Mutational Analysis of the Tyrosine Kinome in Colorectal Cancers

Tyrosine kinases (TKs) are central regulators of signaling pathways that control differentiation, transcription, cell cycle progression, apoptosis, motility, and invasion (1). Although a few TK genes have been shown to be mutationally altered in specific human cancers (1), it is not known how many or how often members of the TK gene family are altered in any particular cancer type. In this study, we have used high-throughput sequenc-ing technologies and bioinformatics from the hu-man genome project to address this question. A recent analysis organized the protein ki-nase complement of the human genome (the “kinome”) into a dendrogram containing nine broad groups of genes (2). We selected one major branch of this dendrogram, containing three of the nine major groups, for mutational analysis. These included the 90 tyrosine kinase genes (TK group), the 43 tyrosine kinase–like genes (TKL group), and the 5 receptor guany-late cyclase genes (RGC group). To evaluate whether these genes were genet-ically altered in colorectal cancer, we initially analyzed all exons encoding their predicted kinase domains. A total of 819 exons from all annotated TK, TKL, and RGC genes containing this domain were extracted from genomic databases (3). These exons were polymerase chain reaction (PCR)-amplified from DNA derived from 35 colorectal cancer cell lines and were directly sequenced (3). From the4 megabases (Mb) of sequence infor-mation obtained, we identified 14 genes that con-tained somatic (i.e., tumor-specific) mutations within their kinase domains. These genes were then analyzed for mutations in another 147 colo-rectal cancers (3). We identified 46 mutations in the 14 genes, 2 of which were synonymous; the rest were either nonsynonymous or splice site alterations (Table 1; table S1). All of these mu-tations were shown to be somatic in the cancers that could be assessed by sequencing of DNA from matched normal tissue. Two independent observations support the hy-pothesis that the mutations found in the seven genes mutated in more than one tumor in ou