Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation.

Adult Body Fluids / chemistry Cell Line Cell-Free Nucleic Acids / isolation & purification Circulating MicroRNA / isolation & purification Extracellular Vesicles / metabolism Female Healthy Volunteers Humans Male MicroRNAs / isolation & purification RNA / isolation & purification Reproducibility of Results Sequence Analysis, RNA / methods
extracellular RNA extracellular vesicles lipoprotein ribonucleoprotein

Journal

Cell
ISSN: 1097-4172
Titre abrégé: Cell
Pays: United States
ID NLM: 0413066

Informations de publication

Date de publication:
04 04 2019
Historique:
received: 03 08 2018
revised: 29 12 2018
accepted: 11 03 2019
entrez: 6 4 2019
pubmed: 6 4 2019
medline: 25 1 2020
Statut: ppublish

Résumé

Poor reproducibility within and across studies arising from lack of knowledge regarding the performance of extracellular RNA (exRNA) isolation methods has hindered progress in the exRNA field. A systematic comparison of 10 exRNA isolation methods across 5 biofluids revealed marked differences in the complexity and reproducibility of the resulting small RNA-seq profiles. The relative efficiency with which each method accessed different exRNA carrier subclasses was determined by estimating the proportions of extracellular vesicle (EV)-, ribonucleoprotein (RNP)-, and high-density lipoprotein (HDL)-specific miRNA signatures in each profile. An interactive web-based application (miRDaR) was developed to help investigators select the optimal exRNA isolation method for their studies. miRDar provides comparative statistics for all expressed miRNAs or a selected subset of miRNAs in the desired biofluid for each exRNA isolation method and returns a ranked list of exRNA isolation methods prioritized by complexity, expression level, and reproducibility. These results will improve reproducibility and stimulate further progress in exRNA biomarker development.

Identifiants

DOI: 10.1016/j.cell.2019.03.024 PMID: 30951671 PMC: PMC6557167
pubmed: 30951671
pii: S0092-8674(19)30286-7
doi: 10.1016/j.cell.2019.03.024
pmc: PMC6557167
mid: NIHMS1021236
pii:
doi:

Substances chimiques

Cell-Free Nucleic Acids 0
Circulating MicroRNA 0
MicroRNAs 0
RNA 63231-63-0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

446-462.e16

Subventions

Organisme : NHLBI NIH HHS
ID : R01 HL122547
Pays : United States
Organisme : NCI NIH HHS
ID : P01 CA069246
Pays : United States
Organisme : NCI NIH HHS
ID : P50 CA217685
Pays : United States
Organisme : NCATS NIH HHS
ID : UH3 TR000943
Pays : United States
Organisme : NIDA NIH HHS
ID : U54 DA036134
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL133575
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA217833
Pays : United States
Organisme : NCI NIH HHS
ID : U19 CA179563
Pays : United States
Organisme : NCATS NIH HHS
ID : UH3 TR000901
Pays : United States
Organisme : NCATS NIH HHS
ID : UH3 TR000890
Pays : United States
Organisme : NCI NIH HHS
ID : U19 CA179512
Pays : United States
Organisme : NCATS NIH HHS
ID : UH2 TR000901
Pays : United States
Organisme : NHLBI NIH HHS
ID : K23 HL127099
Pays : United States
Organisme : NCATS NIH HHS
ID : UH3 TR000906
Pays : United States
Organisme : NCATS NIH HHS
ID : UH2 TR000884
Pays : United States
Organisme : NCATS NIH HHS
ID : UH2 TR000906
Pays : United States
Organisme : NICHD NIH HHS
ID : T32 HD007203
Pays : United States
Organisme : NCATS NIH HHS
ID : UH2 TR000943
Pays : United States
Organisme : NCATS NIH HHS
ID : UH2 TR000890
Pays : United States
Organisme : NCI NIH HHS
ID : R35 CA209904
Pays : United States
Organisme : NHLBI NIH HHS
ID : U01 HL126494
Pays : United States
Organisme : NCATS NIH HHS
ID : UH3 TR000884
Pays : United States

Commentaires et corrections

Type : CommentIn

Informations de copyright

Copyright © 2019 Elsevier Inc. All rights reserved.

