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
Tóm tắt
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.
Tài liệu tham khảo
Wales PW. Surgical therapy for short bowel syndrome. Pediatr Surg Int. 2004;20(9):647–57.
Schalamon J, Mayr JM, Hollwarth ME. Mortality and economics in short bowel syndrome. Best Pract Res Clin Gastroenterol. 2003;17(6):931–42.
McMellen ME, Wakeman D, Longshore SW, McDuffie LA, Warner BW. Growth factors: possible roles for clinical management of the short bowel syndrome. Semin Pediatr Surg. 2010;19(1):35–43.
Aprahamian CJ, Chen M, Yang Y, Lorenz RG, Harmon CM. Two-hit rat model of short bowel syndrome and sepsis: independent of total parenteral nutrition, short bowel syndrome is proinflammatory and injurious to the liver. J Pediatr Surg. 2007;42(6):992–7.
Naini BV, Lassman CR. Total parenteral nutrition therapy and liver injury: a histopathologic study with clinical correlation. Hum Pathol. 2012;43(6):826–33.
Nousia-Arvanitakis S, Angelopoulou-Sakadami N, Metroliou K. Complications associated with total parenteral nutrition in infants with short bowel syndrome. Hepatogastroenterology. 1992;39(2):169–72.
Schall KA, Holoyda KA, Grant CN, Levin DE, Torres ER, Maxwell A, Pollack HA, Moats RA, Frey MR, Darehzereshki A, et al. Adult zebrafish intestine resection: a novel model of short bowel syndrome, adaptation, and intestinal stem cell regeneration. Am J Physiol Gastrointest Liver Physiol. 2015;309(3):G135–145.
Kralj JG, Salit ML. Characterization of in vitro transcription amplification linearity and variability in the low copy number regime using External RNA Control Consortium (ERCC) spike-ins. Anal Bioanal Chem. 2013;405(1):315–20.
Busby MA, Stewart C, Miller CA, Grzeda KR, Marth GT. Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression. Bioinformatics. 2013;29(5):656–7.
FastQC [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc]
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, Collins JE, Humphray S, McLaren K, Matthews L, et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature. 2013;496(7446):498–503.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21.
Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2):166–9.
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40.
Gentleman R, Carey V. Visualization and annotation of genomic experiments. NY: Springer; 2003.
Risso D, Ngai J, Speed TP, Dudoit S. Normalization of RNA-seq data using factor analysis of control genes or samples. Nat Biotechnol. 2014;32(9):896–902.
Falcon S, Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics. 2007;23(2):257–8.
McCarthy DJ, Chen Y, Smyth GK. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 2012;40(10):4288–97.
Risso D, Schwartz K, Sherlock G, Dudoit S. GC-content normalization for RNA-Seq data. BMC Bioinf. 2011;12:480.
Bharadwaj S, Tandon P, Meka K, Rivas JM, Jevenn A, Kuo NT, Steiger E. Intestinal failure: adaptation, rehabilitation, and transplantation. J Clin Gastroenterol. 2016;50(5):366–72.
Kim WR, Stock PG, Smith JM, Heimbach JK, Skeans MA, Edwards EB, Harper AM, Snyder JJ, Israni AK, Kasiske BL. OPTN/SRTR 2011 annual data report: liver. Am J Transplant. 2013;13(1):73–102.
Taylor JA, Martin CA, Nair R, Guo J, Erwin CR, Warner BW. Lessons learned: optimization of a murine small bowel resection model. J Pediatr Surg. 2008;43(6):1018–24.
McDuffie LA, Bucher BT, Erwin CR, Wakeman D, White FV, Warner BW. Intestinal adaptation after small bowel resection in human infants. J Pediatr Surg. 2011;46(6):1045–51.
Benhamou PH, Canarelli JP, Richard S, Cordonnier C, Postel JP, Grenier E, Leke A, Dupont C. Human recombinant growth hormone increases small bowel lengthening after massive small bowel resection in piglets. J Pediatr Surg. 1997;32(9):1332–6.
de Segura IA G, Aguilera MJ, Codesal J, Codoceo R, De-Miguel E. Comparative effects of growth hormone in large and small bowel resection in the rat. J Surg Res. 1996;62(1):5–10.
Lemmey AB, Martin AA, Read LC, Tomas FM, Owens PC, Ballard FJ. IGF-I and the truncated analogue des-(1–3) IGF-I enhance growth in rats after gut resection. Am J Physiol. 1991;260(2 Pt 1):E213–219.
Martin GR, Wallace LE, Sigalet DL. Glucagon-like peptide-2 induces intestinal adaptation in parenterally fed rats with short bowel syndrome. Am J Physiol Gastrointest Liver Physiol. 2004;286(6):G964–972.
O’Loughlin E, Winter M, Shun A, Hardin JA, Gall DG. Structural and functional adaptation following jejunal resection in rabbits: effect of epidermal growth factor. Gastroenterology. 1994;107(1):87–93.
Shulman DI, Hu CS, Duckett G, Lavallee-Grey M. Effects of short-term growth hormone therapy in rats undergoing 75% small intestinal resection. J Pediatr Gastroenterol Nutr. 1992;14(1):3–11.
