RNA-Seq analysis of cancer models with altered SLX4/XPF reveals links to migration, DNA damage response, EMT, and drug sensitivity

SLX4 and XPF are two proteins involved in DNA repair mechanisms, but for which other properties are possible. After a study on phenotypes of cell models with various expressions of the two proteins, we conducted RNA sequencing analysis on five cell models of different origin (A549, NCI-H1703, COLO-357, HT-29 and HEK-293T). Our results show a much higher transcriptional impact on p53 mutant cell lines than on p53 wild type cells. We also present various signatures or scores based on selected genes, and although interesting differences are observed, no general conclusions can be made for all cell lines. Our study and results add data and knowledge to the roles of SLX4 and XPF in cell biology and represent an important background for new and confirmational studies. RNA-seq profiling of wildtype A549, NCI-H1703, COLO-357, HT-29 and HEK-293T and their knockdown derivatives (SLX4- and/or XPF-deficient cell lines using CRISPR/Cas9 technology)