Références

Cell. 2019 Apr 4;177(2):463-477.e15
pubmed: 30951672
Int J Mol Med. 2017 Sep;40(3):834-844
pubmed: 28737826
J Extracell Vesicles. 2014 Nov 06;3:25011
pubmed: 25396408
J Med Genet. 2014 Aug;51(8):526-9
pubmed: 24996905
Proc Natl Acad Sci U S A. 2016 Feb 23;113(8):E968-77
pubmed: 26858453
Mol Ther. 2017 Mar 1;25(3):679-693
pubmed: 28159509
Am J Physiol Heart Circ Physiol. 2017 Dec 1;313(6):H1162-H1167
pubmed: 28916639
Nucleic Acids Res. 2011 Sep 1;39(16):7223-33
pubmed: 21609964
Nat Cell Biol. 2008 Dec;10(12):1470-6
pubmed: 19011622
Sci Rep. 2017 Feb 21;7:41184
pubmed: 28220888
RNA. 2013 May;19(5):712-22
pubmed: 23525801
BMC Genomics. 2018 May 5;19(1):331
pubmed: 29728066
RNA Biol. 2012 Aug;9(8):1066-75
pubmed: 22858679
Methods Mol Biol. 2018;1680:237-255
pubmed: 29030853
RNA Biol. 2017 Jan 2;14(1):58-72
pubmed: 27791479
BMC Bioinformatics. 2015 May 22;16:169
pubmed: 25994840
Science. 1998 Nov 6;282(5391):1145-7
pubmed: 9804556
Nat Cell Biol. 2011 Apr;13(4):423-33
pubmed: 21423178
PLoS One. 2009;4(3):e4802
pubmed: 19277126
Cancer. 1992 Apr 1;69(7):1664-73
pubmed: 1312890
Circulation. 2015 Jun 23;131(25):2202-2216
pubmed: 25995320
Genome Biol. 2014;15(12):550
pubmed: 25516281
Clin Chem. 2018 Jul;64(7):1085-1095
pubmed: 29685897
Nat Biotechnol. 2018 Sep;36(8):746-757
pubmed: 30010675
Am J Hum Genet. 2017 Nov 2;101(5):803-814
pubmed: 29100091
Nat Methods. 2015 May;12(5):453-7
pubmed: 25822800
Am J Hum Genet. 2017 Dec 7;101(6):1034
pubmed: 29220675
Nat Commun. 2016 Apr 26;7:11106
pubmed: 27112789
Nat Cell Biol. 2018 Mar;20(3):332-343
pubmed: 29459780
J Extracell Vesicles. 2014 Mar 26;3:
pubmed: 24683445
Sci Rep. 2017 Mar 17;7:44061
pubmed: 28303895
Nucleic Acids Res. 2018 Sep 28;46(17):9081-9093
pubmed: 29893896
Nat Commun. 2018 Sep 25;9(1):3906
pubmed: 30254196
J Extracell Vesicles. 2014 Mar 25;3:
pubmed: 24678386
Stem Cells. 2008 Jun;26(6):1506-16
pubmed: 18403753
Biotechniques. 2015 Jul 01;59(1):13-7
pubmed: 26156779
Proc Natl Acad Sci U S A. 2013 Mar 12;110(11):4255-60
pubmed: 23440203
Nat Cell Biol. 2007 Jun;9(6):654-9
pubmed: 17486113
Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14888-93
pubmed: 25267620
Cell Mol Life Sci. 2018 Aug;75(15):2873-2886
pubmed: 29441425
EMBO Rep. 2007 Nov;8(11):1052-60
pubmed: 17932509
PLoS One. 2010 Oct 08;5(10):e13247
pubmed: 20949044
Bioinformatics. 2016 Aug 15;32(16):2481-9
pubmed: 27153631
Nucleic Acids Res. 2018 Jan 4;46(D1):D152-D159
pubmed: 29186503

Auteurs

Srimeenakshi Srinivasan (S)

Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.

Ashish Yeri (A)

Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.

