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miRNA Expression Analyses in Prostate Cancer Clinical Tissues
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Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total

J S Hall1, J Taylor, H R Valentine

  • 1Translational Radiobiology Group, School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Christie Hospital NHS Trust, Wilmslow Road, Manchester M20 4BX, UK.

British Journal of Cancer
|July 19, 2012
PubMed
Abstract

Insights

Sample age significantly impacts messenger RNA (mRNA) expression profiling in formalin-fixed paraffin-embedded (FFPE) tissues. MicroRNA (miRNA) profiling offers a robust alternative, effectively analyzing older FFPE samples where mRNA data is compromised.

Area of Science:

  • Oncology
  • Molecular Biology
  • Genomics

Background:

  • Degradation of formalin-fixed paraffin-embedded (FFPE) samples poses challenges for accurate mRNA expression profiling.
  • Exploring factors influencing FFPE mRNA profiling success is crucial for reliable biomarker discovery.
  • Investigating novel approaches to overcome limitations in FFPE sample analysis is warranted.

Purpose of the Study:

  • To identify predictors of successful mRNA expression profiling in FFPE samples.
  • To evaluate an alternative method for gene expression analysis in aged FFPE tissues.
  • To assess the feasibility of microRNA (miRNA) profiling in FFPE samples of varying ages.

Main Methods:

  • Hybridization of bladder and cervix carcinoma FFPE samples to Affymetrix Exon arrays.
  • Assessment of technical success using percentage detection above background (%DABG).
  • Evaluation of biological signal by distinguishing tumor subtypes and measuring specific microRNAs (miR-205) via qRT-PCR and array-based profiling.

Main Results:

  • Sample age, not RNA quality controls, correlated with profiling success (%DABG).
  • mRNA expression profiling showed lost biological signal in older samples.
  • MicroRNA (miRNA) profiling demonstrated high correlation (R=0.95) and effectively distinguished tumor subtypes, outperforming mRNA profiling in older FFPE samples.

Conclusions:

  • Sample age is the primary determinant of successful mRNA profiling in FFPE specimens.
  • MicroRNA (miRNA) profiling provides a viable solution for analyzing gene expression in older FFPE samples.
  • miRNA analysis is robust and overcomes the limitations associated with sample degradation in FFPE tissues.

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