title: The transcriptome of nitrofen-induced pulmonary hypoplasia in the rat model of congenital diaphragmatic hernia.
abstract: We currently do not know how the herbicide nitrofen induces lung hypoplasia and congenital diaphragmatic hernia in rats. Our aim was to compare the differentially expressed transcriptome of nitrofen-induced hypoplastic lungs to control lungs in embryonic day 13 rat embryos before the development of embryonic diaphragmatic defects.
  
  
  
  Using next-generation sequencing technology, we identified the expression profile of microRNA (miRNA) and mRNA genes. Once the dataset was validated by both RT-qPCR and digital-PCR, we conducted gene ontology, miRNA target analysis, and orthologous miRNA sequence matching for the deregulated miRNAs in silico.
  
  
  
  Our study identified 186 known mRNA and 100 miRNAs which were differentially expressed in nitrofen-induced hypoplastic lungs. Sixty-four rat miRNAs homologous to known human miRNAs were identified. A subset of these genes may promote lung hypoplasia in rat and/or human, and we discuss their associations. Potential miRNA pathways relevant to nitrofen-induced lung hypoplasia include PI3K, TGF-β, and cell cycle kinases.
  
  
  
  Nitrofen-induced hypoplastic lungs have an abnormal transcriptome that may lead to impaired development.
authors.affiliation: Department of Physiology and Pathophysiology, University of Manitoba and Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.
authors.forename: Thomas H
authors.initials: TH
authors.lastname: Mahood
authors.affiliation: Department of Physiology and Pathophysiology, University of Manitoba and Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.|Ain Shams University Faculty of Women for Arts, Sciences and Education, Cairo, Egypt.
authors.forename: Dina R
authors.identifier: 0000-0001-9130-1965
authors.initials: DR
authors.lastname: Johar
authors.affiliation: Department of Physiology and Pathophysiology, University of Manitoba and Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.|Department of Surgery, Paediatrics & Child Health, University of Manitoba, Winnipeg, Manitoba, Canada.
authors.forename: Barbara M
authors.initials: BM
authors.lastname: Iwasiow
authors.affiliation: Department of Biochemistry and Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada.|Next Generation Sequencing Platform, Children's Hospital Research Institute of Manitoba and Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba, Canada.
authors.forename: Wayne
authors.initials: W
authors.lastname: Xu
authors.affiliation: Department of Physiology and Pathophysiology, University of Manitoba and Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.|Department of Surgery, Paediatrics & Child Health, University of Manitoba, Winnipeg, Manitoba, Canada.
authors.forename: Richard
authors.identifier: 0000-0002-0108-3157
authors.initials: R
authors.lastname: Keijzer
mesh_terms: D000818:Animals; D005260:Female; D018507:Gene Expression Regulation, Developmental; D065630:Hernias, Diaphragmatic, Congenital / Q000378:metabolism* / Q000473:pathology; D006801:Humans; D008168:Lung / Q000187:drug effects / Q000196:embryology / Q000473:pathology*; D035683:MicroRNAs / Q000378:metabolism; D010647:Phenyl Ethers / Q000009:adverse effects; D019869:Phosphatidylinositol 3-Kinases / Q000378:metabolism; D016133:Polymerase Chain Reaction; D012333:RNA, Messenger / Q000378:metabolism; D051381:Rats; D017422:Sequence Analysis, DNA; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome; D016212:Transforming Growth Factor beta / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D010647:Phenyl Ethers; D012333:RNA, Messenger; D016212:Transforming Growth Factor beta; D019869:Phosphatidylinositol 3-Kinases; C007350:nitrofen