| Literature DB >> 35885926 |
Gang Feng1, Guozheng Liang1, Yaqian Zhang1, Jicong Hu1, Chuandong Zhou1, Jiawen Li1, Wenfeng Zhang1, Han Shen1, Fenglin Wu1, Changli Tao1, Yan Liu2, Hongwei Shao1.
Abstract
Licorice has previously been shown to affect gene expression in cells; however, the underlying mechanisms remain to be clarified. We analyzed the microRNA expression profile of serum from mice treated by gavage with licorice decoction, and obtained 11 differentially expressed microRNAs (DEmiRNAs). We also screened differentially expressed genes (DEgenes) based on RNA-Seq data, and 271 common genes were identified by intersection analysis of the predicted target genes of 11 DEmiRNAs and the DEgenes. The miRNA-gene network showed that most of the hub genes were immune-related. KEGG enrichment analysis of the 271 genes identified three significant pathways, and the 21 genes involved in these three pathways, and the 11 DEmiRNAs, were constructed into a miRNA pathway-target gene network, in which mmu-miR-27a-3p stood out. Compared to ImmPort, there were 13 immune genes within the above group of 21 genes, and three intersected with the mmu-miR-27a-3p predicted target genes, Cd28, Grap2 and Cxcl12, of which the expression of Cd28 changed most significantly. We confirmed the regulation of Cd28 by mmu-miR-27a-3p using a dual-luciferase assay, and further confirmed that overexpression of mmu-miR-27a-3p could significantly downregulate the expression of Cd28 in lymphocytes. These results indicate that mmu-miR-27a-3p could be involved in the licorice-mediated regulation of the expression of Cd28 in mice.Entities:
Keywords: Cd28; gene expression; licorice; miRNA; mmu-miR-27a-3p; regulation
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Year: 2022 PMID: 35885926 PMCID: PMC9317804 DOI: 10.3390/genes13071143
Source DB: PubMed Journal: Genes (Basel) ISSN: 2073-4425 Impact factor: 4.141
Figure 1Screening of DEmiRNAs and prediction of target genes. (A) Volcano plot of differential miRNAs with |log(fold change)| ≥ 1.5, p ≤ 0.01 as screening criteria. (B) Expression changes of 11 DEmiRNAs. (C) The predicted target genes of 11 DEmiRNAs using multiMiR R package and miRWalk 3.0 online tools. (D) GO enrichment of common target genes using two prediction methods. (E) KEGG enrichment of common target genes using two prediction methods.
Figure 2Screening of DEgenes based on RNA-Seq. (A) Volcano plot of differential miRNAs with |log (fold change)| ≥ 1.5, p ≤ 0.01 as screening criteria. (B) Distribution of upregulated and downregulated DEgenes. (C) The interaction network between DEgenes generated using the STRING online tool and visualized with Cytoscape 3.9.0, in which the core genes were identified using Cytohubba plugin. (D) GO enrichment of DEgenes. (E) KEGG enrichment of DEgenes.
Figure 3Comparative analysis of DEgenes and the predicted target genes of 11 DEmiRNAs. (A) The intersection between DEgenes and the predicted target genes of 11 DEmiRNAs. (B) Correlation analysis between 271 common genes and 11 DEmiRNAs identified 243 negatively correlated genes. The miRNA–mRNA relationship was visualized with Cytoscape 3.9.0, in which the core genes were identified using the Cytohubba plugin. (C) GO enrichment of 271 common genes. (D) KEGG enrichment of 271 common genes.
Figure 4Identification of key miRNAs and target gene prediction. (A) The miRNA–gene interaction network between 11 DEmiRNAs and 21 DEgenes involved in the above three KEGG pathways. (B) The intersection between DEmiRNAs that have negative regulatory relationships with more genes in A and the DEmiRNAs identified using the stricter screening criteria (|log(fold difference)| ≥ 2, p ≤ 0.01). (C) The intersection between 21 DEgenes involved in the above three KEGG pathways and 15 immune-related genes derived from ImmPort database identified 13 common genes, which were compared with the 67 predicted target genes of mmu-miRNA-27a-3p; among the 271 common genes mentioned above, this resulted in the identification of three common genes. Changes in expression of the three common genes are shown.
Figure 5Regulation of Cd28 gene expression by mmu-miRNA-27a-3p. (A) A miRNA-27a-3p binding site with the Cd28 3′UTR was predicted using starBase 3.0 and a mutant binding site was designed as a control. (B) Amplification of the Cd28 3′UTR and the preparation of mutant Cd28 3′UTR by overlap PCR. (C) The RL/FL ratio of each group. (D) The normalized ratio of each group. (E) Flow cytometric analysis of the expression of Cd28 on splenic lymphocytes from C57 mice transfected with mmu-miR-27a-3p mimics. The ratio and mean fluorescence intensity (MFI) were analyzed. (F) qRT-PCR detection of Cd28 in C57 mice spleen lymphocytes. **, p < 0.01; ***, p < 0.001; ****, p < 0.0001.