Extracellular vesicles from Heligmosomoides bakeri and Trichuris muris contain distinct microRNA families and small RNAs that could underpin different functions in the host.
Extracellular RNA
Extracellular vesicle
Gastrointestinal nematode
Helminth
RNA interference
microRNA
siRNA
Journal
International journal for parasitology
ISSN: 1879-0135
Titre abrégé: Int J Parasitol
Pays: England
ID NLM: 0314024
Informations de publication
Date de publication:
08 2020
08 2020
Historique:
received:
07
05
2020
revised:
18
06
2020
accepted:
19
06
2020
pubmed:
14
7
2020
medline:
22
6
2021
entrez:
14
7
2020
Statut:
ppublish
Résumé
Extracellular vesicles (EVs) have emerged as a ubiquitous component of helminth excretory-secretory products that can deliver parasite molecules to host cells to elicit immunomodulatory effects. RNAs are one type of cargo molecule that can underpin EV functions, hence there is extensive interest in characterising the RNAs that are present in EVs from different helminth species. Here we outline methods for identifying all of the small RNAs (sRNA) in helminth EVs and address how different methodologies may influence the sRNAs detected. We show that different EV purification methods introduce relatively little variation in the sRNAs that are detected, and that different RNA library preparation methods yielded larger differences. We compared the EV sRNAs in the gastrointestinal nematode Heligmosomoides bakeri with those in EVs from the distantly related gastrointestinal nematode Trichuris muris, and found that many of the sRNAs in both organisms derive from repetitive elements or intergenic regions. However, only in H. bakeri do these RNAs contain a 5' triphosphate, and Guanine (G) starting nucleotide, consistent with their biogenesis by RNA-dependent RNA polymerases (RdRPs). Distinct microRNA (miRNA) families are carried in EVs from each parasite, with H. bakeri EVs specific for miR-71, miR-49, miR-63, miR-259 and miR-240 gene families, and T. muris EVs specific for miR-1, miR-1822 and miR-252, and enriched for miR-59, miR-72 and miR-44 families, with the miR-9, miR-10, miR-80 and let-7 families abundant in both. We found a larger proportion of miRNA reads derive from the mouse host in T. muris EVs, compared with H. bakeri EVs. Our report underscores potential biases in the sRNAs sequenced based on library preparation methods, suggests specific nematode lineages have evolved distinct sRNA synthesis/export pathways, and highlights specific differences in EV miRNAs from H. bakeri and T. muris that may underpin functional adaptation to their host niches.
Identifiants
pubmed: 32659276
pii: S0020-7519(20)30164-8
doi: 10.1016/j.ijpara.2020.06.002
pmc: PMC7435682
pii:
doi:
Substances chimiques
MicroRNAs
0
RNA, Helminth
0
RNA, Small Interfering
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
719-729Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/J004243/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : Z03128/Z/16/Z/WT
Pays : United Kingdom
Organisme : National Centre for the Replacement, Refinement and Reduction of Animals in Research
ID : NC/P001521/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : Z10661/Z/18/Z/WT
Pays : United Kingdom
Organisme : Wellcome Trust
ID : WT104915MA
Pays : United Kingdom
Organisme : Wellcome Trust
ID : WT 097394/Z/11/Z
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/K001744/1
Pays : United Kingdom
Informations de copyright
Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.
