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Background  Gastric cancer is the third most common malignancy affecting the general population worldwide. Aberrant activation of KRAS is a key factor in the development of many types of tumor, however, oncogenic mutations of  KRAS  are infrequent in gastric cancer. We have developed a novel quantitative method of analysis of DNA copy number, termed digital genome scanning (DGS), which is based on the enumeration of short restriction fragments, and does not involve PCR or hybridization. In the current study, we used DGS to survey copy-number alterations in gastric cancer cells.    Methods  DGS of gastric cancer cell lines was performed using the sequences of 5000 to 15000 restriction fragments. We screened 20 gastric cancer cell lines and 86 primary gastric tumors for  KRAS  amplification by quantitative PCR, and investigated  KRAS  amplification at the DNA, mRNA and protein levels by mutational analysis, real-time PCR, immunoblot analysis, GTP-RAS pull-down assay and immunohistochemical analysis. The effect of  KRAS  knock-down on the activation of p44/42 MAP kinase and AKT and on cell growth were examined by immunoblot and colorimetric assay, respectively.    Results  DGS analysis of the HSC45 gastric cancer cell line revealed the amplification of a 500-kb region on chromosome 12p12.1, which contains the  KRAS  gene locus. Amplification of the  KRAS  locus was detected in 15% (3/20) of gastric cancer cell lines (8–18-fold amplification) and 4.7% (4/86) of primary gastric tumors (8–50-fold amplification).  KRAS  mutations were identified in two of the three cell lines in which  KRAS  was amplified, but were not detected in any of the primary tumors. Overexpression of KRAS protein correlated directly with increased  KRAS  copy number. The level of GTP-bound KRAS was elevated following serum stimulation in cells with amplified wild-type  KRAS , but not in cells with amplified mutant  KRAS . Knock-down of  KRAS  in gastric cancer cells that carried amplified wild-type  KRAS  resulted in the inhibition of cell growth and suppression of p44/42 MAP kinase and AKT activity.    Conclusion  Our study highlights the utility of DGS for identification of copy-number alterations. Using DGS, we identified  KRAS  as a gene that is amplified in human gastric cancer. We demonstrated that gene amplification likely forms the molecular basis of overactivation of KRAS in gastric cancer. Additional studies using a larger cohort of gastric cancer specimens are required to determine the diagnostic and therapeutic implications of  KRAS  amplification and overexpression.

bmc cancer

A novel method, digital genome scanning detects KRAS gene amplification in gastric cancers: involvement of overexpressed wild-type KRAS in downstream signaling and cancer cell growth