Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel

Abstract

Chromosome rearrangement, a hallmark of cancer, has profound effects on carcinogenesis and tumor phenotype. We used a panel of 60 human cancer cell lines (the NCI-60) as a model system to identify relationships among DNA copy number, mRNA expression level, and drug sensitivity. For each of 64 cancer-relevant genes, we calculated all 4,096 possible Pearson's correlation coefficients relating DNA copy number (assessed by comparative genomic hybridization using bacterial artificial chromosome microarrays) and mRNA expression level (determined using both cDNA and Affymetrix oligonucleotide microarrays). The analysis identified an association of ERBB2 overexpression with 3p copy number, a finding supported by data from human tumors and a mouse model of ERBB2-induced carcinogenesis. When we examined the correlation between DNA copy number for all 353 unique loci on the bacterial artificial chromosome microarray and drug sensitivity for 118 drugs with putatively known mechanisms of action, we found a striking negative correlation (-0.983; 95% bootstrap confidence interval, -0.999 to -0.899) between activity of the enzyme drug L-asparaginase and DNA copy number of genes near asparagine synthetase in the ovarian cancer cells. Previous analysis of drug sensitivity and mRNA expression had suggested an inverse relationship between mRNA levels of asparagine synthetase and L-asparaginase sensitivity in the NCI-60. The concordance of pharmacogenomic findings at the DNA and mRNA levels strongly suggests further study of L-asparaginase for possible treatment of a low-synthetase subset of clinical ovarian cancers. The DNA copy number database presented here will enable other investigators to explore DNA transcript-drug relationships in their own domains of research focus.

Figure 1

Genomic image maps showing the Pearson's correlation of DNA copy number with gene expression level across the NCI-60 cell lines. Genes are listed on the axes in chromosomal order (corresponding to the order in Table 1). A, correlation of DNA copy number with expression levels measured using cDNA arrays. B, correlation of DNA copy number with expression levels measured using Affymetrix oligonucleotide arrays. C, correlation of DNA copy number with itself. Red and blue indicate high and low correlations, respectively. Top right, chromosome numbers from 1 to X.

Figure 2

Clustered image map showing the Pearson's correlation of DNA copy number with drug sensitivity across the NCI-60 cell lines. A, clustered image map showing the correlation for 353 genes and the −log(GI₅₀) of 118 “mechanism of action” drugs. The negative correlation of DNA copy number for ABCB1 (MDR1) and substrates of P-glycoprotein is highlighted in yellow and enlarged in B. Red and blue indicate high and low correlations, respectively. Cluster trees of both axes with labels can be viewed in Supplementary Figs. S3 and S4 (available at http://mct.aacrjournals.org).

Figure 3

Relationship of _L-asparaginase activity to asparagine synthetase (ASNS) expression level and DNA copy number in the NCI-60 cell lines. A, _L-asparaginase activity [from data in Scherf et al. (12)] versus asparagine synthetase expression level. These data generated the hypothesis that a subset of ovarian cancers might respond to _L-asparaginase. B, _L-asparaginase activity versus DNA copy number for a clone (MET) near asparagine synthetase on chromosome 7. Blue, pink, and gray data points are from leukemic, ovarian, and other cancer cell types, respectively. The blue and pink lines represent linear least-squares fits. CIs for the correlation coefficient estimates are given in Results.