title: Short bowel syndrome results in increased gene expression associated with proliferation, inflammation, bile acid synthesis and immune system activation: RNA sequencing a zebrafish SBS model.
abstract: Much of the morbidity associated with short bowel syndrome (SBS) is attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition (TPN). We hypothesized that acute SBS alone has significant effects on gene expression beyond epithelial proliferation, and tested this in a zebrafish SBS model.
  
  
  
  In a model of SBS in zebrafish (laparotomy, proximal stoma, distal ligation, n = 29) or sham (laparotomy alone, n = 28) surgery, RNA-Seq was performed after 2 weeks. The proximal intestine was harvested and RNA isolated. The three samples from each group with the highest amount of RNA were spiked with external RNA controls consortium (ERCC) controls, sequenced and aligned to reference genome with gene ontology (GO) enrichment analysis performed. Gene expression of ctnnb1, ccnb1, ccnd1, cyp7a1a, dkk3, ifng1-2, igf2a, il1b, lef1, nos2b, saa1, stat3, tnfa and wnt5a were confirmed to be elevated in SBS by RT-qPCR.
  
  
  
  RNA-seq analysis identified 1346 significantly upregulated genes and 678 significantly downregulated genes in SBS zebrafish intestine compared to sham with Ingenuity analysis. The upregulated genes were involved in cell proliferation, acute phase response signaling, innate and adaptive immunity, bile acid regulation, production of nitric oxide and reactive oxygen species, cellular barrier and coagulation. The downregulated genes were involved in folate synthesis, gluconeogenesis, glycogenolysis, fatty-acid oxidation and activation and drug and steroid metabolism. RT-qPCR confirmed gene expression differences from RNA-Sequencing.
  
  
  
  Changes of gene expression after 2 weeks of SBS indicate complex and extensive alterations of multiple pathways, some previously implicated as effects of TPN. The systemic sequelae of SBS alone are significant and indicate multiple targets for investigating future therapies.
authors.affiliation: Division of Pediatric Surgery and Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles and USC Keck School of Medicine, Los Angeles, CA, 90027, USA.
authors.forename: Kathy A
authors.initials: KA
authors.lastname: Schall
authors.affiliation: Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Saban Research Institute, Children's Hospital Los Angeles and USC Keck School of Medicine, Los Angeles, CA, 90027, USA.
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Thornton
authors.affiliation: Division of Pediatric Surgery and Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles and USC Keck School of Medicine, Los Angeles, CA, 90027, USA.
authors.forename: Mubina
authors.initials: M
authors.lastname: Isani
authors.affiliation: Division of Pediatric Surgery and Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles and USC Keck School of Medicine, Los Angeles, CA, 90027, USA.
authors.forename: Kathleen A
authors.initials: KA
authors.lastname: Holoyda
authors.affiliation: Division of Pediatric Surgery and Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles and USC Keck School of Medicine, Los Angeles, CA, 90027, USA.
authors.forename: Xiaogang
authors.initials: X
authors.lastname: Hou
authors.affiliation: Division of Cardiothoracic Surgery, Saban Research Institute, Children's Hospital Los Angeles and USC Keck School of Medicine, Los Angeles, CA, 90027, USA.
authors.forename: Ching-Ling
authors.initials: CL
authors.lastname: Lien
authors.affiliation: Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Saban Research Institute, Children's Hospital Los Angeles and USC Keck School of Medicine, Los Angeles, CA, 90027, USA.
authors.forename: Brendan H
authors.initials: BH
authors.lastname: Grubbs
authors.affiliation: Division of Pediatric Surgery and Developmental Biology and Regenerative Medicine, Saban Research Institute, Children's Hospital Los Angeles and USC Keck School of Medicine, Los Angeles, CA, 90027, USA. tgrikscheit@chla.usc.edu.|Department of Surgery, Children's Hospital Los Angeles, 4650 Sunset Blvd, Mailstop 100, Los Angeles, CA, 90027, USA. tgrikscheit@chla.usc.edu.
authors.forename: Tracy C
authors.initials: TC
authors.lastname: Grikscheit
mesh_terms: D000818:Animals; D001647:Bile Acids and Salts / Q000378:metabolism*; D049109:Cell Proliferation; D016000:Cluster Analysis; D004195:Disease Models, Animal; D015870:Gene Expression; D020869:Gene Expression Profiling; D007107:Immune System / Q000276:immunology* / Q000378:metabolism*; D007249:Inflammation / Q000235:genetics / Q000276:immunology / Q000378:metabolism / Q000473:pathology; D007413:Intestinal Mucosa / Q000378:metabolism / Q000473:pathology; D017423:Sequence Analysis, RNA; D012778:Short Bowel Syndrome / Q000209:etiology* / Q000378:metabolism* / Q000473:pathology; D015027:Zebrafish
chemical_list: D001647:Bile Acids and Salts
keywords: Cell proliferation; Inflammation; Innate and adaptive immunity; Intestinal resection; RNA sequencing; Short bowel syndrome