Phospho-RNA-seq: a modified small RNA-seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma

EMBO J. 2019 Jun 3;38(11):e101695. doi: 10.15252/embj.2019101695. Epub 2019 May 3.


Extracellular RNAs (exRNAs) in biofluids have attracted great interest as potential biomarkers. Although extracellular microRNAs in blood plasma are extensively characterized, extracellular messenger RNA (mRNA) and long non-coding RNA (lncRNA) studies are limited. We report that plasma contains fragmented mRNAs and lncRNAs that are missed by standard small RNA-seq protocols due to lack of 5' phosphate or presence of 3' phosphate. These fragments were revealed using a modified protocol ("phospho-RNA-seq") incorporating RNA treatment with T4-polynucleotide kinase, which we compared with standard small RNA-seq for sequencing synthetic RNAs with varied 5' and 3' ends, as well as human plasma exRNA Analyzing phospho-RNA-seq data using a custom, high-stringency bioinformatic pipeline, we identified mRNA/lncRNA transcriptome fingerprints in plasma, including tissue-specific gene sets. In a longitudinal study of hematopoietic stem cell transplant patients, bone marrow- and liver-enriched exRNA genes were tracked with bone marrow recovery and liver injury, respectively, providing proof-of-concept validation as a biomarker approach. By enabling access to an unexplored realm of mRNA and lncRNA fragments, phospho-RNA-seq opens up new possibilities for plasma transcriptomic biomarker development.

Keywords: RNA‐seq; cell‐free RNA; extracellular RNA; liquid biopsy.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Biomarkers / analysis
  • Biomarkers / blood*
  • Blood Chemical Analysis / methods
  • Cell-Free Nucleic Acids / analysis*
  • Cell-Free Nucleic Acids / blood
  • Computational Biology / methods
  • Gene Expression Profiling / methods
  • Humans
  • MicroRNAs / analysis
  • MicroRNAs / blood*
  • RNA, Long Noncoding / analysis*
  • RNA, Long Noncoding / blood
  • RNA, Messenger / analysis*
  • RNA, Messenger / blood
  • RNA-Seq / methods*
  • Sequence Analysis, RNA / methods


  • Biomarkers
  • Cell-Free Nucleic Acids
  • MicroRNAs
  • RNA, Long Noncoding
  • RNA, Messenger