Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease

Nature Communications
Xu ZhangDaniel Figeys

Abstract

Alterations in gut microbiota have been implicated in the pathogenesis of inflammatory bowel disease (IBD), however factors that mediate the host-microbiota interactions remain largely unknown. Here we collected mucosal-luminal interface samples from a pediatric IBD inception cohort and characterized both the human and microbiota proteins using metaproteomics. We show that microbial proteins related to oxidative stress responses are upregulated in IBD cases compared to controls. In particular, we demonstrate that the expression of human proteins related to oxidative antimicrobial activities is increased in IBD cases and correlates with the alteration of microbial functions. Additionally, we reveal that many of these human proteins are present and show altered abundance in isolated free extracellular vesicles (EVs). Therefore, our study suggests that the alteration of intestinal EV proteomes is associated with the aberrant host-microbiota interactions in IBD.

References

Feb 19, 2002·Chemical Reviews·Sheila S. David, Scott D. Williams
Sep 6, 2005·Mutation Research·Graham C Walker
Oct 6, 2005·Journal of Pediatric Gastroenterology and Nutrition·Jeffrey HyamsUNKNOWN Pediatric Inflammatory Bowel Disease Collaborative Research Group
Jan 27, 2007·Genome Research·Daniel H HusonStephan C Schuster
Mar 24, 2007·Science·Rodolphe BarrangouPhilippe Horvath
Aug 12, 2008·Gastroenterology·Gwenola Vernier-MassouilleJean Frédéric Colombel
Sep 24, 2008·World Journal of Gastroenterology : WJG·Michael WagnerMarie Carlson
Oct 16, 2008·Gastroenterology·Michael D KappelmanJonathan A Finkelstein
Oct 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·Harry SokolPhilippe Langella
Oct 31, 2008·The ISME Journal·Nathan C VerberkmoesJanet K Jansson
Mar 19, 2009·American Journal of Physiology. Endocrinology and Metabolism·Caroline Bauchart-ThevretDouglas G Burrin
Apr 21, 2009·Nature Methods·Jacek R WiśniewskiMatthias Mann
May 1, 2002·FEMS Microbiology Ecology·Julien LoubinouxAlain E Faou
Nov 17, 2009·Gastroenterology Clinics of North America·Cary G Sauer, Subra Kugathasan
Jun 22, 2010·Inflammatory Bowel Diseases·Eric I BenchimolAnne M Griffiths
Jul 14, 2010·Biochemical and Biophysical Research Communications·Felipe A ArenasClaudio C Vásquez
Nov 5, 2010·Nature·Josiane E GarneauSylvain Moineau
Feb 8, 2011·Journal of Clinical Biochemistry and Nutrition·Michael J Davies
Jun 17, 2011·Nature·Bernard KhorRamnik J Xavier
Jun 28, 2011·Genome Biology·Nicola SegataCurtis Huttenhower
Feb 22, 2012·Digestive Diseases and Sciences·Ibrahim MasoodiKartar Singh
Mar 28, 2012·Nature Reviews. Gastroenterology & Hepatology·Marianne H FraherEamonn M M Quigley
Oct 13, 2012·Bioinformatics·Limin FuWeizhong Li
Nov 17, 2012·Journal of Proteome Research·Bart MesuerePeter Dawyndt
Feb 20, 2013·The Journal of Cell Biology·Graça Raposo, Willem Stoorvogel
Jan 1, 2012·Journal of Extracellular Vesicles·Richard J SimpsonSuresh Mathivanan
Dec 19, 2013·Nature Reviews. Gastroenterology & Hepatology·Joannie RuelJean-Frédéric Colombel
Mar 19, 2014·Cell Host & Microbe·Dirk GeversRamnik J Xavier
Jul 7, 2014·Nature Biotechnology·Junhua LiUNKNOWN MetaHIT Consortium
Nov 13, 2014·Bioinformatics·Dae-Kyum KimYong Song Gho
Apr 22, 2015·Nucleic Acids Research·Jianguo XiaDavid S Wishart
Apr 23, 2015·International Journal of Molecular Medicine·Rafal SzatanekMonika Baj-Krzyworzeka
May 2, 2015·Molecular Nutrition & Food Research·Jie YinGuoyao Wu
Jun 18, 2015·Inflammatory Bowel Diseases·Christel ChehoudGary D Wu
Sep 12, 2015·The ISME Journal·Frédéric RaymondJacques Corbeil
Oct 4, 2015·The Journal of Allergy and Clinical Immunology·Han SongHeenam Stanley Kim

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Citations

Jul 20, 2019·Proteomics·Danielle L PetersDaniel Figeys
Aug 30, 2019·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Zhanguo LiuPeng Chen
Jan 21, 2020·Journal of Mass Spectrometry : JMS·Alan A Doucette, Jessica L Nickerson
May 2, 2019·Biometals : an International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine·Kelly GrzywaczAlain Stintzi
Jun 9, 2020·Briefings in Bioinformatics·Jing TangFeng Zhu
Sep 14, 2019·Nature Communications·Leyuan LiDaniel Figeys
May 16, 2020·Biological Reviews of the Cambridge Philosophical Society·Dickson K W OcanseyFei Mao
Sep 20, 2020·Biomolecules·Loredana LeggioNunzio Iraci
Mar 9, 2019·Applied Microbiology and Biotechnology·Ishu Khangwal, Pratyoosh Shukla
Feb 19, 2019·Gastroenterology Research and Practice·Arash AssadsangabiAlan Lobo
Jul 31, 2019·International Journal of Molecular Sciences·Zuzana KubiritovaRoman Gardlik
Nov 28, 2019·Journal of Immunology Research·Huihui XuHongyan Zhao
Mar 27, 2020·NPJ Biofilms and Microbiomes·Shuping LongLiang Qiao
Jul 2, 2020·MSystems·Carlos G GonzalezJoshua E Elias
Feb 6, 2019·Therapeutic Advances in Gastroenterology·Jonathan P SegalJulian R Marchesi
Feb 6, 2019·Proceedings of the National Academy of Sciences of the United States of America·Spencer C PeckDavid Schleheck
Apr 8, 2020·Frontiers in Immunology·Charles Caër, Mary Jo Wick
Apr 23, 2020·Frontiers in Microbiology·Ameen EetemadiIlias Tagkopoulos
Aug 23, 2020·Diagnostics·Małgorzata Krzystek-KorpackaKatarzyna Neubauer
Dec 16, 2020·Acta Physiologica·Alexandre VillardRamaroson Andriantsitohaina
Jan 22, 2021·Current Opinion in Genetics & Development·Karoliina StefaniusKim Orth
Feb 13, 2021·Critical Reviews in Microbiology·Shruti AhlawatKrishna Kant Sharma

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Datasets Mentioned

BETA
UP000005945

Methods Mentioned

BETA
PCA
biopsies
PCR
transmission electron microscopy
biopsy

Software Mentioned

MetaboAnalyst
MetaPro
PERMAOVA
ZetaView
Prism
Cytoscape
MEGAN
Unipet
MetaLab
R

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