Références
Nat Commun. 2015 Nov 25;6:8864
pubmed: 26602609
Int J Parasitol. 2020 Aug;50(9):707-718
pubmed: 32659277
J Extracell Vesicles. 2017 Mar 7;6(1):1286095
pubmed: 28326170
J Infect Dis. 2015 Nov 15;212(10):1636-45
pubmed: 25985904
PLoS Pathog. 2019 Jun 4;15(6):e1007817
pubmed: 31163079
J Vis Exp. 2015 Apr 06;(98):e52412
pubmed: 25867600
Cell. 2018 Mar 22;173(1):20-51
pubmed: 29570994
J Immunol. 1998 Apr 1;160(7):3453-61
pubmed: 9531306
Nucleic Acids Res. 2018 Jan 4;46(D1):D335-D342
pubmed: 29112718
J Extracell Vesicles. 2018 Nov 23;7(1):1535750
pubmed: 30637094
Nat Commun. 2017 Nov 23;8(1):1741
pubmed: 29170498
Exp Parasitol. 2017 Jul;178:30-36
pubmed: 28533110
Mol Biochem Parasitol. 2017 Jul;215:2-10
pubmed: 27899279
Plant Physiol. 2020 Jan;182(1):51-62
pubmed: 31636103
Immunol Cell Biol. 2018 May 29;:
pubmed: 29808496
Nat Commun. 2014 Nov 25;5:5488
pubmed: 25421927
Nat Commun. 2019 May 28;10(1):2344
pubmed: 31138806
Front Microbiol. 2017 Mar 16;8:377
pubmed: 28360889
Mob DNA. 2015 Jun 02;6:11
pubmed: 26045719
Methods Mol Biol. 2019;1962:1-14
pubmed: 31020551
Curr Opin Microbiol. 2018 Dec;46:73-79
pubmed: 30172862
Parasite Immunol. 2018 Jul;40(7):e12536
pubmed: 29746004
J Extracell Vesicles. 2018 Jan 21;7(1):1428004
pubmed: 29410780
Cell Rep. 2017 May 23;19(8):1545-1557
pubmed: 28538175
Genome Biol. 2009;10(3):R25
pubmed: 19261174
Nucleic Acids Res. 2002 Jan 1;30(1):207-10
pubmed: 11752295
Parasitol Res. 2015 May;114(5):1865-73
pubmed: 25855345
Immunity. 2017 Oct 17;47(4):739-751.e5
pubmed: 29045903
Annu Rev Nutr. 2016 Jul 17;36:301-36
pubmed: 27215587
Nucleic Acids Res. 2012 Jan;40(1):37-52
pubmed: 21911355
J Extracell Vesicles. 2015 Oct 05;4:28665
pubmed: 26443722
Int J Parasitol. 2020 Aug;50(9):635-645
pubmed: 32652128
Semin Immunopathol. 2012 Nov;34(6):815-28
pubmed: 23053395
BMC Biol. 2018 May 14;16(1):52
pubmed: 29759067
Nucleic Acids Res. 2018 Sep 28;46(17):9081-9093
pubmed: 29893896
Elife. 2020 May 22;9:
pubmed: 32441255
PLoS Pathog. 2019 Dec 30;15(12):e1008090
pubmed: 31887135
J Extracell Vesicles. 2019 Feb 14;8(1):1578116
pubmed: 30815237
Int J Parasitol. 2016 Nov;46(12):799-808
pubmed: 27590846
PLoS Negl Trop Dis. 2019 Nov 26;13(11):e0007811
pubmed: 31770367
PLoS Biol. 2015 Feb 10;13(2):e1002061
pubmed: 25668728
Front Genet. 2019 Apr 26;10:364
pubmed: 31080456
RNA Biol. 2017 Apr 3;14(4):436-441
pubmed: 28125361
Nat Genet. 2019 Jan;51(1):163-174
pubmed: 30397333
Cell Host Microbe. 2016 Jan 13;19(1):32-43
pubmed: 26764595
Trends Parasitol. 2010 Nov;26(11):524-9
pubmed: 20729145
Science. 2019 Feb 22;363(6429):817-818
pubmed: 30792291
PLoS Negl Trop Dis. 2015 Sep 24;9(9):e0004069
pubmed: 26401956
Trends Parasitol. 2015 Oct;31(10):477-489
pubmed: 26433251
PLoS Pathog. 2011 Jan 06;7(1):e1001248
pubmed: 21253577
BMC Genomics. 2012 Jan 04;13:4
pubmed: 22216965
Nucleic Acids Res. 2019 Apr 23;47(7):3594-3606
pubmed: 30820541
PLoS One. 2015 May 05;10(5):e0126049
pubmed: 25942392
Semin Immunopathol. 2012 Nov;34(6):829-46
pubmed: 23053394
Nat Rev Immunol. 2014 Oct;14(10):667-85
pubmed: 25234148
RNA. 2013 Jun;19(6):740-51
pubmed: 23610128
Bioinformatics. 2013 Nov 15;29(22):2933-5
pubmed: 24008419