Genome-wide expression profiling of CRC cells (SW620) upon TIMELESS loss expression and/or ZEB1 down regulation

Colorectal cancer (CRC) is the third most common cancer worldwide. Recent studies pinpointed TIMELESS (TIM) to be crucially involved in replication protection/genomic stability, DNA damage response (DDR) and coordination of mitotic kinase activation with DNA replication termination. Here we present the first direct evidence of a TIM-ZEB1 axis which control key pathological processes in CRC. We found that loss of TIM expression unleashes ZEB1 which triggers epithelial-to-mesenchymal transition program, cell migration/invasion increase and acquirement of stem-like phenotype of CRC cells. Besides, deranged TIM-ZEB1 axis sets off accumulation of DNA damage and delays DNA damage recovery. It is worth noting that the aggressive and genetically unstable ‘CMS4 - colorectal cancer molecular subtype’ matched with low-TIM expressing CRCs and that patients with low-TIM and high-ZEB1 expression have an adverse outcome. Our results support a critical role for TIM-ZEB1 axis derangement and modulation in determining aggressive disease and poor prognosis in CRC patients. We analyzed the transcriptional profile of SW620 colon cancer cell line and of SW620 TIM-KD (p.LKO.1#1 - TRCN0000153760; Sigma-Aldrich, S.Louis, MO, USA), SW620 ZEB1-KD (p.LKO.1#2 - TRCN0000017565;Sigma-Aldrich), and SW620 ZEB1/TIM-KDs cells. A total of 6 different experimental conditions were analyzed in this study. We performed biological replicates for a total of 12 samples profiled.