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Identification of candidate cancer genes involved in human retinoblastoma by data mining

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Abstract

Objective

The objective of this study was to discover potential cancer-related genes involved in retinoblastoma (RB) tumorigenesis.

Materials and methods

Using a data-mining tool called cDNA Digital Gene Expression Displayer (DGED) and serial analysis of gene expression DGED from the Cancer Genome Anatomy Project (CGAP) database, eight cDNA libraries and five serial analysis of gene expression libraries from retinoblastoma (RB) solid tumors and normal retina tissues were analyzed. The deregulated genes were classified into major families using information from Gene Ontology. Several candidate cancer-related genes were analyzed by real-time reverse transcription polymerase chain reaction (RT-PCR) and immunohistochemistry (IHC) on tissue microarrays (TMA) of RB and human normal retina samples.

Results

A total of 260 genes with deregulated expression emerged when examined by DGED from the CGAP database. Functional classification of these genes not only provided an interesting insight into RB tumorigenesis but also facilitated target identification for RB therapeutics. Several candidate genes were confirmed by real-time RT-PCR and IHC analysis on TMA and were found to be associated with RB genesis through text-mining in Information Hyperlinked over Proteins. The results also implicated MCM7 and WIF1 as promising therapeutic targets for RB, but further validation is needed.

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Acknowledgements

We thank the patients and corneal donors for their participation in this study. This work was supported in part by the National Basic Research Program of China (2007CB5119005), National Natural Science Foundation of China (30471867), the Program for Innovative Researcher Team in Science and Technology in Fujian Province University (FMU-RT001), Fujian Provincial Natural Science Foundation (C0510009, C0520003), and Science Development Foundation of Fujian Medical University (FJGXY04020).

Conflict of interest statement

The authors declare that they have no competing interests.

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Authors and Affiliations

  1. Biomedical Engineering Center, Molecular Medicine Research Center, Fujian Medical University, Fuzhou, Fujian, China

    Juhua Yang

  2. Department of Genetics, National Research Institute for Family Planning, Peking Union Medical College, 100081, Beijing, China

    Juhua Yang, Jian-Jun Zhao & Xu Ma

  3. Department of Ophthalmology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China

    Yihua Zhu

  4. Cancer Research Institute, Central South University, Changsha, Hunan, China

    Wei Xiong

  5. Molecular Medicine Research Center of Fujian Medical University, Key Laboratory of Infection and Oncology, Fujian Province University, 350004, Fuzhou, Fujian, China

    Jian-Yin Lin

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  1. Juhua Yang
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Correspondence to Jian-Yin Lin or Xu Ma.

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Juhua Yang and Jian-Jun Zhao contribute equally to the article.

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Yang, J., Zhao, JJ., Zhu, Y. et al. Identification of candidate cancer genes involved in human retinoblastoma by data mining. Childs Nerv Syst 24, 893–900 (2008). https://doi.org/10.1007/s00381-008-0595-7

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  • DOI: https://doi.org/10.1007/s00381-008-0595-7

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