An Evolutionarily Conserved Synthetic Lethal Interaction Network Identifies FEN1 as a Broad-Spectrum Target for Anticancer Therapeutic Development

Abstract

Harnessing genetic differences between cancerous and noncancerous cells offers a strategy for the development of new therapies. Extrapolating from yeast genetic interaction data, we used cultured human cells and siRNA to construct and evaluate a synthetic lethal interaction network comprised of chromosome instability (CIN) genes that are frequently mutated in colorectal cancer. A small number of genes in this network were found to have synthetic lethal interactions with a large number of cancer CIN genes; these genes are thus attractive targets for anticancer therapeutic development. The protein product of one highly connected gene, the flap endonuclease FEN1, was used as a target for small-molecule inhibitor screening using a newly developed fluorescence-based assay for enzyme activity. Thirteen initial hits identified through in vitro biochemical screening were tested in cells, and it was found that two compounds could selectively inhibit the proliferation of cultured cancer cells carrying inactivating mutations in CDC4, a gene frequently mutated in a variety of cancers. Inhibition of flap endonuclease activity was also found to recapitulate a genetic interaction between FEN1 and MRE11A, another gene frequently mutated in colorectal cancers, and to lead to increased endogenous DNA damage. These chemical-genetic interactions in mammalian cells validate evolutionarily conserved synthetic lethal interactions and demonstrate that a cross-species candidate gene approach is successful in identifying small-molecule inhibitors that prove effective in a cell-based cancer model.

FEN1 knockdown improves trastuzumab sensitivity in human epidermal growth factor 2-positive breast cancer cells

“…High expression of FEN1 is associated with clinicopathological significance and poor survival (26), suggesting that FEN1 has an important role in the development of breast cancer. It has previously been demonstrated that anticancer therapies are able to induce FEN1 expression (5), and inhibition of FEN1 combined with DNA injury agents results in increased inhibition of proliferation via endogenous DNA damage (12,(27)(28)(29). In the present study, it was demonstrated that trastuzumab promoted the activation of HER2 and AKT, and concurrently upregulated FEN1 protein expression in BT474 breast cancer cells.…”

Meeting report – 9th IRIC International Symposium on Molecular Targets in Cancer Genomics

“…Several interesting interactions emerged, including SLIs between the FEN1 flap endonuclease and genes whose homologs are frequently mutated in colorectal cancer, such as MRE11A and CDC4. Interestingly, small molecule inhibition of FEN1 in cancer cells with mutated MRE11A or CDC4 recapitulated the SLI phenotype identified in yeast (van Pel et al, 2013a). This result emphasizes the importance of model organisms in the identification of clinically relevant synthetic lethal interactions in human tumors.…”

DNA Repair Endonucleases: Physiological Roles and Potential as Drug Targets

“…99 A study in colorectal cancer cell lines revealed that FEN1 inhibition by a number of small molecules had a synthetically lethal effect in cells deficient in the ubiquitin ligase CDC4. 115 Interestingly, in a recent study, curcumin, the active ingredient in turmeric, has been shown to restrict cell proliferation in breast cancer cell lines through inhibition of FEN1 activity. 116 It was shown that curcumin upregulates expression of the transcription factor NF-E2-related factor 2 (nrf2).…”