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[Cancer Research 58, 5009-5013, November 15, 1998]
© 1998 American Association for Cancer Research
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Gene Expression Profiling of Alveolar Rhabdomyosarcoma with cDNA Microarrays

Javed Khan, Richard Simon, Michael Bittner, Yidong Chen, Stephen B. Leighton1, Thomas Pohida, Paul D. Smith, Yuan Jiang, Gerald C. Gooden, Jeffrey M. Trent and Paul S. Meltzer2

Cancer Genetics Branch, National Human Genome Research Institute [J. K., M. B., Y. C., Y. J., G. C. G., J. M. T., P. S. M.], Biometric Research Branch, National Cancer Institute [R. S.], Biomedical Engineering and Instrumentation Program, National Center for Research Resources [S. B. L., P. D. S.], Computational Bioscience and Engineering Laboratory, Office of Research Services [T. P.], NIH, Bethesda, Maryland 20892

Several forms of human sarcoma, lymphoma, and leukemia are characterized by somatically acquired chromosome translocations that result in fusion genes that encode chimeric transcription factors with oncogenic properties. We have used cDNA microarrays containing 1238 cDNAs to investigate the gene expression profile of a group of seven alveolar rhabdomyosarcoma (ARMS) cell lines characterized by the presence of the PAX3-FKHR fusion gene. Using the method of multidimensional scaling to represent the relationships among the cell lines in two-dimensional Euclidean space, we determined that ARMS cells show a consistent pattern of gene expression, which allows the cells to be clustered together. By searching across the seven ARMS cell lines, we found that 37 of 1238 genes were most consistently expressed in ARMS relative to a reference cell line. Only three of these genes have been previously reported to be expressed in ARMS. Among these 37 were genes related to both primary (PAX3-FKHR) and secondary (CDK4) genetic alterations in ARMS. These results in ARMS demonstrate the potential of cDNA microarray technology to elucidate tumor-specific gene expression profiles in human cancers.

1 Present address: Beecher Instruments, Silver Spring, MD 20910.

2 To whom requests for reprints should be addressed, at National Human Genome Research Institute/NIH, Building 49, Room 4A10, 49 Convent Drive, Bethesda, MD 20892-4470. Phone: (301) 402-2023; Fax: (301) 402-2040; E-mail: pmeltzer@nhgri.nih.gov.

Received 8/ 7/98. Accepted 10/ 1/98.




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Q. M. Guo, R. L. Malek, S. Kim, C. Chiao, M. He, M. Ruffy, K. Sanka, N. H. Lee, C. V. Dang, and E. T. Liu
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P. Kauraniemi, I. Hedenfalk, K. Persson, D. J. Duggan, M. Tanner, O. Johannsson, H. Olsson, J. M. Trent, J. Isola, and A. Borg
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F. Forozan, E. H. Mahlamäki, O. Monni, Y. Chen, R. Veldman, Y. Jiang, G. C. Gooden, S. P. Ethier, A. Kallioniemi, and O.-P. Kallioniemi
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W. J. Fredericks, K. Ayyanathan, M. Herlyn, J. R. Friedman, and F. J. Rauscher III
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