Transcriptomic and proteomic analysis of the mechanisms underlying the role of the CCT3 gene in breast cancer

Background: Breast cancer has surpassed lung cancer as the most common cancer in the world. Our previous research showed that silencing the expression of the CCT3 gene significantly decreased the proliferation and metastasis of breast cancer cells, but the mechanism is still unclear. In this study, we investigated CCT3 gene and protein expression by transcriptomics and proteomics to explore the mechanism underlying its function. Methods: MDA-MB-231 cells were transfected with CCT3-siRNA to knock down the expression of the CCT3 gene. qRT‒PCR was used to measure the efficiency of the suppression. We used RNA-seq and tandem mass tag proteomics analysis to identify differentially expressed genes and proteins, respectively. The possible biological consequences were determined by bioinformatics analysis. Results: The mRNA expression of CCT3 decreased by 87.6% in MDA-MB-231 cells transfected with shCCT3 lentivirus. RNA-seq identified 449 differentially expressed genes after transfection with shCCT3, including 240 upregulated genes and 209 downregulated genes, and 61 differentially expressed proteins (33 upregulated and 28 downregulated) were identified by TMT proteomics analysis. GO and KEGG enrichment revealed the biological and molecular functions in CCT3-knockdown cells. Conjoint analysis revealed the expression of several genes and proteins, such as RPUSD4, LUC7L3, HELLS, ARL1, and SPINT2. Conclusions: We explored the molecular mechanism by which the proliferation and metastasis of breast cancer cells are promoted after the expression of CCT3 is inhibited through transcriptomics and proteomics, and we initially identified several key genes and proteins. The functional verification of these genes requires further research.