A functional genomics approach to the mode of action of apratoxin A


The cyanobacterial metabolite apratoxin A (1) demonstrates potent cytotoxicity against tumor cell lines by a hitherto unknown mechanism. We have used functional genomics to elucidate the molecular basis for this activity. Gene expression profiling and DNA content analysis showed that apratoxin A induces G1-phase cell cycle arrest and apoptosis. Cell-based functional assays with a genome-wide collection of expression cDNAs showed that ectopic induction of fibroblast growth factor receptor (FGFR) signaling attenuates the apoptotic activity of apratoxin A. This natural product inhibited phosphorylation and activation of STAT3, a downstream effector of FGFR signaling. It also caused defects in FGF-dependent processes during zebrafish development, with concomitant reductions in expression levels of the FGF target gene mkp3. We conclude that apratoxin A mediates its antiproliferative activity through the induction of G1 cell cycle arrest and an apoptotic cascade, which is at least partially initiated through antagonism of FGF signaling via STAT3.

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Figure 1: Characterization of the biological effects of apratoxin A.
Figure 2: Genome-scale cDNA overexpression screen to identify proteins that confer resistance to apratoxin A.
Figure 3: Clusters of genes that are highly expressed in the cell lines most resistant to apratoxin A (OVCAR5, SK-MEL-2, OVCAR4) compared with four of the most susceptible cell lines (HT29, RPMI-8226, SR, LOX IMVI).
Figure 4: Effect of apratoxin A on STAT3 phosphorylation and transcriptional STAT3 activity in U2OS cells.
Figure 5: In vitro angiogenesis assay.
Figure 6: Effect of apratoxin A on zebrafish embryo development.


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This work was supported by the Novartis Research Foundation (to P.G.S.), the US National Institutes of Health (NIH; to J.C.I.B.), the Irving S. Sigal Postdoctoral Fellowship (to H.L.), and an Inbiomed Fellowship (to R.M.R.). We would like to thank J. Zhang and S. Ho for the sample preparation for GeneChip analysis, A. Gutierrez for technical assistance in the logistics of the cDNA screen, S. White and A. Villar for providing reporter plasmids, P. McClurg for statistical analysis, C. Trussell for assisting in the FACS analysis, G. Xia for executing the FGFR kinase assay and for providing PD173074 and G. Hampton, E. Saez, T. Murphy and A. Willingham for helpful discussions. We would like to thank Y. Kawakami and Á. Raya for their support and helpful discussions regarding the zebrafish study, and C. Rodriguez for technical assistance in obtaining the zebrafish pictures. We also thank D. Newman for providing the NCI-60 data and for running the COMPARE analysis.

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Correspondence to Hendrik Luesch or Peter G Schultz.

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Supplementary information

Supplementary Table 1

Activity of apratoxin A in the NCI-60 cytotoxicity assays. (PDF 33 kb)

Supplementary Table 2

Correlation of transcriptional changes induced in HT29 cells by various stress treatments and apratoxin A treatment (12 h). (PDF 60 kb)

Supplementary Table 3

cDNAs that attenuate the cytotoxicity of apratoxin A upon overexpression, grouped by their putative resistance mechanism. (PDF 31 kb)

Supplementary Table 4

Genes identified by hierarchical cluster analysis which are overexpressed in cancer cell lines most resistant to apratoxin A. (PDF 21 kb)

Supplementary Methods (PDF 89 kb)

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Luesch, H., Chanda, S., Raya, R. et al. A functional genomics approach to the mode of action of apratoxin A. Nat Chem Biol 2, 158–167 (2006). https://doi.org/10.1038/nchembio769

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