A bioinformatics analysis of differentially expressed genes in Huh7 cells with low expression of Mindin
10.3969/j.issn.1001-5256.2019.10.028
- VernacularTitle:基于生物信息学分析Mindin低表达Huh7细胞的差异表达基因
- Author:
Xin ZHANG
1
;
Muqi WANG
;
Wenjun WANG
Author Information
1. Department of Infectious Diseases, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China
- Publication Type:Research Article
- Keywords:
Mindin;
transcriptome;
signal transduction;
computational biology
- From:
Journal of Clinical Hepatology
2019;35(10):2272-2277
- CountryChina
- Language:Chinese
-
Abstract:
ObjectiveTo perform a transcriptomic study of Huh7 cells with low expression of Mindin, and to investigate the biological effects of Mindin. MethodsThe Mindin interference sequence was designed, synthesized, and introduced into Huh7 cells via the lentiviral vector GV248. Real-time quantitative PCR was used to measure the inhibitory effect on Mindin transcription level. Huh7 cells with low expression of Mindin were obtained and a transcriptomic study was performed for such cells and their control cells. Bioinformatics was used to analyze abnormally expressed genes, and pathway analysis was used to investigate the possible biological functions involving Mindin. The t-test was used for comparison of continuous data between groups. ResultsCompared with the control cells, Huh7 cells transfected with the lentivirus containing interference sequence had a knockdown efficiency of Mindin mRNA of 63.8% (P=0.003). Huh7 cells with stable low expression of Mindin had a significantly higher cell migration rate than the control cells (3.511±0.538 vs 1.701±0.765, t=-3.355, P=0.03). Compared with the control cells, Huh7 cells with low expression of Mindin had 2888 upregulated genes and 2516 downregulated genes. Gene ontology analysis and pathway analysis were performed for 895 differentially expressed genes with ｜log2FC｜>2.0 and P＜005. The pathway analysis showed that the top 10 biological functions involving Mindin were tumor signaling pathway, chemokine signaling pathway, systemic lupus erythematosus, glycerophospholipid metabolism, neuroactive ligand-receptor interaction, hypertrophic cardiomyopathy, glycerolipid metabolism, MAPK signaling pathway, complement and coagulation cascades, and basal cell carcinoma. ConclusionHuh7 cells with low expression of Mindin are successfully constructed. Mindin has wide biological functions including tumors, chemokines, and lipid metabolism.
