Transcriptional profiling of oral squamous cell carcinoma using formalin-fixed paraffin-embedded samples

A. Saleh, R. B. Zain, H. Hussaini, F. Ng, V. Tanavde, S. Hamid, A. T. Chow, G. S. Lim, M. T. Abraham, S. H. Teo, S. C. Cheong

    Research output: Contribution to journalArticle

    22 Citations (Scopus)

    Abstract

    Despite the advances in cancer treatment, the 5-year survival rate for oral cancer has not changed significantly for the past 40 years and still remains among the worst of all anatomic sites. Gene expression microarrays have been used successfully in the identification of genetic alterations in cancer development, however, these have hitherto been limited by the need for specimens with good quality intact RNA. Here, we demonstrated the use of formalin-fixed paraffin-embedded tissues in microarray experiments to identify genes differentially expressed between cancerous and normal oral tissues. Forty-three tissue samples were macrodissected and gene expression analyses were conducted using the Illumina DASL assay. We report RNA yield of 2.4 and 0.8 μg/mm3 from tumour and normal tissues, respectively and this correlated directly with the tissue volume used for RNA extraction. Using unsupervised hierarchical clustering, distinct gene expression profiles for tumour and normal samples could be generated, and differentially expressed genes could be identified. The majority of these genes were involved in regulation of apoptosis and cell cycle, metastasis and cell adhesion including BCL2A1, BIRC5, MMP1, MMP9 and ITGB4. Representative genes were further validated in independent samples suggesting that these genes may be directly associated with oral cancer development. The ability to conduct microarrays on formalin-fixed paraffin-embedded specimens represents a significant advancement that could open up avenues for finding genes that could be used as prognostication and predictive tools for cancer.

    Original languageEnglish
    Pages (from-to)379-386
    Number of pages8
    JournalOral Oncology
    Volume46
    Issue number5
    DOIs
    Publication statusPublished - May 2010

    Fingerprint

    Paraffin
    Formaldehyde
    Squamous Cell Carcinoma
    Genes
    Mouth Neoplasms
    RNA
    Neoplasms
    Gene Expression
    Transcriptome
    Cell Adhesion
    Cluster Analysis
    Cell Cycle
    Apoptosis
    Neoplasm Metastasis

    Keywords

    • Formalin-fixed paraffin-embedded tissues
    • Gene expression profiling
    • Microarray
    • Oral squamous cell carcinoma

    ASJC Scopus subject areas

    • Oncology
    • Oral Surgery
    • Cancer Research

    Cite this

    Saleh, A., Zain, R. B., Hussaini, H., Ng, F., Tanavde, V., Hamid, S., ... Cheong, S. C. (2010). Transcriptional profiling of oral squamous cell carcinoma using formalin-fixed paraffin-embedded samples. Oral Oncology, 46(5), 379-386. https://doi.org/10.1016/j.oraloncology.2010.02.022

    Transcriptional profiling of oral squamous cell carcinoma using formalin-fixed paraffin-embedded samples. / Saleh, A.; Zain, R. B.; Hussaini, H.; Ng, F.; Tanavde, V.; Hamid, S.; Chow, A. T.; Lim, G. S.; Abraham, M. T.; Teo, S. H.; Cheong, S. C.

    In: Oral Oncology, Vol. 46, No. 5, 05.2010, p. 379-386.

    Research output: Contribution to journalArticle

    Saleh, A, Zain, RB, Hussaini, H, Ng, F, Tanavde, V, Hamid, S, Chow, AT, Lim, GS, Abraham, MT, Teo, SH & Cheong, SC 2010, 'Transcriptional profiling of oral squamous cell carcinoma using formalin-fixed paraffin-embedded samples', Oral Oncology, vol. 46, no. 5, pp. 379-386. https://doi.org/10.1016/j.oraloncology.2010.02.022
    Saleh, A. ; Zain, R. B. ; Hussaini, H. ; Ng, F. ; Tanavde, V. ; Hamid, S. ; Chow, A. T. ; Lim, G. S. ; Abraham, M. T. ; Teo, S. H. ; Cheong, S. C. / Transcriptional profiling of oral squamous cell carcinoma using formalin-fixed paraffin-embedded samples. In: Oral Oncology. 2010 ; Vol. 46, No. 5. pp. 379-386.
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