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. 2018 Feb 28;12:393-408.
doi: 10.2147/DDDT.S155993. eCollection 2018.

Integration of microRNA-mRNA Profiles and Pathway Analysis of Plant Isoquinoline Alkaloid Berberine in SGC-7901 Gastric Cancers Cells

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Free PMC article

Integration of microRNA-mRNA Profiles and Pathway Analysis of Plant Isoquinoline Alkaloid Berberine in SGC-7901 Gastric Cancers Cells

Yanhong Yang et al. Drug Des Devel Ther. .
Free PMC article

Abstract

Purpose: Berberine (BBR) is a traditional Chinese medicine normally used for gastroenteritis, and recent research found that it could fight against tumors. In this study, we focused on integrating miRNA sequencing and RNA sequencing of SGC-7901 gastric cancer cells treated by BBR to elucidate their underlying mechanisms.

Materials and methods: WST-1 assay and flow cytometry were used to check the effects of BBR on SGC-7901. miRNA sequencing and RNA sequencing were used to establish the miRNA and mRNA profiles of BBR-treated SGC-7901.

Results: The results showed that BBR could inhibit the proliferation of SGC-7901 cells and induce G1 arrest in cell cycle phase and apoptosis. A total of 1,960 upregulated genes and 4,837 downregulated genes were identified in the RNA sequencing and 347 upregulated and 93 downregulated miRNAs in the miRNA sequencing. A total of 78 novel miRNAs were also found. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed that the genes were related to pathways in cancer and metabolism. We also analyzed the miRNA-mRNA network of genes grouped into cell cycle, apoptosis, inflammation, metabolism, cell junction, acetylization process, TGF-β pathway, and Wnt signaling pathway.

Conclusion: BBR could inhibit the proliferation of SGC-7901 cells and induce apoptosis. Integrated analysis of microRNA-mRNA profiles is a promising approach to validate gene expression patterns associated with malignant phenotype and study the mechanisms of anticancer.

Keywords: RNA sequencing; berberine; gastric cancer; integrated analysis; microRNA sequencing.

Conflict of interest statement

Disclosure The authors report no conflicts of interest in this work.

Figures

Figure 1
Figure 1
Effect of BBR on the proliferation of SGC-7901 cells by WST-1 assay. Note: The proliferation of SGC-7901 cells was inhibited by different concentrations of BBR treated for (A) 12 and (B) 24 h, respectively. Abbreviation: BBR, berberine.
Figure 2
Figure 2
Effect of BBR at different concentrations on the cell cycle of SGC-7901 cells as detected by flow cytometry. Notes: (A) Control; (B) 5 µmol/L; (C) 10 µmol/L; (D) 20 µmol/L. (E) The histogram showed that the cells treated by BBR at different concentrations were accumulated in G1 phase, and less cells entered S phase. *P<0.05, **P<0.01. Abbreviation: BBR, berberine.
Figure 3
Figure 3
Effect of BBR at different concentrations on apoptosis of SGC-7901 cells as detected by flow cytometry. Notes: (A) Control; (B) 5 µmol/L; (C) 10 µmol/L; (D) 20 µmol/L. (E) The histogram showed that BBR could induce the apoptosis of SGC-7901, and the apoptosis was more obvious with the higher concentration. *P<0.01. Abbreviation: BBR, berberine.
Figure 4
Figure 4
The scatter plot of the mRNA expression profile of SGC-7901 cells treated by BBR. Note: A total of 1,960 upregulated genes and 4,837 downregulated genes were identified. Abbreviation: BBR, berberine.
Figure 5
Figure 5
The presentation of GO classification of the mRNA expression profile. Abbreviations: GO, Gene Ontology; BBR, berberine.
Figure 6
Figure 6
The presentation of KEGG assignments of differentially expressed genes. Abbreviation: KEGG, Kyoto Encyclopedia of Genes and Genomes.
Figure 7
Figure 7
The miRNA expression profile of SGC-7901 cells treated by BBR. Note: A total of 347 upregulated and 93 downregulated miRNAs were identified. Abbreviation: BBR, berberine.
Figure 8
Figure 8
The presentation of GO classification of the upregulated or downregulated miRNA target genes. Abbreviations: GO, Gene Ontology; BBR, berberine.
Figure 9
Figure 9
The presentation of KEGG assignments of the upregulated or downregulated miRNA target genes. Abbreviation: KEGG, Kyoto Encyclopedia of Genes and Genomes.
Figure 10
Figure 10
The presentation of KEGG assignments of the upregulated or downregulated novel miRNA target genes. Abbreviation: KEGG, Kyoto Encyclopedia of Genes and Genomes.
Figure 11
Figure 11
The merged heatmap of genes related to cell cycle, apoptosis, inflammation, metabolism, TGF-β pathway, Wnt signaling pathway, cell junction, and acetylization.
Figure 12
Figure 12
The merged miRNA–RNA relation network of genes related to cell cycle, apoptosis, inflammation, metabolism, TGF-β pathway, Wnt signaling pathway, cell junction, and acetylization.
Figure 12
Figure 12
The merged miRNA–RNA relation network of genes related to cell cycle, apoptosis, inflammation, metabolism, TGF-β pathway, Wnt signaling pathway, cell junction, and acetylization.

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