Somatic mutations affect key pathways in lung adenocarcinoma

Abstract

Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers--including NF1, APC, RB1 and ATM--and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment.

Figure 1. Significantly mutated genes in lung adenocarcinomas

The height of the bars represents the number of somatic mutations in each indicated gene in 188 tumour and normal pairs. Standard, gene-specific and category-based tests were used for this analysis (Supplementary Information). Ten genes were found to be significantly mutated by all three statistical methods (red bars), 7 genes by at least two methods (blue bars) and 9 genes by one of the three methods (green bars), for up to 26 significantly mutated genes in total.

Figure 2. Diagrams of mutations found in the members of several receptor families in lung adenocarcinomas

a-e, Mutations in members of the EGF (a), EPH (b), FGF (c), NTRK (d) and VEGF (e) receptor families are shown. Protein domains are determined by using HMMPFAM. The PFAM domains include `L' (receptor ligand binding domain), Fn3 (fibronectin type III domain), Ig (immunoglobulin domain), LRR (leucine rich repeat domain), LRRNT (leucine rich repeat amino-terminal domain), PTK (protein tyrosine kinase domain) and SAM (sterile α-motif). The locations of mutations are indicated by diamonds, circles and triangles, with filled shapes representing new mutations and open shapes denoting known mutations. The size of the shapes is positively proportional to the degree of conservation at the mutated residue. Representative scheme for each family is constructed based on the ClustalW2 alignment. Recurrent mutations are outlined in black.

Figure 3. Concurrent and mutual exclusion of mutations observed across genes in lung adenocarcinomas

Tumours with and without mutations in the indicated genes are labelled in red and blue in the corresponding columns, respectively. Tumours from smokers (former and current) and from individuals who have never smoked are labelled in yellow and green, respectively. Tumours without smoking status are labelled in grey.

Figure 4. Mutation distributions in individual lung adenocarcinoma genomes

a, Tumours with mutations in PRKDC showed higher than average mutation rates, and conversely tumours with mutations in EGFR had lower than average mutation rates. b, Smokers have on average threefold higher mutation rates compared to individuals who have never smoked.

Figure 5. DNA copy number, gene expression, and mutation distributions in lung adenocarcinomas

a-d, Copy number, gene expression and mutation status at TP53 (a), APC (b), EGFR (c) and KRAS (d) loci in 41 lung adenocarcinomas. Normalized gene expression and log₂ DNA copy number ratio in each sample were determined as described in Supplementary Information.

Figure 6. Significantly mutated pathways in lung adenocarcinomas

Genetic alterations in lung adenocarcinoma frequently occur in genes of the MAPK signalling, p53 signalling, Wnt signalling, cell cycle and mTOR pathways. Oncoproteins are indicated in pink to red and tumour suppressor proteins are shown in light to dark blue. The darkness of the colours is positively correlated to the percentage of tumours with genetic alterations. Frequency of genetic alterations for each of these pathway members in 188 tumours is indicated. Genes (EGFR, FGFR1, FGFR4, KDR, EPHA3, KRAS, NRAS, MDM2 and CDK6) lying in regions of focal amplification were analysed for the percentage of samples with copy number amplification. Samples with greater than 2.5 and fewer than 1.5 DNA copies were considered as amplified and deleted, respectively. Selected components of each pathway are shown in the figure.