The severity of the toxic side effects of chemotherapy varies among patients, and much of this variation is likely genetically based. Here, we use the model system Drosophila melanogaster to genetically dissect the toxicity of methotrexate (MTX), a drug used primarily to treat childhood acute lymphoblastic leukemia and rheumatoid arthritis. We use the Drosophila Synthetic Population Resource, a panel of recombinant inbred lines derived from a multiparent advanced intercross, and quantify MTX toxicity as a reduction in female fecundity. We identify three quantitative trait loci (QTL) affecting MTX toxicity; two colocalize with the fly orthologs of human genes believed to mediate MTX toxicity and one is a novel MTX toxicity gene with a human ortholog. A fourth suggestive QTL spans a centromere. Local single-marker association scans of candidate gene exons fail to implicate amino acid variants as the causative single-nucleotide polymorphisms, and we therefore hypothesize the causative variation is regulatory. In addition, the effects at our mapped QTL do not conform to a simple biallelic pattern, suggesting multiple causative factors underlie the QTL mapping results. Consistent with this observation, no single single-nucleotide polymorphism located in or near a candidate gene can explain the QTL mapping signal. Overall, our results validate D. melanogaster as a model for uncovering the genetic basis of chemotoxicity and suggest the genetic basis of MTX toxicity is due to a handful of genes each harboring multiple segregating regulatory factors.

The severity of the toxic side effects of chemotherapy shows a great deal of interindividual variability, and much of this variation is likely genetically based. Simple DNA tests predictive of toxic side effects could revolutionize the way chemotherapy is carried out. Due to the challenges in identifying polymorphisms that affect toxicity in humans, we use Drosophila fecundity following oral exposure to carboplatin, gemcitabine and mitomycin C as a model system to identify naturally occurring DNA variants predictive of toxicity. We use the Drosophila Synthetic Population Resource (DSPR), a panel of recombinant inbred lines derived from a multiparent advanced intercross, to map quantitative trait loci affecting chemotoxicity. We identify two QTL each for carboplatin and gemcitabine toxicity and none for mitomycin. One QTL is associated with fly orthologs of a priori human carboplatin candidate genes ABCC2 and MSH2, and a second QTL is associated with fly orthologs of human gemcitabine candidate genes RRM2 and RRM2B. The third, a carboplatin QTL, is associated with a posteriori human orthologs from solute carrier family 7A, INPP4A&B, and NALCN. The fourth, a gemcitabine QTL that also affects methotrexate toxicity, is associated with human ortholog GPx4. Mapped QTL each explain a significant fraction of variation in toxicity, yet individual SNPs and transposable elements in the candidate gene regions fail to singly explain QTL peaks. Furthermore, estimates of founder haplotype effects are consistent with genes harboring several segregating functional alleles. We find little evidence for nonsynonymous SNPs explaining mapped QTL; thus it seems likely that standing variation in toxicity is due to regulatory alleles. CHEMOTHERAPEUTIC agents are among the most toxic medications administered to humans (Alley et al. 2002). The toxicity caused by these medications may become severe enough that patients are forced to adjust dosing or switch to a different chemotherapeutic medication, while the disease progresses. Although diet, medical history, age, and other environmental factors of the patient may explain a portion of the toxicity (Gajewski et al. 1989;Meirow and Nugent 2001; Rothenberg et al. 2003;Watters and McLeod 2003;Lee et al. 2005), we have shown that there is a significant genetic component governing the toxic effect of several drugs in Drosophila melanogaster (Kislukhin et al. 2012). Here we use the D. melanogaster model system to dissect the genetic basis of toxicity for three front-line chemotherapeutics: carboplatin, gemcitabine hydrochloride (gemcitabine), and mitomycin C.Carboplatin is a platinum-containing compound used primarily to treat ovarian cancer. It is also sometimes used to treat lung, breast, bladder, and endometrial cancer; head and neck cancer; cancer of the cervix and testicles; certain types of brain cancer; Wilms' tumor; neuroblastoma; and retinoblastoma (Wheate et al. 2010). Gemcitabine is an antimetabolite used primarily in combination with other chemotherapy drugs to treat ovarian...