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Biological Chemistry

Technique eases analysis of damaged RNA

New method allows researchers to analyze gene expression in preserved tissue biopsy samples

by Stu Borman
July 10, 2017 | APPEARED IN VOLUME 95, ISSUE 28

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Credit: CNRI/Science Source
A new RNA analysis technique could help researchers assess gene expression in preserved tissues such as this slice of a skin tumor.
Credit: CNRI/Science Source
A new RNA analysis technique could help researchers assess gene expression in preserved tissues such as this slice of a skin tumor.

When doctors take biopsies of a patient’s tissue, they often fix the tissue with formalin and embed it in wax to preserve it. But this process chemically modifies and fragments mRNAs in the tissue, making it difficult to analyze the mRNAs later to, for example, study gene expression patterns. This mRNA analysis typically involves reverse transcription, which requires long stretches of unmodified mRNA and subsequent amplification of the resulting complementary DNAs. An alternative gene expression analysis technique made by Nano­String can handle damaged mRNAs, but it uses expensive instrumentation and proprietary reagents and has limited sensitivity, says Ben Larman of Johns Hopkins University School of Medicine. Larman and coworkers now report a competitive technique, called ligation in situ hybridization (LISH), that they think could be less expensive and more sensitive than Nano­String’s (Nucleic Acids Res. 2017, DOI: 10.1093/nar/gkx471). In LISH, researchers design probes containing mostly DNA sequences that complement mRNA sequences of interest. Adding these probes to damaged mRNAs allows scientists to turn the mRNAs into sequences of mostly DNA that can be amplified and sequenced without reverse transcription.

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