In order to characterize patterns of global transcriptional deregulation in primary colon carcinomas, we performed gene expression profiling of some 300 rectal and colon carcinomas, and, as expected, identified comprehensive lists of deregulated genes. Genes that are upregulated are potentially required for the viability of colorectal cancer cells, and can therefore be considered oncogenes. Our systematic comparison of colon and rectal carcinomas also revealed a significant overlap of genomic imbalances and transcriptional deregulation, including activation of the Wnt/b-catenin signaling cascade, suggesting similar pathogenic pathways. The functional validation of novel targets was performed in cell lines established from colorectal carcinomas that recapitulate the genomic and gene expression changes that we have previously observed in primary colorectal cancers (CRC). We used a combined functional genomics and systems biology approach to identify such anti-CRC targets. Genes that are highly overexpressed in tumor cells can be required for tumor cell survival, and have the potential to be selective therapeutic targets. In an attempt to identify such targets, we assesd the consequences of RNAi-mediated silencing of overexpressed genes that were selected from 300 gene expression profiles from colorectal cancers (CRC) and matched normal mucosa. In order to identify credible models for in-depth functional analysis, we first confirmed the overexpression of these genes in 25 different CRC cell lines. We then identified five candidate genes based on how profoundly they reduced the viability of CRC cell lines when silenced with either siRNAs or shRNAs;the genes are HMGA1, TACSTD2, RRM2, RPS2, and NOL5A. These genes were further studied by systematic analysis of comprehensive gene expression profiles generated following siRNA-mediated silencing. Exploration of these RNAi-specific gene expression signatures allowed the identification of the functional space in which the five genes operate, and showed enrichment for cancer specific signaling pathways, some known to be involved in CRC. By comparing the expression of the RNAi signature genes with their respective expression levels in an independent set of primary rectal carcinomas we could recapitulate these defined RNAi signatures, therefore establishing the biological relevance of our observations. This strategy identified the signaling pathways that are affected by the prominent oncogenes HMGA1 and TACSTD2, established a yet unknown link between RRM2 and PLK1, and identified RPS2 and NOL5A as promising potential therapeutic targets in CRC.Broad chromosomal copy number alterations-aneuploidy-define the genomic landscape of cancer cells. In colorectal carcinomas chromosome 13 is one of the most commonly gained chromosomes in. Despite the prevalence of this aneuploidy, it is not clear which gene or genes are the targets of this chromosomal imbalance and the identification of oncogenic drivers behind these imbalances, however, remains a formidable task. Using an integrated genomic approach (i.e, integrating copy numbr changes with gene expression patterns), RNA interference based gene silencing, and targeted functional analyses, we identified novel oncogenes responsible for colorectal tumorigenesis. The systematic integration of genomic copy number changes with gene expression profiles in colorectal carcinomas revealed 44 highly overexpressed genes mapping to localized amplicons on chromosome 13, which is recurrently gained. RNA interference based silencing identified eight candidates whose loss of function resulted in viability reduction of at least 20% in colorectal cancer cell lines. The functional space of these genes was established by global expression profiling after RNAi exposure. One candidate, LNX2, is involved in regulating NOTCH signaling;silencing LNX2 resulted in reduced NOTCH levels, in downregulation of the transcription factor TCF7L2, and in markedly reduced WNT-signaling. Genomic amplification of chromosome 13 and overexpression of LNX2 therefore constitutively activates the WNT-pathway, generating evidence for an aberrant NOTCH-WNT axis in colorectal cancer.Combined therapeutic targeting could therefore take advantage of the addiction of colorectal tumors to these specific pathways, and hence increase therapeutic efficacy.
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