic analysis of the specific signatures regulated by SNT against UC. SNT was predicted to be effective in inflammatory bowel disease, UC, and several other diseases. In the rats with UC, SNT decreased the disease activity index and colon mucosal damage index compared to the untreated UC model rats. Additionally, SNT reversed the upregulated levels of serum tumor necrosis factor (TNF)-α, prostaglandin E 2 (PGE 2 ), interleukin (IL)-6, and nitric oxide (NO) in UC model rats. The proteomic analysis identified 78 proteins that were differentially regulated by SNT in the rats with UC, which were associated with the Gene Ontology terms sulfur compound binding, calcium ion binding, and Toll-like receptor (TLR)-4 binding. Among these differentially regulated proteins, C-reactive protein (CRP) and collagen alpha-1(XII) chain (COL12A1) were found to be signature proteins associated with the efficacy of SNT against UC. This study represents the first precise investigation of the efficacy and mechanisms of SNT against UC, and shows that SNT is a promising candidate for personalized management of UC.

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Section: Discussionmentioning

confidence: 99%

Systematic Investigation of the Efficacy of Sinitang Decoction Against Ulcerative Colitis

Wang

et al. 2020

Front. Pharmacol.

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“…As an indispensable part of bioinformatics, gene expression microarrays have been extensively used to study cancer-related genes and provide broad prospects for drug-based molecular targeting, molecular prediction, and molecular therapy 18. A series of biomarkers have been presented potentially as the diagnosis and prognosis in cervical cancer and other cancers 19,20…”

Section: Discussionmentioning

confidence: 99%

<p>Identification of candidate biomarkers correlated with the diagnosis and prognosis of cervical cancer via integrated bioinformatics analysis</p>

Dai

Chen

Wang

et al. 2019

OTT

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Background: Cervical carcinoma is one of the most common malignant gynecological tumors and is associated with high rates of morbidity and mortality. Early diagnosis and early treatment can reduce the mortality rate of cervical cancer. However, there is still no specific biomarkers for the diagnosis and detection of cervical cancer prognosis. Therefore, it is greatly urgent in searching biomarkers correlated with the diagnosis and prognosis of cervical cancer. Results: The mRNA and microRNA expression profile datasets (GSE7803, GSE9750, GSE63514, and GSE30656) were downloaded from the Gene Expression Omnibus database (GEO). The three microarray datasets were integrated to one via integrated bioinformatics. Differentially expressed genes (DEGs) and microRNAs (DEMs) were obtained by R software. The protein–protein interaction (PPI) networks of the DEGs were performed from the STRING database and further visualized by Cytoscape software. A total of 83 DEGs and 14 DEMs were screened from the microarray expression profile datasets. The miRNAs validated to be associated with cervical cancer were obtained using HMDD online website and the target genes of DEMs were identified using the miRWalk2.0 online database. ESR1, PPP1R3C, NSG1 , and TMPRSS11D were the gene targets of hsa-miR-21; the targets of hsa-miR-16 were GYS2, ENDOU , and KLF4 . These targets were all downregulated in cervical cancer. Finally, we verified the expression of those targets in cervical tissues from TCGA and GTEx databases and analyzed their relationship with survival of cervical cancer patients. In the end, the expression of key genes in cervical cancer tissues was verified via experiment method, we found KLF4 and ESR1 were downregulated in tumor tissues. Conclusion: This study indicates that KLF4 and ESR1 are downregulated by the upregulated miR21 and miRNA16 in cervical cancer, respectively, using bioinformatics analysis, and the lower expression of KLF4 and ESR1 is closely related to the poor prognosis. They might be of clinical significance for the diagnosis and prognosis of cervical cancer, and provide effective targets for the treatment of cervical cancer.

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“…[22,23] In addition, many miRNAs were predicted using the WebGestalt toolkit [24] then validated to be important in acute ischemic stroke. [25–27] Bioinformatics analysis was also performed to explore the underlying functions, pathways, and networks of the differentially expressed miRNAs and targeted genes in various types of cancer such as hepatocellular carcinoma, [28] gastric carcinoma, [29] breast cancer, [30] prostate cancer, [31] and so on. Many miRNAs identified as potential biomarkers based on bioinformatics analysis were further confirmed by reverse transcription quantitative PCR and other functional experiments.…”

Section: Discussionmentioning

confidence: 99%

Identification of miRNAs-genes regulatory network in diabetic nephropathy based on bioinformatics analysis

et al. 2019

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MicroRNAs (miRNAs) play a great contribution to the development of diabetic nephropathy (DN). The aim of this study was to explore potential miRNAs-genes regulatory network and biomarkers for the pathogenesis of DN using bioinformatics methods. Gene expression profiling data related to DN (GSE1009) was obtained from the Gene Expression Omnibus (GEO) database, and then differentially expressed genes (DEGs) between DN patients and normal individuals were screened using GEO2R, followed by a series of bioinformatics analyses, including identifying key genes, conducting pathway enrichment analysis, predicting and identifying key miRNAs, and establishing regulatory relationships between key miRNAs and their target genes. A total of 600 DEGs associated with DN were identified. An additional 7 key DEGs, including 6 downregulated genes, such as vascular endothelial growth factor α ( VEGFA ) and COL4A5 , and 1 upregulated gene ( CCL19 ), were identified in another dataset (GSE30528) from glomeruli samples. Pathway analysis showed that the down- and upregulated DEGs were enriched in 14 and 6 pathways, respectively, with 7 key genes mainly involved in extracellular matrix–receptor interaction, PI3K/Akt signaling, focal adhesion, and Rap1 signaling. The relationships between miRNAs and target genes were constructed, showing that miR-29 targeted COL4A and VEGFA, miR-200 targeted VEGFA, miR-25 targeted ITGAV, and miR-27 targeted EGFR. MiR-29 and miR-200 may play important roles in DN. VEGFA and COL4A5 were targeted by miR-29 and VEGFA by miR-200, which may mediate multiple signaling pathways leading to the pathogenesis and development of DN.

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Bioinformatics analysis of differentially expressed miRNA-related mRNAs and their prognostic value in breast carcinoma

Cited by 10 publications

References 37 publications

Systematic Investigation of the Efficacy of Sinitang Decoction Against Ulcerative Colitis

Systematic Investigation of the Efficacy of Sinitang Decoction Against Ulcerative Colitis

<p>Identification of candidate biomarkers correlated with the diagnosis and prognosis of cervical cancer via integrated bioinformatics analysis</p>

Identification of miRNAs-genes regulatory network in diabetic nephropathy based on bioinformatics analysis

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