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Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing

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  • Thomas Conrad, Berlin Institute for Medical Systems Biology at the MDC Berlin-Buch
  • ,
  • Evgenia Ntini, Max Planck Institute for Molecular Genetics
  • ,
  • Benjamin Lang, University of Barcelona
  • ,
  • Luca Cozzuto, University of Barcelona
  • ,
  • Jesper B. Andersen, Biotech Research and Innovation Centre (BRIC), University of Copenhagen
  • ,
  • Jens U. Marquardt, University Medical Centre Schleswig-Holstein
  • ,
  • Julia Ponomarenko, University of Barcelona, Pompeu Fabra University
  • ,
  • Gian Gaetano Tartaglia, University of Barcelona, Pompeu Fabra University
  • ,
  • Ulf A. Vang Ørom

MicroRNA expression is important for gene regulation and deregulated microRNA expression is often observed in diseases such as cancer. The processing of primary microRNA transcripts is an important regulatory step in microRNA biogenesis. Due to low expression level and association with chromatin, primary microRNAs are challenging to study in clinical samples where input material is limited. Here, we present a high-sensitivity targeted method to determine processing efficiency of several hundred primary microRNAs from total RNA that requires relatively few RNA sequencing reads. We validate the method using RNA from HeLa cells and show the applicability to clinical samples by analyzing RNA from normal liver and hepatocellular carcinoma. We identify 24 primary microRNAs with significant changes in processing efficiency from normal liver to hepatocellular carcinoma, among those the highly expressed miRNA-122 and miRNA-21, demonstrating that differential processing of primary microRNAs is occurring and could be involved in disease.With our method presented here we provide means to study pri-miRNA processing in disease from clinical samples.

Original languageEnglish
Pages (from-to)1726-1730
Number of pages5
Publication statusPublished - Nov 2020

    Research areas

  • Clinical samples, HCC, Liver, miRNA biogenesis, Primary miRNAs, RNA sequencing

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