A gene-alteration profile of human lung cancer cell lines

Abstract

Aberrant proteins encoded from genes altered in tumors drive cancer development and may also be therapeutic targets. Here we derived a comprehensive gene-alteration profile of lung cancer cell lines. We tested 17 genes in a panel of 88 lung cancer cell lines and found the rates of alteration to be higher than previously thought. Nearly all cells feature inactivation at TP53 and CDKN2A or RB1, whereas BRAF, MET, ERBB2, and NRAS alterations were infrequent. A preferential accumulation of alterations among histopathological types and a mutually exclusive occurrence of alterations of CDKN2A and RB1 as well as of KRAS, epidermal growth factor receptor (EGFR), NRAS, and ERBB2 were seen. Moreover, in non-small-cell lung cancer (NSCLC), concomitant activation of signal transduction pathways known to converge in mammalian target of rapamycin (mTOR) was common. Cells with single activation of ERBB2, PTEN, or MET signaling showed greater sensitivity to cell-growth inhibition induced by erlotinib, LY294002, and PHA665752, respectively, than did cells featuring simultaneous activation of these pathways, underlining the need for combined therapeutic strategies in targeted cancer treatments. In conclusion, our gene-alteration landscape of lung cancer cell lines provides insights into how gene alterations accumulate and biological pathways interact in cancer.

Figure 1

Gene alterations in lung cancer cell lines. A: Profile of genes altered in human lung cancer cell lines. The presence of alterations is indicated by gray bars. Black squares indicate no data. The black lines in the PIK3CA oncogene refer to the two variants of unknown oncogenic potential. The histopathology is also shown. B: PIK3CA and MET variants in the RERF-LC-OK and HCC15 cell lines. Nucleotide numbering reflects cDNA numbering with +1 corresponding to the A of the ATG transition initiation codon in the reference sequence C: MET gene amplification in lung cancer cell lines revealed by quantitative PCR. The relative MET copy number was determined by comparison with an unrelated control locus, MDH2, on chromosome 7q11. Cells with MET amplification are indicated with an arrow. D: Western blot anti-phospho-MET (pMET^Y1234/Y1235) and anti-MET (MET) in the indicated cell lines. Constitutive MET activation is present in the EBC-1 and Calu-3 cells, but not in the HCC15 and H1963 cells, which carry gene variants of unknown biological significance.

Figure 2

Genotype of the cell lines and sensitivity to specific inhibitors. A: The IC₅₀ (µM) for each compound (RAPA, rapamycin; LY, LY294002, PHA, PHA665752; and Erlo, erlotinib) is indicated within the boxes. Treatments were applied for 72 hr. B: Immunoblotting analysis depicting the decreased phosphorylation of the indicated protein upon administering increasing concentrations of the compound. Treatments were applied for 24hr.

Figure 3

Cell-growth inhibition upon administering combined LY294002 and erlotinib treatment. Lines represent the cell survival relative to untreated controls of the MTT assays in the H1650 and H460 cells treated with increasing concentrations of LY294002, alone or with 5 µM erlotinib for 72 hr. Error bars indicate the standard deviation of three replicates.