Transcriptome analysis of riboclibin on BTG1 gene in cervical cancer cell culture

The aim of this study was to investigate the mechanism of action of ribociclib on the B cell translocation gene (BTG) 1 gene in cervical cancer cell culture by transcriptome analysis. To identify new molecular targets for cervical cancer treatment and prognosis, transcriptome analysis was performed after RNA isolation on six samples, three replicates each, from HeLa cell lines treated with ribociclib (experimental) and those not treated with ribociclib (control). After normalization, the edgeR R package and the Quasi-Likelihood model were used to determine differential gene expression (DGE) between groups. The TopGO package and the Kolmogorov-Smirnov (KS) statistical test were used for gene ontology analysis. The cluster Profiler package was used for pathway analysis. R scripts were used for statistical comparisons within and between groups, data visualization applications, and report generation. Within the scope of the study, RNA sequencing was performed on a total of six different samples, with three replicates in each group. The distributions of Reads per Kilobase (RPK) and Transcripts per Million (TPM) values obtained after normalization and filtering were similar. In both groups, the majority of genes were concentrated at low expression levels, and a small number of genes were observed at high expression levels. Following DGE analysis, when comparing the control and experimental groups, among the genes with statistically significant differences in the False Discovery Rate (FDR), 1434 genes showed significant increases in expression and 1273 genes showed significant decreases in expression (p<0.05). In the transcriptome analysis of the top 15 genes with the lowest FDR values, a significant decrease in the expression of IGFBP3, NDRG1, ATP1B3, MT-CYB, BNIP3P1, and CD83 was observed, while an increase in the expression of PIM3, CCN1, HERPUD1, EIF1, ID1, ASNS, HMGB2, MSMO1, and ID1 was observed. In the volcano plot of the different gene expressions in the comparison of the two groups, IGFBP3, BNIP3P1, MT-CYB, NDRG1, and ATP1B3 were among the genes with statistically significant differences (FDR<0.05) according to logFC and FDR values of all genes. A significant decrease was observed in the ATP1B3, IGFBP3, and NDRG1 genes with the lowest FDR values after ribociclib treatment compared to the control cell group. Significant changes were observed in genes related to molecular function, cellular components, and biological processes. In the expression analysis of genes showing significant changes (FDR<0.05), it was determined that 1434 genes showing significant increases were significantly clustered in 22 pathways, and 1273 genes showing significant decreases were significantly clustered in 15 pathways. Conclusion in Ribociclib treatment in Hela cell culture has been shown to both suppress the cell cycle and induce significant transcriptomic changes in the cell, affecting gene regulation mechanisms, cellular metabolism, protein synthesis, exosomes, and triggering metabolic reprogramming. More effective and durable responses can be achieved with treatment options such as metabolic and immunomodulatory agents in the treatment of cervical cancer. Keywords: cervical cancer, Hela, ribociclib, transcriptome analysis