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Transcriptome analyses of benign and malignant prostate epithelial cells in formalin-fixed paraffin-embedded whole-mounted radical prostatectomy specimens

Prostate Cancer and Prostatic Diseases volume 11, pages 194–197 (2008)Cite this article

Abstract

Formalin-fixed paraffin-embedded (FFPE) prostate specimens are rich sources of molecular pathological information. However, FFPE-based microarray analysis of tissue samples may be hampered by the degradation and chemical alteration of RNA molecules due to the preservation procedure. In this report, we employed a probe analyses of Affymetrix oligonucleotide arrays at individual probe level to compensate for the potential loss of gene identifications associated with compromised mRNA quality in FFPE preparations. Furthermore, to increase the sample quality, we utilized laser capture microdissection of prostate tumor and benign epithelial cells. Remarkably, combination of these approaches recapitulated the common prostate cancer-associated gene expression alteration. Identification of prostate cancer associated-gene expression alterations such as AMACR, Kallikrein gene family and genes associated with androgen signaling such as PDEF and STEAP were consistent with previous findings reported in prostate cancer. These data suggest that combination of laser capture dissection with computational enhancement of microarray data may be useful for the assessment of gene expression changes in FFPE prostate cancer specimens.

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Acknowledgements

We thank Ms. Denise Young for preparation of the prostate samples.

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Author notes

  1. B Furusato and S Shaheduzzaman: These authors have contributed equally to this work.

Authors and Affiliations

  1. Department of Genitourinary Pathology, Armed Forces Institute of Pathology, Washington, DC, USA

    B Furusato & I A Sesterhenn

  2. Department of Surgery Uniformed Services, Center for Prostate Disease Research, University of the Health Sciences, Rockville, MD, USA

    B Furusato, S Shaheduzzaman, G Petrovics, A Dobi, L Ravindranath & S Srivastava

  3. Genomatix Software GmbH, Munich, Germany

    M Seifert & T Werner

  4. Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, MD, USA

    M E Nau & M Vahey

  5. Urology Service, Walter Reed Army Medical Center, Washington, DC, USA

    D G McLeod

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  1. B Furusato
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  2. S Shaheduzzaman
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  3. G Petrovics
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  4. A Dobi
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  5. M Seifert
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  6. L Ravindranath
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  7. M E Nau
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  8. T Werner
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  9. M Vahey
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  10. D G McLeod
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  11. S Srivastava
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  12. I A Sesterhenn
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Corresponding author

Correspondence to I A Sesterhenn.

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The authors indicated no potential conflicts of interest.

Supplementary Information accompanies the paper on the Prostate Cancer and Prostatic Diseases website (http://www.nature.com/pcan)

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Furusato, B., Shaheduzzaman, S., Petrovics, G. et al. Transcriptome analyses of benign and malignant prostate epithelial cells in formalin-fixed paraffin-embedded whole-mounted radical prostatectomy specimens. Prostate Cancer Prostatic Dis 11, 194–197 (2008). https://doi.org/10.1038/sj.pcan.4501007

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  • DOI: https://doi.org/10.1038/sj.pcan.4501007

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