A Comparison of GAPDH and ACTB As Internal Control for Gene Expression Studies in Different Cancer Cell Lines

Housekeeping genes are used as internal controls to normalize the expression of target genes in gene expression studies. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and Actin beta (ACTB) are frequently preferred as housekeeping genes in gene expression studies. Due to the general alterations in the gene expression pattern in cancer cases, the selection of the appropriate housekeeping genes for these studies are challenging. In this study, we aimed to analyze the expression of the well-known housekeeping genes GAPDH and ACTB in 6 different cancer cell lines. Furthermore, the relative gene expression of the selected target gene (Tissue inhibitor of metalloproteinases 2-TIMP2) was normalized separately using GAPDH and ACTB and the obtained results were compared with each other. Finally, the stability of GAPDH and ACTB was analyzed using the in-silico tool, Bestkeeper. As a result of the study, it is found that the expression of GAPDH and ACTB were significantly different in the Jurkat (p< 0.01), MOLT4 (p< 0.05), REH (p< 0.001) and HT29 (p< 0.001) cell lines. Based on this finding, significantly different relative target gene expression values were obtained in different cell lines depending on whether the selected housekeeping gene was GAPDH or ACTB. In addition, GAPDH was found to show less variation among the samples used in all cell lines and more stability based on Bestkeeper analysis. These results support that the appropriate housekeeping gene selection, especially in cancer cell lines, may be an effective factor in obtaining accurate results for the studies in the field provide guidance to researchers. Keywords: Cancer cell lines, Gene expression, Housekeeping genes, GAPDH, ACTB