Pike See Cheah (PS)

Neurology and Radiology Services and Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA; Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Malaysia.

Allen Chung (A)

Department of Surgery, University of California, San Francisco and VA Medical Center San Francisco, San Francisco, CA 94121, USA.

Kirsty Danielson (K)

Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.

Peter De Hoff (P)

Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.

Justyna Filant (J)

Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Clara D Laurent (CD)

Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.

Lucie D Laurent (LD)

Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.

Rogan Magee (R)

Computational Medicine Center, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA, USA.

Courtney Moeller (C)

Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.

Venkatesh L Murthy (VL)

Department of Medicine, Division of Cardiovascular Medicine, Frankel Cardiovascular Center, University of Michigan, Ann Arbor, MI, USA.

Parham Nejad (P)

Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.

Anu Paul (A)

Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.

Isidore Rigoutsos (I)

Computational Medicine Center, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA, USA.

Rodosthenis Rodosthenous (R)

Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.

Ravi V Shah (RV)

Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.

Bridget Simonson (B)

Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.

Cuong To (C)

Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.

David Wong (D)

Department of Surgery, University of California, San Francisco and VA Medical Center San Francisco, San Francisco, CA 94121, USA.

Irene K Yan (IK)

Mayo Clinic Florida, Jacksonville, FL, USA.

Xuan Zhang (X)

Neurology and Radiology Services and Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.

Leonora Balaj (L)

Neurology and Radiology Services and Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA; Department of Neurosurgery, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.

Xandra O Breakefield (XO)

Neurology and Radiology Services and Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.

George Daaboul (G)

NanoView Biosciences, Boston, MA, USA.

Roopali Gandhi (R)

Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.

Jodi Lapidus (J)

Oregon Health Sciences University, Portland, OR, USA.

Eric Londin (E)

Computational Medicine Center, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA, USA.

Tushar Patel (T)

Mayo Clinic Florida, Jacksonville, FL, USA.

Robert L Raffai (RL)

Department of Surgery, University of California, San Francisco and VA Medical Center San Francisco, San Francisco, CA 94121, USA.

Anil K Sood (AK)

Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Roger P Alexander (RP)

Pacific Northwest Research Institute, Seattle, WA 98122, USA.

Saumya Das (S)

Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.

Louise C Laurent (LC)

Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA. Electronic address: llaurent@ucsd.edu.

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female

Evaluation of Low-Value Services Across Major Medicare Advantage Insurers and Traditional Medicare.

Ciara Duggan, Adam L Beckman, Ishani Ganguli et al.
1.00
Humans United States Aged Cross-Sectional Studies Medicare Part C

Effectiveness of Virtual Yoga for Chronic Low Back Pain: A Randomized Clinical Trial.

Hallie Tankha, Devyn Gaskins, Amanda Shallcross et al.
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH

questionsmedicales.fr › Personnes › Tranches d'âge › Adulte › Small RNA Sequencing across Diverse Biofluids...
questionsmedicales.fr › Liquides et sécrétions biologiques › Liquides biologiques › Small RNA Sequencing across Diverse Biofluids...
questionsmedicales.fr › Cellules › Cellules cultivées › Lignée cellulaire › Small RNA Sequencing across Diverse Biofluids...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › Acides nucléiques acellulaires › Small RNA Sequencing across Diverse Biofluids...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN non traduit › Petit ARN non traduit › microARN › MicroARN circulant › Small RNA Sequencing across Diverse Biofluids...
questionsmedicales.fr › Cellules › Structures cellulaires › Espace extracellulaire › Vésicules extracellulaires › Small RNA Sequencing across Diverse Biofluids...
questionsmedicales.fr › Personnes › Bénévoles › Volontaires sains › Small RNA Sequencing across Diverse Biofluids...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Small RNA Sequencing across Diverse Biofluids...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN non traduit › Petit ARN non traduit › microARN › Small RNA Sequencing across Diverse Biofluids...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › Small RNA Sequencing across Diverse Biofluids...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Méthodologie en recherche épidémiologique › Reproductibilité des résultats › Small RNA Sequencing across Diverse Biofluids...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › Small RNA Sequencing across Diverse Biofluids...