Radio-
chemotherapy with 5-flu orouracil (5-FU) is the standard of care treatment for patients with
colorectal cancer, but it is only effective for a third of them. Despite our understanding of the mechanism of action of
5-FU, drug resistance remains a significant limitation to the clinical use of
5-FU, as both intrinsic and acquired chemoresistance represents the major obstacles for the success of 5-FU-based
chemotherapy. In order to identify the mechanism of acquired resistance,
5-FU chemoresistance was induced in CRC cell lines by passaging cells with increasing concentrations of
5-FU. To study global molecular changes, quantitative proteomics and transcriptomics analyses were performed on these cell lines, comparing the resistant cells as well as the effect of chemo and
radiotherapy. Interestingly, a very high proportion of downregulated genes were annotated as
transcription factors coding for Krüppel-associated box (KRAB) domain-containing zinc-finger
proteins (KZFPs), the largest family of transcriptional repressors. Among nearly 350 KRAB-ZFPs, almost a quarter were downregulated after the induction of a 5-FU-resistance including a common one between the three CRC cell lines, ZNF649, whose role is still unknown. To confirm the observations of the proteomic and transcriptomic approaches, the abundance of 20 different KZFPs and control mRNAs was validated by RT-qPCR. In fact, several KZFPs were no longer detectable using qPCR in cell lines resistant to
5-FU, and the KZFPs that were downregulated only in one or two cell lines showed similar pattern of expression as measured by the omics approaches. This proteomic, transcriptomic and genomic analysis of intrinsic and acquired resistance highlights a possible new mechanism involved in the cellular adaptation to
5-FU and therefore identifies potential new therapeutic targets to overcome this resistance.