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The combination of paclitaxel (PTX) and topoisomerase I inhibitors such as camptothecin (CPT) constitutes a therapeutic strategy based on anticipated synergism. However, previous in vitro studies have generated contradictory findings for this strategy. The interaction between these drugs can be synergistic or antagonistic, depending on the cell type examined. To gain additional insight into this promising yet controversial strategy, we investigated the interaction between PTX and CPT in three different cell lines (PANC-1, MDA-MB-231 and HL-60) and explored possible underlying mechanisms of synergy or antagonism. Using a novel solubilizing natural compound, rubusoside, water-insoluble PTX and CPT were solubilized to enable the comparison of the effects of single drugs and their combination on cell viability. Intracellular drug concentrations were quantified to examine the effect of CPT on cellular uptake and accumulation of PTX. Flow cytometry and quantitative real-time PCR gene array analyses were used to explore the mechanisms behind the interaction between PTX and CPT. Our studies confirmed that rubusoside-solubilized PTX or CPT maintained cytotoxicity, causing significant reductions in cell viability. However, the efficacy of the combination of PTX and CPT produced varied results based on the cell line tested. CPT antagonistically reduced the cytotoxic activity of PTX in PANC-1 and MDA-MB-231 cells. The effect of CPT on the cytotoxicity of PTX was less pronounced in HL-60 cells, showing neither synergy nor antagonism. Analysis of apoptosis by flow cytometry revealed that upon co-treatment with CPT, apoptosis induced by PTX was attenuated in PANC-1 and MDA-MB-231 cells. In agreement with our cytotoxicity findings, no synergistic or antagonistic effects on apoptosis were observed in HL-60 cells. The antagonism in PANC-1 and MDA-MB-231 cells was not a result of reduced PTX uptake and accumulation because the amount of intracellular PTX was not altered upon co-treatment with CPT. Moreover, higher expression of anti-apoptosis-related transcripts (BCL2L10, CFLAR, HIP1 and TRADD) in PANC-1 cells was observed upon combination treatment over PTX treatment alone. Although exact underlying mechanisms are unknown, the suspected CPT-dependent reduction of intracellular PTX accumulation was ruled out. The findings of antagonism and increased anti-apoptotic gene transcription serve as a precaution to the design of combination drug strategies where a synergistic interaction may not exist.