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A bioinformatical and functional approach to identify novel strategies for chemoprevention of colorectal cancer

Heijink, D. M., Fehrmann, R. S. N., de Vries, E. G. E., Koornstra, J. J., Oosterhuis, D., van der Zee, A. G. J., Kleibeuker, J. H. & de Jong, S., Apr-2011, In : ONCOGENE. 30, 17, p. 2026-2036 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

Comparing normal colorectal mucosa and adenomas focusing on deregulated pathways obtains insight into the biological processes of early colorectal carcinogenesis. Publicly available microarray expression data from 26 normal mucosa and 47 adenoma samples were analyzed. Biological pathways enriched in adenomas were identified with Gene Set Enrichment Analysis (GSEA). The analysis revealed 10, 11 and 16 gene sets distinguishing adenomas from normal mucosa according to Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Map Annotator and Pathway Profiler (GenMAPP) and Biocarta databases, respectively. Biological pathways known to be involved in colon carcinogenesis such as cell cycle (P = 0.002) and Wnt signaling (P = 0.007) were enriched in adenomas. In addition, we found enrichment of novel pathways such as retinoblastoma (Rb) pathway (P = 0.002), Src pathway (P = 0.004), folate biosynthesis (P = 0.019) and Hedgehog signaling (P = 0.037) in adenomas. Microarray results for Rb and Src pathway genes were validated by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) on mRNA isolated from an independent set of adenoma and normal colon samples. A high correlation between microarray data and qRT-PCR expression data was found. The relevance of targeting of identified pathways was shown using the Rb pathway inhibitors roscovitine and PD-0332991 and the Src pathway inhibitor dasatinib. All inhibitors used induced cell growth reduction in adenoma cells. This study shows a bioinformatical and functional approach leading to potentially new options for chemoprevention of colorectal cancer. Oncogene (2011) 30, 2026-2036; doi:10.1038/onc.2010.578; published online 10 January 2011

Original languageEnglish
Pages (from-to)2026-2036
Number of pages11
JournalONCOGENE
Volume30
Issue number17
Publication statusPublished - Apr-2011

    Keywords

  • pathways, microarray, gene set enrichment, adenoma, chemoprevention, DEPENDENT KINASE INHIBITOR, GENE-EXPRESSION, CELL-LINES, PROTEIN-KINASE, COLON-CANCER, EARLY EVENT, DNA-DAMAGE, RB-PATHWAY, CYCLIN D1, ADENOMAS

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