Profiling and discovery of novel miRNAs from formalin-fixed, paraffin-embedded melanoma and nodal specimens

J Mol Diagn. 2009 Sep;11(5):420-9. doi: 10.2353/jmoldx.2009.090041.

Abstract

Archived formalin-fixed, paraffin-embedded human tumors are widely available and represent a unique source of morphologically defined material. Formalin-fixed, paraffin-embedded tissue is known to contain a wealth of molecular information in the form of microRNAs (miRNAs), which could be correlated with clinical outcome for improved prognostication and/or treatment response. miRNAs are endogenous, noncoding RNAs ( approximately 22 nucleotides) and may function as tumor suppressors or oncogenes. A reliable, robust methodology is needed to take full advantage of archived human cancers, especially for those where fresh-frozen tumor banks are unavailable, for example, malignant melanoma. To this end, we applied a simple-to-use protocol for extracting total RNA from various formalin-fixed, paraffin-embedded specimens (colon, liver, prostate, thyroid, uterus, and skin), optimized for small RNA recovery. Using a "poison primer" strategy (ie, primer silencing), we blocked the amplification of ribosomal RNA, enabling the successful sequencing of 17 novel and 53 known miRNAs (including small RNAs) from 10-year-old archived normal skin, cutaneous scalp melanoma, and sentinel lymph nodes (both negative and positive for metastasis) excised from a 52-year-old man. The cloning incidence provided an estimation of the level of specific miRNA expression, which was confirmed by Northern analysis and quantitative real-time polymerase chain reaction. This methodology can therefore be used to facilitate miRNA discovery from archived human cancers.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Blotting, Northern
  • Child
  • Formaldehyde / chemistry*
  • Humans
  • In Vitro Techniques
  • Male
  • Melanoma / genetics
  • Melanoma / pathology*
  • MicroRNAs / analysis
  • MicroRNAs / genetics*
  • Middle Aged
  • Neoplasms / genetics
  • Neoplasms / pathology*
  • Paraffin Embedding / methods*
  • Polymerase Chain Reaction
  • Tissue Fixation / methods*

Substances

  • MicroRNAs
  • Formaldehyde