Vanderhoof JA, McCusker RH, Clark R, Mohammadpour H, Blackwood DJ, Harty RF, Park JH. Truncated and native insulinlike growth factor I enhance mucosal adaptation after jejunoileal resection. Gastroenterology. 1992;102(6):1949–56.
Wallis K, Walters JR, Gabe S. Short bowel syndrome: the role of GLP-2 on improving outcome. Curr Opin Clin Nutr Metab Care. 2009;12(5):526–32.
Sun RC, Diaz-Miron JL, Choi PM, Sommovilla J, Guo J, Erwin CR, Warner BW. Both epidermal growth factor and insulin-like growth factor receptors are dispensable for structural intestinal adaptation. J Pediatr Surg. 2015;50(6):943–7.
Feng Y, Barrett M, Hou Y, Yoon HK, Ochi T, Teitelbaum DH. Homeostasis alteration within small intestinal mucosa after acute enteral refeeding in total parenteral nutrition mouse model. Am J Physiol Gastrointest Liver Physiol. 2016;310(4):G273–284.
Beck PL, Rosenberg IM, Xavier RJ, Koh T, Wong JF, Podolsky DK. Transforming growth factor-beta mediates intestinal healing and susceptibility to injury in vitro and in vivo through epithelial cells. Am J Pathol. 2003;162(2):597–608.
Ko TC, Sheng HM, Reisman D, Thompson EA, Beauchamp RD. Transforming growth factor-beta 1 inhibits cyclin D1 expression in intestinal epithelial cells. Oncogene. 1995;10(1):177–84.
Das LM, Torres-Castillo MD, Gill T, Levine AD. TGF-beta conditions intestinal T cells to express increased levels of miR-155, associated with down-regulation of IL-2 and itk mRNA. Mucosal Immunol. 2013;6(1):167–76.
Romagnani S. Th1/Th2 cells. Inflamm Bowel Dis. 1999;5(4):285–94.
Monteleone G, Holloway J, Salvati VM, Pender SL, Fairclough PD, Croft N, MacDonald TT. Activated STAT4 and a functional role for IL-12 in human Peyer’s patches. J Immunol. 2003;170(1):300–7.
Biber JL, Jabbour S, Parihar R, Dierksheide J, Hu Y, Baumann H, Bouchard P, Caligiuri MA, Carson W. Administration of two macrophage-derived interferon-gamma-inducing factors (IL-12 and IL-15) induces a lethal systemic inflammatory response in mice that is dependent on natural killer cells but does not require interferon-gamma. Cell Immunol. 2002;216(1–2):31–42.
Godshall CJ, Lentsch AB, Peyton JC, Scott MJ, Cheadle WG. STAT4 is required for antibacterial defense but enhances mortality during polymicrobial sepsis. Clin Diagn Lab Immunol. 2001;8(6):1044–8.
Ralls MW, Demehri FR, Feng Y, Woods Ignatoski KM, Teitelbaum DH. Enteral nutrient deprivation in patients leads to a loss of intestinal epithelial barrier function. Surgery. 2015;157(4):732–42.
Sukhotnik I, Haj B, Pollak Y, Dorfman T, Bejar J, Matter I. Effect of bowel resection on TLR signaling during intestinal adaptation in a rat model. Surg Endosc. 2016;30:4416–24.
Kuhn KA, Manieri NA, Liu TC, Stappenbeck TS. IL-6 stimulates intestinal epithelial proliferation and repair after injury. PLoS One. 2014;9(12):e114195.
Sun L, Ye RD. Serum amyloid A1: Structure, function and gene polymorphism. Gene. 2016;583(1):48–57.
Hasegawa M, Yada S, Liu MZ, Kamada N, Munoz-Planillo R, Do N, Nunez G, Inohara N. Interleukin-22 regulates the complement system to promote resistance against pathobionts after pathogen-induced intestinal damage. Immunity. 2014;41(4):620–32.
Puder M, Valim C, Meisel JA, Le HD, de Meijer VE, Robinson EM, Zhou J, Duggan C, Gura KM. Parenteral fish oil improves outcomes in patients with parenteral nutrition-associated liver injury. Ann Surg. 2009;250(3):395–402.
Kliewer SA, Mangelsdorf DJ. Bile Acids as Hormones: The FXR-FGF15/19 Pathway. Dig Dis. 2015;33(3):327–31.
Tomlinson E, Fu L, John L, Hultgren B, Huang X, Renz M, Stephan JP, Tsai SP, Powell-Braxton L, French D, et al. Transgenic mice expressing human fibroblast growth factor-19 display increased metabolic rate and decreased adiposity. Endocrinology. 2002;143(5):1741–7.
Mutanen A, Heikkila P, Lohi J, Raivio T, Jalanko H, Pakarinen MP. Serum FGF21 increases with hepatic fat accumulation in pediatric onset intestinal failure. J Hepatol. 2014;60(1):183–90.
Wu J, Chen J, Wu W, Shi J, Zhong Y, van Tol EA, Tang Q, Cai W. Enteral supplementation of bovine lactoferrin improves gut barrier function in rats after massive bowel resection. Br J Nutr. 2014;112(4):486–92.