Whole-genome studies identify solute carrier transporters in cellular susceptibility to paclitaxel

Abstract

Objective Clinical use of paclitaxel is limited by variable responses and the potential for significant toxicity. To date, studies of association between variants in candidate genes and paclitaxel effects have yielded conflicting results. We sought to evaluate relationships between global gene expression and paclitaxel sensitivity. Methods We utilized well-genotyped lymphoblastoid cell lines derived from the International HapMap Project to evaluate relationships between cellular susceptibility to paclitaxel and global gene expression. Cells were exposed to varying concentrations of paclitaxel to evaluate paclitaxel-induced cytotoxicity and apoptosis. Among the top genes, we identified solute carrier (SLC) genes associated with paclitaxel sensitivity and narrowed down the list to those that had single nucleotide polymorphisms (SNPs) associated with both their expression level of the SLC gene and also with paclitaxel sensitivity. We performed independent validation in an independent set of cell lines and also conducted functional studies using RNA interference. Results Of all genes associated with paclitaxel-induced cytotoxicity at p<0.05 (1713 genes), there was a significant enrichment of SLC genes (31 genes). A subset of SLC genes, namely SLC31A2, SLC43A1, SLC35A5, and SLC41A2, were associated with paclitaxel sensitivity and had regulating SNPs that were also associated with paclitaxel-induced cytotoxicity. Multivariate modeling demonstrated that those 4 SLC genes jointly explain 20% of the observed variability in paclitaxel susceptibility. Using RNA interference, we demonstrated increased paclitaxel susceptibility with knockdown of 3 SLC genes, SLC31A2, SLC35A5, and SLC41A2. Conclusions Our findings are novel and lend further support to the role of transporters, specifically solute carriers in mediating cellular susceptibility to paclitaxel.

Pharmacoethnicity in Paclitaxel-Induced Sensory Peripheral Neuropathy

“…Cytotoxicity was determined using an AlamarBlue (Invitrogen, nologies Inc.; Carlsbad, CA, USA) cellular growth inhibition assay as described (19). Mean area under the paclitaxel concentration-cell survival percentage curve (AUC) was determined by at least 6 replicates from 2 independent experiments and used as the phenotype in the GWAS.…”

“…AUC values for each cell line were log 2 -transformed before statistical analysis to form an approximately normal distribution. Paclitaxel cytotoxicity data of CEU (n = 77), YRI (n = 87) and ASW (n = 83) are previously published (19). For each population, a linear regression was calculated to determine the correlation between the AUC for each replicate; the correlation for CEU, YRI, ASW, CHB and JPT was 0.83, 0.86, 0.81, 0.83 and 0.82, respectively.…”

Sample size calculation for studies with grouped survival data

“…Njiaju et al 5 used lymphoblastoid cell lines (LCL) to study in vitro drug toxicity of paclitaxel, a treatment for cancer. The goal was to identify genetic loci that are associated with drug induced toxicities.…”

“…In the experiments, only a finite number of doses are tested, and thus, the LD50 of the drug can only be determined to be between two adjacent doses. See the work of Njiaju et al 5 for a specific example. Here, LD50 is not a “survival time” itself, but the data can be analyzed using techniques for grouped survival data.…”

The marriage of quantitative genetics and cell biology

“…Paclitaxel has long been used in the treatment regimens of multiple cancers, and we suspected that sensitivity or toxicity to this drug might be affected by the TUBB6 SNP. While mining the data in a previously published study in LCLs 23 found no association between cell death induced by paclitaxel in the LCLs and the TUBB6 SNP, we suspect that effects could be being masked by variation in drug transporter expression. It is still worth examining in patients undergoing cancer treatment where paclitaxel can cause sensory neuropathy, especially at higher doses.…”