Proteomics analysis in A375 melanoma cells before and after short hairpin RNA-mediated Cbl-b gene silencing

Abstract

Objective To analyze differentially expressed proteins in A375 melanoma cells before and after short hairpin RNA (shRNA) -mediated Cbl-b gene silencing. Methods The label-free quantitative proteomics approach was performed to identify differentially expressed proteins between A375 cells transfected with lentiviral vectors containing Cbl-b shRNA (Cbl-b shRNA group) and those with control lentiviral vectors (control group) . Then, the properties of differentially expressed proteins were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) enrichment analysis. Western blot analysis was conducted to determine the expression of differential proteins (EphA2 and GSK3β) and phosphorylated protein kinase (p-AKT) after shRNA-mediated Cbl-b gene silencing. Statistical analysis was carried out by t test of two independent-samples for comparison of protein expression abundance between the two groups with SPSS 23.0 software. Additionally, the results of GO and KEGG enrichment analysis were analyzed by Fisher′s exact test. Results A total of 3 449 proteins were identified and quantified, and 74 of them were differentially expressed between the Cbl-b shRNA group and control group. Compared with the control group, 52 proteins were up-regulated and 22 were down-regulated in the Cbl-b shRNA group. GO enrichment analysis of differential proteins revealed that the top five significantly enriched biological processes were integrin-mediated cell adhesion, single-organism metabolic process, regulation of integrin-mediated cell adhesion, regulation of protein-targeting mitochondria and nucleic acid metabolic process. The top five significantly enriched molecular functions included DNA binding, 2-iron, 2-sulfur cluster binding, signaling receptor activity, cadherin binding and cell adhesion molecule binding. The top five significantly enriched cell components included nucleosome, DNA packaging complex, photoreceptor connecting cilium, DNA-protein complex and extracellular region part. KEGG enrichment analysis demonstrated that the top five significantly enriched melanoma-related signaling pathways were folate biosynthesis, axon guidance, extracellular matrix-receptor interaction, adherens junction and Wnt signaling pathways. As Western blot analysis revealed, the Cbl-b shRNA group showed lower protein expression of EphA2 (0.369) , but higher protein expression of GSK3β (3.524) compared with the control group (1) , which were consistent with the results of proteomics analysis. Additionally, the protein expression of p-AKT was down-regulated in Cbl-b shRNA group (0.453) compared with the control group (1) . Conclusion Cbl-b may be involved in the occurrence of melanoma through a variety of biological pathways, and the EphA2/PI3K/AKT signaling pathway may be one important pathway. Key words: Melanoma; Ubiquitin-protein ligases; Proto-oncogene proteins cbl-b; RNA, small interfering; Proteomics