PUBLICATION

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

Authors

Schall, K.A., Thornton, M.E., Isani, M., Holoyda, K.A., Hou, X., Lien, C.L., Grubbs, B.H., Grikscheit, T.C.

ID

ZDB-PUB-170126-8

Date

2017

Source

BMC Genomics 18: 23 (Journal)

Registered Authors

Lien, Ching-Ling (Ellen)

Keywords

Cell proliferation, Inflammation, Innate and adaptive immunity, Intestinal resection, RNA sequencing, Short bowel syndrome

Datasets

GEO:GSE83195

MeSH Terms

Bile Acids and Salts/metabolism*
Gene Expression*
Inflammation/genetics
Inflammation/immunology
Inflammation/metabolism
Inflammation/pathology
Short Bowel Syndrome/etiology*
Short Bowel Syndrome/metabolism*
Short Bowel Syndrome/pathology
Zebrafish
Disease Models, Animal
Gene Expression Profiling
Animals
Intestinal Mucosa/metabolism
Intestinal Mucosa/pathology
Sequence Analysis, RNA
Immune System/immunology*
Immune System/metabolism*
Cell Proliferation
Cluster Analysis

(all 20)

PubMed

28118819 Full text @ BMC Genomics

Abstract

Background 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.

Methods 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.

Results 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.

Conclusion 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.

Genes / Markers

Figures

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Expression

Gene	Antibody	Fish	Conditions	Stage	Anatomy	Assay	Figure
ccnb1		EKW	resection: intestine	Adult	intestine	RTPCR	Fig. 2
ccnd1		EKW	resection: intestine	Adult	intestine	RTPCR	Fig. 2
ctnnb1	ab2-ctnnb1	EKW	resection: intestine	Adult	intestine proximal region	IHC	Fig. S1
ctnnb1		EKW	resection: intestine	Adult	intestine	RTPCR	Fig. 2
cyp7a1		EKW	resection: intestine	Adult	intestine	RTPCR	Fig. 3
dkk3b		EKW	resection: intestine	Adult	intestine	RTPCR	Fig. 2
ifng1		EKW	resection: intestine	Adult	intestine	RTPCR	Fig. 2
igf2a		EKW	resection: intestine	Adult	intestine	RTPCR	Fig. 2
il1b		EKW	resection: intestine	Adult	intestine	RTPCR	Fig. 2
lef1		EKW	resection: intestine	Adult	intestine	RTPCR	Fig. 2

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Phenotype

Fish	Conditions	Stage	Phenotype	Figure
EKW	resection: intestine	Adult	intestine ccnb1 expression increased amount, abnormal	Fig. 2
EKW	resection: intestine	Adult	intestine ccnd1 expression increased amount, abnormal	Fig. 2
EKW	resection: intestine	Adult	intestine ctnnb1 expression increased amount, abnormal	Fig. 2
EKW	resection: intestine	Adult	intestine cyp7a1 expression increased amount, abnormal	Fig. 3
EKW	resection: intestine	Adult	intestine dkk3b expression increased amount, abnormal	Fig. 2
EKW	resection: intestine	Adult	intestine ifng1 expression increased amount, abnormal	Fig. 2
EKW	resection: intestine	Adult	intestine igf2a expression increased amount, abnormal	Fig. 2
EKW	resection: intestine	Adult	intestine il1b expression increased amount, abnormal	Fig. 2
EKW	resection: intestine	Adult	intestine lef1 expression increased amount, abnormal	Fig. 2
EKW	resection: intestine	Adult	intestine nos2b expression increased amount, abnormal	Fig. 3

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Mutations / Transgenics

Human Disease / Model

Human Disease	Fish	Conditions	Evidence
short bowel syndrome	EKW	resection: intestine	TAS

Sequence Targeting Reagents

Fish

Fish
EKW

Antibodies

Name	Type	Antigen Genes	Isotypes	Host Organism
Ab2-ctnnb1	polyclonal	ctnnb1		Rabbit

Orthology

Engineered Foreign Genes

Mapping

Schall et al., 2017 ZDB-PUB-170126-8 PMID:28118819

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 et al., 2017

ZDB-PUB-170126-8
PMID:28118819