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Iterative Microarray and RNA Interference–Based Interrogation of the Src-Induced Invasive Phenotype

¹ Department of Surgery, H. Lee Moffit Cancer Center & Research Institute, College of Medicine, University of South Florida, Tampa, Florida; ² Penn State Cancer Institute, Penn State College of Medicine, Hershey, Pennsylvania; ³ Department of Functional Genomics, Institute for Genomic Research, Rockville, Maryland; and ⁴ Department of Pharmacology, George Washington University Medical Center, Washington, District of Columbia

Requests for reprints: Norman H. Lee, Department of Functional Genomics, The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850. Phone: 301-795-7585; Fax: 301-838-0208; E-mail: nhlee{at}tigr.org and Timothy J. Yeatman, Department of Surgery, H. Lee Moffit Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612. E-mail: yeatman{at}moffit.usf.edu.

Src kinase has long been recognized as a factor in the progression of colorectal cancer and seems to play a specific role in the development of the metastatic phenotype. In spite of numerous studies conducted to elucidate the exact role of Src in cancer progression, downstream targets of Src remain poorly understood. Gene expression profiling has permitted the identification of large sets of genes that may be functionally interrelated but it is often unclear as to which molecular pathways they belong. Here we have developed an iterative approach to experimentally reconstruct a network of gene activity regulated by Src and contributing to the invasive phenotype. Our strategy uses a combination of phenotypic anchoring of gene expression profiles and loss-of-function screening by way of RNA-mediated interference. Using a panel of human colon cancer cell lines exhibiting differential Src-specific activity and invasivity, we identify the first two levels of gene transcription responsible for the invasive phenotype, where first-tier genes are controlled by Src activity and the second-tier genes are under the influence of the first tier. Specifically, perturbation of first-tier gene activity by either pharmacologic inhibition of Src or RNA-mediated interference–directed knockdown leads to a loss of invasivity and decline of second-tier gene activity. The targeting of first-tier genes may be bypassed altogether because knockdown of second-tier genes led to a similar loss of invasive potential. In this manner, numerous members of a "transcriptional cascade" pathway for metastatic activity have been identified and functionally validated.

Key Words: Src • invasion • microarrays • gene expression • RNAi

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