Characterization of a method for profiling gene expression in cells recovered from intact human prostate tissue using RNA linear amplification

Y. Ding, L. Xu, S. Chen, B. D. Jovanovic, I. B. Helenowski, D. L. Kelly, W. J. Catalona, X. J. Yang, M. Pins, V. Ananthanarayanan, Raymond Bergan

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

Coupling array technology to laser capture microdissection (LCM) has the potential to yield gene expression profiles of specific cell populations within tissue. However, remaining problems with linear amplification preclude accurate expression profiling when using the low nanogram amounts of RNA recovered after LCM of human tissue. We describe a novel robust method to reliably amplify RNA after LCM, allowing direct probing of 12K gene arrays. The fidelity of amplification was demonstrated by comparing the ability of amplified RNA (aRNA) versus that of native RNA to identify differentially expressed genes between two different cell lines, demonstrating a 99.3% concordance between observations. Array findings were validated by quantitative polymerase chain reaction analysis of a randomly selected subset of 32 genes. Using LCM to recover normal (N=5 subjects) or cancer (N=3) cell populations from intact human prostate tissue, three differentially expressed genes were identified. Independent investigators have previously identified differential expression of two of these three genes, hepsin and beta-microseminoprotein, in prostate cancer. Taken together, the current study demonstrates that accurate gene expression profiling can readily be performed on specific cell populations present within complex tissue. It also demonstrates that this approach efficiently identifies biologically relevant genes.

Original languageEnglish (US)
Pages (from-to)379-391
Number of pages13
JournalProstate Cancer and Prostatic Diseases
Volume9
Issue number4
DOIs
StatePublished - Dec 2006
Externally publishedYes

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Gene Expression Profiling
Laser Capture Microdissection
Prostate
RNA
Genes
Population
Transcriptome
Prostatic Neoplasms
Research Personnel
Technology
Cell Line
Polymerase Chain Reaction
Neoplasms

ASJC Scopus subject areas

  • Oncology
  • Urology

Cite this

Characterization of a method for profiling gene expression in cells recovered from intact human prostate tissue using RNA linear amplification. / Ding, Y.; Xu, L.; Chen, S.; Jovanovic, B. D.; Helenowski, I. B.; Kelly, D. L.; Catalona, W. J.; Yang, X. J.; Pins, M.; Ananthanarayanan, V.; Bergan, Raymond.

In: Prostate Cancer and Prostatic Diseases, Vol. 9, No. 4, 12.2006, p. 379-391.

Research output: Contribution to journalArticle

Ding, Y, Xu, L, Chen, S, Jovanovic, BD, Helenowski, IB, Kelly, DL, Catalona, WJ, Yang, XJ, Pins, M, Ananthanarayanan, V & Bergan, R 2006, 'Characterization of a method for profiling gene expression in cells recovered from intact human prostate tissue using RNA linear amplification', Prostate Cancer and Prostatic Diseases, vol. 9, no. 4, pp. 379-391. https://doi.org/10.1038/sj.pcan.4500888
Ding, Y. ; Xu, L. ; Chen, S. ; Jovanovic, B. D. ; Helenowski, I. B. ; Kelly, D. L. ; Catalona, W. J. ; Yang, X. J. ; Pins, M. ; Ananthanarayanan, V. ; Bergan, Raymond. / Characterization of a method for profiling gene expression in cells recovered from intact human prostate tissue using RNA linear amplification. In: Prostate Cancer and Prostatic Diseases. 2006 ; Vol. 9, No. 4. pp. 379-391.
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