Phospho-RNA-seq: a modified small RNA-seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma.
RNA‐seq
cell‐free RNA
extracellular RNA
liquid biopsy
Journal
The EMBO journal
ISSN: 1460-2075
Titre abrégé: EMBO J
Pays: England
ID NLM: 8208664
Informations de publication
Date de publication:
03 06 2019
03 06 2019
Historique:
received:
05
02
2019
revised:
14
04
2019
accepted:
15
04
2019
pubmed:
6
5
2019
medline:
8
1
2020
entrez:
5
5
2019
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 31053596
pii: embj.2019101695
doi: 10.15252/embj.2019101695
pmc: PMC6545557
pii:
doi:
Substances chimiques
Biomarkers
0
Cell-Free Nucleic Acids
0
MicroRNAs
0
RNA, Long Noncoding
0
RNA, Messenger
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Validation Study
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NCI NIH HHS
ID : P30 CA046592
Pays : United States
Organisme : NHLBI NIH HHS
ID : T32 HL007622
Pays : United States
Organisme : NHLBI NIH HHS
ID : U01 HL126499
Pays : United States
Informations de copyright
© 2019 The Authors. Published under the terms of the CC BY 4.0 license.
Références
N Engl J Med. 2006 Aug 10;355(6):570-80
pubmed: 16899777
PLoS One. 2017 Jan 6;12(1):e0164644
pubmed: 28060806
Proc Natl Acad Sci U S A. 2014 May 20;111(20):7361-6
pubmed: 24799715
Biochemistry. 1977 Nov 15;16(23):5120-6
pubmed: 199248
Nat Biotechnol. 2018 Sep;36(8):746-757
pubmed: 30010675
Sci Rep. 2017 Mar 17;7:44061
pubmed: 28303895
Cell Rep. 2018 Oct 30;25(5):1346-1358
pubmed: 30380423
Cell. 2017 Jul 13;170(2):352-366.e13
pubmed: 28709002
Proc Natl Acad Sci U S A. 1965 Jul;54(1):158-65
pubmed: 5323016
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Nat Genet. 2015 Mar;47(3):199-208
pubmed: 25599403
Wiley Interdiscip Rev RNA. 2014 Jul-Aug;5(4):537-48
pubmed: 24687772
Methods. 2008 Jan;44(1):3-12
pubmed: 18158127
J Biol Chem. 1966 Jun 25;241(12):2923-32
pubmed: 4287929
PeerJ. 2018 Apr 2;6:e4600
pubmed: 29629248
Bioinformatics. 2019 Jun 1;35(11):1966-1967
pubmed: 30346488
Nat Rev Cancer. 2011 Jun;11(6):426-37
pubmed: 21562580
Nucleic Acids Res. 2016 May 5;44(8):3865-77
pubmed: 26921406
Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):5003-8
pubmed: 21383194
Science. 2001 Sep 21;293(5538):2269-71
pubmed: 11486053
BMC Genomics. 2013 May 10;14:319
pubmed: 23663360
Clin Biochem. 1972 Dec;5(4):198-200
pubmed: 4674387
Biochemistry. 2011 Sep 20;50(37):7835-41
pubmed: 21838247
Nature. 2000 Aug 17;406(6797):747-52
pubmed: 10963602
Nat Commun. 2016 Apr 26;7:11106
pubmed: 27112789
Cell. 2016 Mar 10;164(6):1226-1232
pubmed: 26967288
BMC Bioinformatics. 2008 Jun 09;9:271
pubmed: 18541026
PLoS One. 2013 Jun 07;8(6):e64795
pubmed: 23762257
Nat Rev Genet. 2009 Jan;10(1):57-63
pubmed: 19015660
Nucleic Acids Res. 2017 Dec 1;45(21):12140-12151
pubmed: 29069500
Nat Methods. 2008 Jul;5(7):621-8
pubmed: 18516045
Biol Direct. 2013 Jul 04;8:16
pubmed: 23826734
Nature. 2003 Sep 25;425(6956):415-9
pubmed: 14508493
Nat Methods. 2013 Jul;10(7):623-9
pubmed: 23685885
Nat Genet. 2008 May;40(5):499-507
pubmed: 18443585
Nat Rev Mol Cell Biol. 2014 Aug;15(8):509-24
pubmed: 25027649
Front Genet. 2012 Apr 20;3:56
pubmed: 22529849
Bioinformatics. 2015 Aug 15;31(16):2614-22
pubmed: 25847007
BMC Bioinformatics. 2008 Dec 29;9:559
pubmed: 19114008
Front Neurosci. 2018 Sep 05;12:625
pubmed: 30233304
Genome Res. 2011 Feb;21(2):265-75
pubmed: 21177965
Methods Mol Biol. 2015;1276:211-28
pubmed: 25665566
Sci Rep. 2016 Jan 20;6:19413
pubmed: 26786760
Proc Natl Acad Sci U S A. 2018 Jun 5;115(23):E5334-E5343
pubmed: 29777089
Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10513-8
pubmed: 18663219
N Engl J Med. 2007 Jan 4;356(1):11-20
pubmed: 17202451
Front Immunol. 2018 May 16;9:1012
pubmed: 29867984
RNA Biol. 2014;11(7):817-28
pubmed: 24922482
PLoS Comput Biol. 2011 Jul;7(7):e1002111
pubmed: 21779159
PLoS One. 2008;3(11):e3694
pubmed: 19002258
Mol Cell. 2010 Jul 9;39(1):133-44
pubmed: 20603081