Genomics

Dataset Information

42

Short Bowel Syndrome (SBS) has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model


ABSTRACT: Purpose: Most of the morbidity associated with short bowel syndrome (SBS) are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition (TPN). We hypothesized that acute SBS alone has significant systemic effects, and tested this in a zebrafish SBS model. Methods: With IACUC approval, adult male wild-type zebrafish underwent SBS (laparotomy, proximal stoma, distal ligation,n=3) or sham (laparotomy alone,n=3) surgery. After 2 weeks, the proximal intestine was harvested, RNA isolated and external RNA controls consortium (ERCC) controls spiked into each sample, sequenced and aligned to reference genome with gene ontology (GO) enrichment analysis performed. CyclinD1, CyclinB1, SAA1, IFN-gamma, and CYP7A1 gene expression were confirmed by qPCR. Results: RNA-seq analysis identified 1346 up-regulated genes and 678 down-regulated genes in SBS zebrafish compared to sham. The up-regulated genes were involved in acute phase response signaling, complement system, coagulation, cell proliferation, cellular barrier, production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down-regulated genes were involved in folate synthesis, gluconeogenesis, glycogenolysis, fatty-acid oxidation & activation, and drug & steroid metabolism. CyclinD1 gene expression was 2-fold higher, CyclinB1 2.8-fold higher, SAA1 4.5-fold higher, IFN-gamma 2.1-fold higher, and CYP7A1 25-fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways, some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.

INSTRUMENT(S): Illumina NextSeq 500 (Danio rerio)

SUBMITTER: Tracy Grikscheit  

PROVIDER: GSE83195 | GEO | 2017-03-08

SECONDARY ACCESSION(S): PRJNA325275

REPOSITORIES: GEO

Dataset's files

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GSE83195_RAW.tar Raw
GSE83195_SBS_v_Sham_DE_RawCounts_RPKM_ERCC_Annotation.csv.gz Csv
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Publications

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.

Schall Kathy A KA   Thornton Matthew E ME   Isani Mubina M   Holoyda Kathleen A KA   Hou Xiaogang X   Lien Ching-Ling CL   Grubbs Brendan H BH   Grikscheit Tracy C TC  

BMC genomics 20170125 1


<h4>Background</h4>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.<h4>Methods</h4>In a model of SBS in zebrafish (laparotomy, proximal stoma, distal ligation, n = 29) or sham (laparotomy alone, n = 28) surgery, RNA-S  ...[more]

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