Identification of genetic variants contributing to cisplatin-induced cytotoxicity by use of a genomewide approach

Abstract

Cisplatin, a platinating agent commonly used to treat several cancers, is associated with nephrotoxicity, neurotoxicity, and ototoxicity, which has hindered its utility. To gain a better understanding of the genetic variants associated with cisplatin-induced toxicity, we present a stepwise approach integrating genotypes, gene expression, and sensitivity of HapMap cell lines to cisplatin. Cell lines derived from 30 trios of European descent (CEU) and 30 trios of African descent (YRI) were used to develop a preclinical model to identify genetic variants and gene expression that contribute to cisplatin-induced cytotoxicity in two different populations. Cytotoxicity was determined as cell-growth inhibition at increasing concentrations of cisplatin for 48 h. Gene expression in 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip Human Exon 1.0 ST Array. We identified six, two, and nine representative SNPs that contribute to cisplatin-induced cytotoxicity through their effects on 8, 2, and 16 gene expressions in the combined, Centre d'Etude du Polymorphisme Humain (CEPH), and Yoruban populations, respectively. These genetic variants contribute to 27%, 29%, and 45% of the overall variation in cell sensitivity to cisplatin in the combined, CEPH, and Yoruban populations, respectively. Our whole-genome approach can be used to elucidate the expression of quantitative trait loci contributing to a wide range of cellular phenotypes.

Figure 1.

Relationship between SNP genotype, gene expression, and cisplatin IC₅₀ in combined CEU and YRI populations. A, Genomewide association between SNP genotypes and log₂-transformed cisplatin IC₅₀ in the combined populations. The X-axis represents the chromosomal location of SNPs. The Y-axis represents the statistical significance of association analysis. The dashed line indicates the significance cutoff (P⩽10^-4). B, Association analysis between SNP genotypes and log₂-transformed gene expression in the combined populations. The X-axis represents the SNP chromosomal location. The Y-axis represents the statistical significance of association analysis. The dashed line indicates the significance cutoff (Bonferroni-corrected P<.05). C, Correlation between log₂-transformed cisplatin IC₅₀ and log₂-transformed DDIT4, NEK2, SHMT2, WDR58, and FRAG1 expression. All five gene expressions are significantly associated with one SNP genotype. This SNP, rs456998, is labeled with an asterisk in panels A and B.

Figure 2.

Relationship between rs8094647, MYC gene expression, and cisplatin IC₅₀ in combined CEU and YRI populations. A, Association between rs8094647 genotype and log₂-transformed cisplatin IC₅₀. B, Association between rs8094647 genotype and log₂-transformed MYC expression. C, Correlation of log₂-transformed MYC expression and log₂ cisplatin IC₅₀. The number of cell lines per genotype is labeled directly above the genotype in panels A and B.

Figure 3.

Relationship between SNP genotype, gene expression, and cisplatin IC₅₀ in CEU population. A, Genomewide association between SNP genotypes and log₂-transformed cisplatin IC₅₀ in CEU population. The X-axis represents the chromosomal location of SNPs. The Y-axis represents the statistical significance of association analysis. The dashed line indicates the significance cutoff (P⩽10^-4). B, Association analysis between SNP genotypes and log₂-transformed gene expression in CEU population. The X-axis represents the SNP chromosomal location. The Y-axis represents the statistical significance of association analysis. The dashed line indicates the significance cutoff (Bonferroni-corrected P<.05). C, Correlation between log₂-transformed cisplatin IC₅₀ and log₂-transformed BHLHB3 expression. SNP rs1649942, which is significantly associated with cisplatin IC₅₀ and BHLHB3 expression, is labeled with an asterisk in panels A and B.

Figure 4.

Relationship between SNP genotype, gene expression, and cisplatin IC₅₀ in YRI population. A, Genomewide association between SNP genotypes and log₂-transformed cisplatin IC₅₀ in YRI population. The X-axis represents the chromosomal location of SNPs. The Y-axis represents the statistical significance of association analysis. The dashed line indicates the significance cutoff (P⩽10^-4). B, Association analysis between SNP genotypes and log₂-transformed gene expression in YRI population. The X-axis represents the SNP chromosomal location. The Y-axis represents the statisticial significance of association analysis. The dashed line indicates the significance cutoff (Bonferroni-corrected P<.05). C, Correlation between log₂-transformed cisplatin IC₅₀ and log₂-transformed FAM57A, WDR54, PFKFB4, GATM, HDAC10, MAPK12, KIAA1799, and PGM1 expression. HDAC10 and MAPK12 share the same transcript cluster ID on exon array, as do KIAA1799 and PGM1. All six transcript clusters are significantly associated with one SNP genotype. This SNP, rs12278731, is labeled with an asterisk in panels A and B.