title: Gene expression profiling in necrotizing enterocolitis reveals pathways common to those reported in Crohn's disease.
abstract: BACKGROUND
  Necrotizing enterocolitis (NEC) is the most frequent life-threatening gastrointestinal disease experienced by premature infants in neonatal intensive care units. The challenge for neonatologists is to detect early clinical manifestations of NEC. One strategy would be to identify specific markers that could be used as early diagnostic tools to identify preterm infants most at risk of developing NEC or in the event of a diagnostic dilemma of suspected disease. As a first step in this direction, we sought to determine the specific gene expression profile of NEC.
  
  
  METHODS
  Deep sequencing (RNA-Seq) was used to establish the gene expression profiles in ileal samples obtained from preterm infants diagnosed with NEC and non-NEC conditions. Data were analyzed with Ingenuity Pathway Analysis and ToppCluster softwares.
  
  
  RESULTS
  Data analysis indicated that the most significant functional pathways over-represented in NEC neonates were associated with immune functions, such as altered T and B cell signaling, B cell development, and the role of pattern recognition receptors for bacteria and viruses. Among the genes that were strongly modulated in neonates with NEC, we observed a significant degree of similarity when compared with those reported in Crohn's disease, a chronic inflammatory bowel disease.
  
  
  CONCLUSIONS
  Gene expression profile analysis revealed a predominantly altered immune response in the intestine of NEC neonates. Moreover, comparative analysis between NEC and Crohn's disease gene expression repertoires revealed a surprisingly high degree of similarity between these two conditions suggesting a new avenue for identifying NEC biomarkers.
authors.affiliation: Department of Anatomy and Cell Biology, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, 3001, 12th Avec North, J1H 5N4, Sherbrooke, QC, Canada. eric.tremblay@usherbrooke.ca.
authors.forename: Éric
authors.initials: É
authors.lastname: Tremblay
authors.affiliation: Department of Anatomy and Cell Biology, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, 3001, 12th Avec North, J1H 5N4, Sherbrooke, QC, Canada. marie-pier.thibault@usherbrooke.ca.
authors.forename: Marie-Pier
authors.initials: MP
authors.lastname: Thibault
authors.affiliation: Division of Neonatology, Department of Pediatrics, CHEO, Ottawa, ON, Canada. eferretti@toh.ca.
authors.forename: Emanuela
authors.initials: E
authors.lastname: Ferretti
authors.affiliation: Department of Pediatrics, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada. corentin.babakissa@usherbrooke.ca.
authors.forename: Corentin
authors.initials: C
authors.lastname: Babakissa
authors.affiliation: Division of Neonatology, Department of Pediatrics, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada. valerie.bertelle@usherbrooke.ca.
authors.forename: Valérie
authors.initials: V
authors.lastname: Bertelle
authors.affiliation: Department of Surgery, CHEO, Ottawa, ON, Canada. mbettolli@cheo.on.ca.
authors.forename: Marcos
authors.initials: M
authors.lastname: Bettolli
authors.affiliation: Division of Gastroenterology, Hepatology & Nutrition, CHEO, Ottawa, ON, Canada. karolina.burghardt@gmail.com.
authors.forename: Karolina Maria
authors.initials: KM
authors.lastname: Burghardt
authors.affiliation: Department of Pediatrics, CHU de Martinique, Fort-de-France, France. jean-francois.colombani@chu-fortdefrance.fr.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Colombani
authors.affiliation: Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada. dgrynspan@cheo.on.ca.
authors.forename: David
authors.initials: D
authors.lastname: Grynspan
authors.affiliation: Department of Nutrition, Centre de recherche, CHU Sainte-Justine, Université de Montréal, Montréal, QC, Canada. emile.levy@recherche-ste-justine.qc.ca.
authors.forename: Emile
authors.initials: E
authors.lastname: Levy
authors.affiliation: Department of Pediatrics, Erasmus MC-Sophia, Rotterdam, The Netherland. pengluerasmusmc@gmail.com.
authors.forename: Peng
authors.initials: P
authors.lastname: Lu
authors.affiliation: Department of Surgery, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada. sandeep.mayer@usherbrooke.ca.
authors.forename: Sandeep
authors.initials: S
authors.lastname: Mayer
authors.affiliation: Department of Anatomy and Cell Biology, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, 3001, 12th Avec North, J1H 5N4, Sherbrooke, QC, Canada. daniel.menard@usherbrooke.ca.
authors.forename: Daniel
authors.initials: D
authors.lastname: Ménard
authors.affiliation: CHU de Rouen, Department of Medical Pediatrics, Rouen, France. olivier.mouterde@chu-rouen.fr.
authors.forename: Olivier
authors.initials: O
authors.lastname: Mouterde
authors.affiliation: Department of Pediatrics, Erasmus MC-Sophia, Rotterdam, The Netherland. i.b.renes@amc.uva.nl.|Emma Children's Hospital-AMC, Amsterdam, The Netherlands. i.b.renes@amc.uva.nl.
authors.forename: Ingrid B
authors.initials: IB
authors.lastname: Renes
authors.affiliation: Division of Gastroenterology, McGill University, Montréal, QC, Canada. digestivelab@hotmail.com.
authors.forename: Ernest G
authors.initials: EG
authors.lastname: Seidman
authors.affiliation: Department of Anatomy and Cell Biology, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, 3001, 12th Avec North, J1H 5N4, Sherbrooke, QC, Canada. jean-francois.beaulieu@usherbrooke.ca.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Beaulieu
mesh_terms: D000998:Antiviral Agents / Q000378:metabolism; D003424:Crohn Disease / Q000150:complications* / Q000235:genetics*; D020345:Enterocolitis, Necrotizing / Q000150:complications* / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D007113:Immunity, Innate / Q000235:genetics; D007231:Infant, Newborn; D008297:Male; D011247:Pregnancy; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics*
chemical_list: D000998:Antiviral Agents