title: Bacterial protein signals are associated with Crohn's disease.
abstract: OBJECTIVE
  No Crohn's disease (CD) molecular maker has advanced to clinical use, and independent lines of evidence support a central role of the gut microbial community in CD. Here we explore the feasibility of extracting bacterial protein signals relevant to CD, by interrogating myriads of intestinal bacterial proteomes from a small number of patients and healthy controls.
  
  
  METHODS
  We first developed and validated a workflow-including extraction of microbial communities, two-dimensional difference gel electrophoresis (2D-DIGE), and LC-MS/MS-to discover protein signals from CD-associated gut microbial communities. Then we used selected reaction monitoring (SRM) to confirm a set of candidates. In parallel, we used 16S rRNA gene sequencing for an integrated analysis of gut ecosystem structure and functions.
  
  
  RESULTS
  Our 2D-DIGE-based discovery approach revealed an imbalance of intestinal bacterial functions in CD. Many proteins, largely derived from Bacteroides species, were over-represented, while under-represented proteins were mostly from Firmicutes and some Prevotella members. Most overabundant proteins could be confirmed using SRM. They correspond to functions allowing opportunistic pathogens to colonise the mucus layers, breach the host barriers and invade the mucosae, which could still be aggravated by decreased host-derived pancreatic zymogen granule membrane protein GP2 in CD patients. Moreover, although the abundance of most protein groups reflected that of related bacterial populations, we found a specific independent regulation of bacteria-derived cell envelope proteins.
  
  
  CONCLUSIONS
  This study provides the first evidence that quantifiable bacterial protein signals are associated with CD, which can have a profound impact on future molecular diagnosis.
authors.affiliation: UMR1319 Micalis, INRA, Jouy-en-Josas, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Juste
authors.affiliation: Chair of Bioinformatics, Boku University Vienna, Vienna, Austria Department of Life Sciences, University of Warwick, Warwickshire, UK.
authors.forename: David P
authors.initials: DP
authors.lastname: Kreil
authors.affiliation: UMR1313 GABI, Iso Cell Express (ICE), INRA, Jouy-en-Josas, France.
authors.forename: Christian
authors.initials: C
authors.lastname: Beauvallet
authors.affiliation: Plate-forme d'Analyse Protéomique de Paris Sud-Ouest (PAPPSO), INRA, Gif-sur-Yvette, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Guillot
authors.affiliation: Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, Strasbourg, France.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Vaca
authors.affiliation: Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, Strasbourg, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Carapito
authors.affiliation: UMR1319 Micalis, INRA, Jouy-en-Josas, France.
authors.forename: Stanislas
authors.initials: S
authors.lastname: Mondot
authors.affiliation: Chair of Bioinformatics, Boku University Vienna, Vienna, Austria.
authors.forename: Peter
authors.initials: P
authors.lastname: Sykacek
authors.affiliation: UMR1319 Micalis, INRA, Jouy-en-Josas, France Gastroenterology and Nutrition Unit, Hôpital Saint-Antoine, AP-HP, Paris, France.
authors.forename: Harry
authors.initials: H
authors.lastname: Sokol
authors.affiliation: UMR1319 Micalis, INRA, Jouy-en-Josas, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Blon
authors.affiliation: UMR1319 Micalis, INRA, Jouy-en-Josas, France.
authors.forename: Pascale
authors.initials: P
authors.lastname: Lepercq
authors.affiliation: UMR1319 Micalis, INRA, Jouy-en-Josas, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Levenez
authors.affiliation: Plate-forme d'Analyse Protéomique de Paris Sud-Ouest (PAPPSO), INRA, Gif-sur-Yvette, France.
authors.forename: Benoît
authors.initials: B
authors.lastname: Valot
authors.affiliation: UR1077, Mathématique Informatique et Génome (MIG), INRA, Jouy-en-Josas, France.
authors.forename: Wilfrid
authors.initials: W
authors.lastname: Carré
authors.affiliation: UR1077, Mathématique Informatique et Génome (MIG), INRA, Jouy-en-Josas, France.
authors.forename: Valentin
authors.initials: V
authors.lastname: Loux
authors.affiliation: UMR1319 Micalis, INRA, Jouy-en-Josas, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Pons
authors.affiliation: UR341, Mathématiques et Informatique Appliquées (MIA), INRA, Jouy-en-Josas, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: David
authors.affiliation: UR341, Mathématiques et Informatique Appliquées (MIA), INRA, Jouy-en-Josas, France.
authors.forename: Brigitte
authors.initials: B
authors.lastname: Schaeffer
authors.affiliation: UMR1319 Micalis, INRA, Jouy-en-Josas, France.
authors.forename: Patricia
authors.initials: P
authors.lastname: Lepage
authors.affiliation: UMR1313 GABI, Iso Cell Express (ICE), INRA, Jouy-en-Josas, France.
authors.forename: Patrice
authors.initials: P
authors.lastname: Martin
authors.affiliation: UMR1319 Micalis, INRA, Jouy-en-Josas, France.
authors.forename: Véronique
authors.initials: V
authors.lastname: Monnet
authors.affiliation: Gastroenterology and Nutrition Unit, Hôpital Saint-Antoine, AP-HP, Paris, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Seksik
authors.affiliation: Gastroenterology and Nutrition Unit, Hôpital Saint-Antoine, AP-HP, Paris, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Beaugerie
authors.affiliation: UMR1319 Micalis, INRA, Jouy-en-Josas, France.
authors.forename: S Dusko
authors.initials: SD
authors.lastname: Ehrlich
authors.affiliation: UR1077, Mathématique Informatique et Génome (MIG), INRA, Jouy-en-Josas, France.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Gibrat
authors.affiliation: Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, Strasbourg, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Van Dorsselaer
authors.affiliation: UMR1319 Micalis, INRA, Jouy-en-Josas, France.
authors.forename: Joël
authors.initials: J
authors.lastname: Doré
mesh_terms: D000328:Adult; D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D001426:Bacterial Proteins / Q000378:metabolism*; D015415:Biomarkers / Q000378:metabolism*; D002853:Chromatography, Liquid; D003424:Crohn Disease / Q000382:microbiology*; D003430:Cross-Sectional Studies; D015180:Electrophoresis, Gel, Two-Dimensional; D005260:Female; D006801:Humans; D007422:Intestines / Q000382:microbiology*; D008297:Male; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D020539:Sequence Analysis, Protein; D053719:Tandem Mass Spectrometry
chemical_list: D001426:Bacterial Proteins; D015415:Biomarkers; D012336:RNA, Ribosomal, 16S
keywords: Crohn's Disease; Enteric Bacterial Microflora; Inflammatory Bowel Disease