A genomic strategy for the functional validation of colorectal cancer genes identifies potential therapeutic targets

Authors

  • Marian Grade,

    1. Department of General and Visceral Surgery, University Medicine Göttingen, Georg-August-University, Göttingen, Germany
    2. Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Md
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  • Amanda B. Hummon,

    1. Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Md
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  • Jordi Camps,

    1. Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Md
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  • Georg Emons,

    1. Department of General and Visceral Surgery, University Medicine Göttingen, Georg-August-University, Göttingen, Germany
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  • Melanie Spitzner,

    1. Department of General and Visceral Surgery, University Medicine Göttingen, Georg-August-University, Göttingen, Germany
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  • Jochen Gaedcke,

    1. Department of General and Visceral Surgery, University Medicine Göttingen, Georg-August-University, Göttingen, Germany
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  • Patrick Hoermann,

    1. Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Md
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  • Reinhard Ebner,

    1. Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Md
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  • Heinz Becker,

    1. Department of General and Visceral Surgery, University Medicine Göttingen, Georg-August-University, Göttingen, Germany
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  • Michael J. Difilippantonio,

    1. Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Md
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  • B. Michael Ghadimi,

    1. Department of General and Visceral Surgery, University Medicine Göttingen, Georg-August-University, Göttingen, Germany
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  • Tim Beissbarth,

    1. Department of General and Visceral Surgery, University Medicine Göttingen, Georg-August-University, Göttingen, Germany
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  • Natasha J. Caplen,

    1. Gene Silencing Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Md
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  • Thomas Ried

    Corresponding author
    1. Section of Cancer Genomics, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Md
    • National Cancer Institute, Genetics Branch, 50 South Drive, Building 50, Room 1408, Bethesda, Maryland 20892, USA

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    • Tel.: +301-594-3118, Fax: +301-435-4428


Abstract

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 combined a functional genomics and a systems biology approach to assess the consequences of RNAi-mediated silencing of overexpressed genes that were selected from 140 gene expression profiles from colorectal cancers (CRCs) 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 that profoundly reduced the viability of CRC cell lines when silenced with either siRNAs or short-hairpin RNAs (shRNAs), i.e., 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.

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