Although our analysis had identified a specific dependency on CCNE1 in amplified lines, we first re-assessed all seven amplicon-associated genes for impact on chemotherapy response in OVCAR-3 and SK-OV-3 using a 72-hour cytotoxicity assay.
We also observed that knockdown of CCNE1 resulted in diminished TPX2 gene expression in 19q12 amplified lines (Figure S4 A) suggestive that TPX2 expression is affected downstream of Cyclin E1.
Consistent with this finding, cisplatin had no differential effect on cell viability in CCNE1 knockdown cells as compared with siRNA controls in two of the three additional 19q12 amplified lines (Kuramochi and OVCAR-4) (Figure 3C).
Although A. brunnescens and A. polypyramis are close relatives and a common origin of the amplified LINEs seems plausible, our phylogenetic data suggest independent amplifications in A. brunnescens and A. polypyramis.
Reduction in cell viability after CCNE1 knockdown was specific to cell lines with 19q12 amplification, with limited or no effect in non-amplified lines, indicating an 'addiction' [25] to CCNE1 deregulation.
In experiments with FGFR-amplified celinesnes, dovitinib decreased pFRS2 and pERK/MAPK and inhibited cell growth in MDA-MB-134 (FGFR1-amplified) and SUM52 (FGFR2-amplified) lines [ 60].
Interestingly, MET-amplified lines with EGFR or HER2 amplification were more sensitive to the combination of foretinib with lapatinib or erlotinib.
These results suggest that dovitinib treatment can inhibit several pro-oncogenic traits in FGFR2-amplified lines, but additional factors may be required for FGFR2-amplified cells to undergo apoptosis upon dovitinib treatment.
FRAX1036 and docetaxel combination treatment of PAK1-amplified lines, MDA-MB-175 and HCC2911, elevated a major apoptotic marker (cleaved PARP) and attenuated a cell cycle regulator (cyclin D1).
Besides inhibiting cell proliferation, dovitinib treatment also induced a significant decrease in soft-agar colony formation in FGFR2-amplified lines (KATO III p=0.002; SNU16 p=0.05; figure 5D and supplementary figure S12, available online only).
