title: Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine.
abstract: Berberine has been identified with anti-proliferative effects on various cancer cells. Many researchers have been trying to elucidate the anti-cancer mechanisms of berberine based on differentially expressed genes. However, differentially alternative splicing genes induced by berberine might also contribute to its pharmacological actions and have not been reported yet. Moreover, the potential functional cross-talking between the two sets of genes deserves further exploration. In this study, RNA-seq technology was used to detect the differentially expressed genes and differentially alternative spliced genes in BEL-7402 cancer cells induced by berberine. Functional enrichment analysis indicated that these genes were mainly enriched in the p53 and cell cycle signalling pathway. In addition, it was statistically proven that the two sets of genes were locally co-enriched along chromosomes, closely connected to each other based on protein-protein interaction and functionally similar on Gene Ontology tree. These results suggested that the two sets of genes regulated by berberine might be functionally cross-talked and jointly contribute to its cell cycle arresting effect. It has provided new clues for further researches on the pharmacological mechanisms of berberine as well as the other botanical drugs.
authors.affiliation: School of Life Science and Technology, Tongji University, Shanghai, People's Republic of China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Sheng
authors.affiliation: School of Life Science and Technology, Tongji University, Shanghai, People's Republic of China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Sun
authors.affiliation: School of Life Science and Technology, Tongji University, Shanghai, People's Republic of China.
authors.forename: Ruixin
authors.initials: R
authors.lastname: Zhu
authors.affiliation: School of Life Science and Technology, Tongji University, Shanghai, People's Republic of China.
authors.forename: Na
authors.initials: N
authors.lastname: Jiao
authors.affiliation: School of Life Science and Technology, Tongji University, Shanghai, People's Republic of China.
authors.forename: Kailin
authors.initials: K
authors.lastname: Tang
authors.affiliation: School of Life Science and Technology, Tongji University, Shanghai, People's Republic of China.
authors.forename: Zhiwei
authors.initials: Z
authors.lastname: Cao
authors.affiliation: School of Life Science and Technology, Tongji University, Shanghai, People's Republic of China.|Key Lab of Systems Biology, Shanghai Institutes for Biological Science, Chinese Academy of Science, Shanghai, People's Republic of China.
authors.forename: Chao
authors.initials: C
authors.lastname: Ma
mesh_terms: D017398:Alternative Splicing; D000970:Antineoplastic Agents / Q000494:pharmacology* / Q000627:therapeutic use; D001599:Berberine / Q000494:pharmacology* / Q000627:therapeutic use; D006528:Carcinoma, Hepatocellular / Q000188:drug therapy / Q000235:genetics* / Q000378:metabolism; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004843:Epistasis, Genetic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008113:Liver Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D059467:Transcriptome
chemical_list: D000970:Antineoplastic Agents; D001599:Berberine