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Identification of SOX4 target genes using phylogenetic footprinting-based prediction from expression microarrays suggests that overexpression of SOX4 potentiates metastasis in hepatocellular carcinoma

Oncogene volume 27, pages 5578–5589 (2008)Cite this article

Abstract

A comprehensive microarray analysis of hepatocellular carcinoma (HCC) revealed distinct synexpression patterns during intrahepatic metastasis. Recent evidence has demonstrated that synexpression group member genes are likely to be regulated by master control gene(s). Here we investigate the functions and gene regulation of the transcription factor SOX4 in intrahepatic metastatic HCC. SOX4 is important in tumor metastasis as RNAi knockdown reduces tumor cell migration, invasion, in vivo tumorigenesis and metastasis. A multifaceted approach integrating gene profiling, binding site computation and empirical verification by chromatin immunoprecipitation and gene ablation refined the consensus SOX4 binding motif and identified 32 binding loci in 31 genes with high confidence. RNAi knockdown of two SOX4 target genes, neuropilin 1 and semaphorin 3C, drastically reduced cell migration activity in HCC cell lines suggesting that SOX4 exerts some of its action via regulation of these two downstream targets. The discovery of 31 previously unidentified targets expands our knowledge of how SOX4 modulates HCC progression and implies a range of novel SOX4 functions. This integrated approach sets a paradigm whereby a subset of member genes from a synexpression group can be regulated by one master control gene and this is exemplified by SOX4 and advanced HCC.

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Acknowledgements

We acknowledge the technical supports provided by the Microarray & Gene Expression Analysis Core Facility of the VGH National Yang-Ming University Genome Research Center (VYMGC). The Gene Expression Analysis Core Facility is supported by National Research Program for Genomic Medicine (NRPGM), National Science Council. RNAi reagents were obtained from the National RNAi Core Facility located at the Institute of Molecular Biology/Genomic Research Center, Academia Sinica (supported by the National Research Program for Genomic Medicine Grants of NSC (NSC 94-3112-B-001-003 and NSC 94-3112-B-001-018-Y). We thank Dr Hua-Chien Chen for providing the PCR primers for the RT-qPCR assays. This work was supported in part by grant (NSC 95-2752-B-010-002-PAE) from National Science Council (Program for Promoting Academic Excellence of Universities Phase II) and a grant from the Ministry of Education, Aim for the Top University Plan to APT and YPC.

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  1. Y-L Liao and Y-M Sun: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan, ROC

    Y-L Liao & A-P Tsou

  2. Institute of Computer Science and Information Engineering, National Central University, Chung-Li, Taiwan, ROC

    Y-M Sun & J-T Horng

  3. Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, ROC

    G-Y Chau

  4. Institute of Anatomy and Cell Biology, National Yang-Ming University, Taipei, Taiwan, ROC

    Y-P Chau

  5. Genomics Research Center, Academia Sinica, Nankang, Taipei, Taiwan, ROC

    T-C Lai, J-L Wang & M Hsiao

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Correspondence to J-T Horng, M Hsiao or A-P Tsou.

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Supplementary Information accompanies the paper on the Oncogene website (http://www.nature.com/onc)

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Liao, YL., Sun, YM., Chau, GY. et al. Identification of SOX4 target genes using phylogenetic footprinting-based prediction from expression microarrays suggests that overexpression of SOX4 potentiates metastasis in hepatocellular carcinoma. Oncogene 27, 5578–5589 (2008). https://doi.org/10.1038/onc.2008.168

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