Molecular characteristics of non-small cell lung cancer

Abstract

We used hierarchical clustering to examine gene expression profiles generated by serial analysis of gene expression (SAGE) in a total of nine normal lung epithelial cells and non-small cell lung cancers. Separation of normal and tumor, as well as histopathological subtypes, was evident by using the 3,921 most abundant transcript tags. This distinction remained when only 115 highly differentially expressed tags were used. Furthermore, these 115 transcript tags clustered into groups suggestive of the unique biological and pathological features of the different tissues examined. Adenocarcinomas were characterized by high-level expression of small airway-associated or immunologically related proteins, whereas squamous cell carcinomas overexpressed genes involved in cellular detoxification or antioxidation. The messages of two p53-regulated genes, p21(WAF1/CIP1) and 14-3-3final sigma, were consistently underexpressed in the adenocarcinomas, suggesting that the p53 pathway itself might be compromised in this cancer type. Gene expression patterns observed by SAGE were consistent with results obtained by quantitative real-time PCR or cDNA array analyses by using a total of 43 lung tumor and normal samples. Thus, although derived from only a few tissue libraries, gene expression profiles obtained by using SAGE most likely represent an unbiased yet distinctive molecular signature for the most common forms of human lung cancer.

Figure 1

Clustering and multidimensional scaling of the SAGE libraries. Only genes with total tag counts of at least 10 are included. (A) Cluster of all nine SAGE libraries. Genes are aligned horizontally, libraries are shown vertically. Red, green, and black indicate genes expressed at high, low, or moderate levels, respectively, in the indicated library. (B) Dendrogram of clustered libraries. (C) Multidimensional scaling indicating the relatedness of the nine libraries.

Figure 2

Clustering and multidimensional scaling of the 115 genes highly differentially expressed (P < 0.001) in nine SAGE libraries. (A) Dendrogram of nine clustered libraries by using 115 differentially expressed genes. (B) Multidimensional scaling of the libraries by using 115 differentially expressed genes. (C) Cluster of the 115 genes (Left) with three main clusters (Right) consisting of genes overexpressed in squamous cell carcinoma (Top), overexpressed in adenocarcinoma (Middle), and underexpressed in adenocarcinoma (Bottom), respectively. † indicates that this tag corresponds to more than one gene of the same family. * indicates that the tag corresponds to more than one distinct gene.

Figure 3

Comparison of genes underexpressed in adenocarcinoma by using Affymetrix genechip and SAGE libraries. (A) Histogram of normalized SAGE data shows the average relative expression levels of seven genes that were underexpressed in adenocarcinoma (shown Lower Right in Fig. 2C). (B) Histogram of genechip data shows the normalized average relative expression levels of the same genes as in A. When a genechip expression value was less than 1, it was set to 1 before normalization. Normalization was done in the same manner as for clustering analysis (see Materials and Methods).