Genetic variants contributing to daunorubicin-induced cytotoxicity

Abstract

Identifying heritable genetic variants responsible for chemotherapeutic toxicities has been challenging due in part to its multigenic nature. To date, there is a paucity of data on genetic variants associated with patients experiencing severe myelosuppression or cardiac toxicity following treatment with daunorubicin. We present a genome-wide model using International HapMap cell lines that integrate genotype and gene expression to identify genetic variants that contribute to daunorubicin-induced cytotoxicity. A cell growth inhibition assay was used to measure variations in the cytotoxicity of daunorubicin. Gene expression was determined using the Affymetrix GeneChip Human Exon 1.0ST Array. Using sequential analysis, we evaluated the associations between genotype and cytotoxicity, those significant genotypes with gene expression and correlated gene expression of the identified candidates with cytotoxicity. A total of 26, 9, and 18 genetic variants were identified to contribute to daunorubicin-induced cytotoxicity through their effect on 16, 9, and 36 gene expressions in the combined, Centre d' Etude du Polymorphisme Humain (CEPH), and Yoruban populations, respectively. Using 50 non-HapMap CEPH cell lines, single nucleotide polymorphisms generated through our model predicted 29% of the overall variation in daunorubicin sensitivity and the expression of CYP1B1 was significantly correlated with sensitivity to daunorubicin. In the CEPH validation set, rs120525235 and rs3750518 were significant predictors of transformed daunorubicin IC(50) (P = 0.005 and P = 0.0008, respectively), and rs1551315 trends toward significance (P = 0.089). This unbiased method can be used to elucidate genetic variants contributing to a wide range of cellular phenotypes.

Figure 1

Relationship between rs10932125, CYP1B1 gene expression, and daunorubicin IC₅₀ in the combined CEU and YRI populations. A, rs10932125 genotype and inverse-transformed daunorubicin IC₅₀ association. B, rs10932125 genotype and log₂-transformed CYP1B1 expression association. C, log₂-transformed CYP1B1 expression and inverse-transformed daunorubicin IC₅₀ correlation.

Figure 2

Relationship between rs3750518, HNRPD gene expression, and daunorubicin IC₅₀ in the CEU population. A, rs3750518 genotype and inverse-transformed daunorubicin IC₅₀ association. B, rs3750518 genotype and log₂-transformed HNRPD expression association. C, log₂-transformed HNRPD expression and inverse-transformed daunorubicin IC₅₀ correlation.

Figure 3

Relationship between rs6603859, TAP2 gene expression, and daunorubicin IC₅₀ in the YRI population. A, rs6603859 genotype and inverse-transformed daunorubicin IC₅₀ association. B, rs6603859 genotype and log₂-transformed TAP2 expression association. C, log₂-transformed TAP2 expression and inverse-transformed daunorubicin IC₅₀ correlation.

Figure 4

Relationship between rs7929521, IKBKE gene expression, and daunorubicin IC₅₀ in the YRI population. A, rs7929521 genotype and inverse-transformed daunorubicin IC₅₀ association. B, rs7929521 genotype and log₂-transformed IKBKE expression association. C, log₂-transformed IKBKE expression and inverse-transformed daunorubicin IC₅₀ correlation.

Figure 5

Relative CYP1B1 expression is correlated with cellular sensitivity to daunorubicin. CYP1B1 relative to endogenous control huB₂M expression is correlated with daunorubicin IC₅₀ in 50 independent non-HapMap CEPH samples.