Predicting chemotherapeutic drug combinations through gene network profiling

Abstract

Contemporary chemotherapeutic treatments incorporate the use of several agents in combination. However, selecting the most appropriate drugs for such therapy is not necessarily an easy or straightforward task. Here, we describe a targeted approach that can facilitate the reliable selection of chemotherapeutic drug combinations through the interrogation of drug-resistance gene networks. Our method employed single-cell eukaryote fission yeast (Schizosaccharomyces pombe) as a model of proliferating cells to delineate a drug resistance gene network using a synthetic lethality workflow. Using the results of a previous unbiased screen, we assessed the genetic overlap of doxorubicin with six other drugs harboring varied mechanisms of action. Using this fission yeast model, drug-specific ontological sub-classifications were identified through the computation of relative hypersensitivities. We found that human gastric adenocarcinoma cells can be sensitized to doxorubicin by concomitant treatment with cisplatin, an intra-DNA strand crosslinking agent, and suberoylanilide hydroxamic acid, a histone deacetylase inhibitor. Our findings point to the utility of fission yeast as a model and the differential targeting of a conserved gene interaction network when screening for successful chemotherapeutic drug combinations for human cells.

Figure 1. Sensitivity score (s-score) of the doxorubicin resistance (DXR) mutants obtained at different durations of drug exposure.

(a) Grey and black bars indicate days 3 and 7, respectively, after drug exposure. (b) Level of hypersensitivity. Dark red, high; red, medium; pink, low; white, not sensitive; and light blue, resistant. DXR genes that were disrupted in the null mutants are listed. HU: hydroxyurea, CPT: camptothecin, MMS: Methyl methanesulfonate, TBZ: thiabendazole, Cis: cisplatin, SAHA: suberoylanilide hydroxamic acid.

Figure 2. Gene network of doxorubicin resistance (DXR) genes.

Linkages between the DXR genes were obtained using String ver. 9.1. The genes are color-coded according to their ontological/functional classification.

Figure 3. Overlap in drug resistance network between the tested drugs and doxorubicin.

The DXR mutants that remained hypersensitivity on day 7 upon exposure to (a) hydroxyurea (HU), (b) camptothecin (CPT), (c) methyl methanesulfonate (MMS), (d) thiabendazole (TBZ), (e) cisplatin, and (f) suberoylanilide hydroxamic acid (SAHA). Strains that showed sensitivity across all drug concentrations tested or only on one of the tested concentrations: red, high to medium sensitivity; pink, weak sensitivity.

Figure 4. Sensitization of human gastric adenocarcinoma (AGS) cells to doxorubicin via concurrent treatment with cisplatin and SAHA.

(a) Cells were co-treated with varying concentrations of cisplatin in the presence of 5 μM SAHA, or 0.1 or 1 μM doxorubicin or with a triple combination of cisplatin, 5 μM SAHA and 0.1 or 1 μM doxorubicin. (b) Dose response effect on the viability of AGS cells was analyzed. Cells were treated with varying concentrations of cisplatin alone (blue), in combination with 5 μM SAHA (red) or 0.1 μM doxorubicin (green), or both 0.1 μM doxorubicin and 5 μM SAHA (purple).