Comparison of genomic signatures of non-small cell lung cancer recurrence between two microarray platforms

Cancer genomic signatures may vary using different platforms. We compared the differential gene expression in non-small cell lung cancer (NSCLC) between two platforms in order to find the most relevant genomic signatures of tumor recurrence.

We analyzed gene expression in frozen lung cancer tissue from 59 selected patients who had undergone surgical resection of NSCLC. These patients were divided into two groups: group R, patients who had a tumor recurrence within four years, n=37; group NR, patients who remained disease-free four years following initial surgery, n=22. Each RNA sample was assayed twice using both Affymetrix and Illumina GeneChip. Data were analyzed by principal component analysis and leave-one-out cross-validation.

Using the same filtering criteria, 13 genes that were differentially expressed between R and NR were identified by Affymetrix, while 21 genes were identified by Illumina GeneChip. In common, a total of six genes were detected by both systems. Using univariate analysis, four (lipocalin 2, LCN2; parathyroid hormone-like hormone, PTHLH; ras-related protein Rab-38, RAB38; and four jointed box 1, FJX1) of these six genes were associated with survival. A risk score of survival was calculated according to the four-gene expression. There was a significant difference in overall survival between low- and high-risk groups.

A four-gene signature is associated with survival among patients with early-stage NSCLC. Further validation of these findings is warranted.