FACS-Assisted Microarray Profiling Implicates Novel Genes and Pathways in Zebrafish Gastrointestinal Tract Development

Stuckenholz, Carsten; Lü, Lili; Thakur, Prakash; Kaminski, Naftali; Bahary, Nathan

doi:10.1053/j.gastro.2009.06.050

Cited by 50 publications

(54 citation statements)

References 58 publications

(71 reference statements)

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“…7 For whole-mount in situ hybridization (ISH), embryos were processed as described. 5 See supplementary text for probes and corresponding accession numbers. Alkaline phosphatase staining for vasculature and whole-mount Oil-red-O (ORO) staining were carried out as described.…”

Section: Methodsmentioning

confidence: 99%

“…3, 4 Gene expression profiles and active pathways during zebrafish GI development are also analogous to those observed in mammalian GI development and cancer. 5 Furthermore, prominent histopathological similarities are seen between zebrafish and mammalian GI diseases, such as fatty liver, cholestasis and neoplasia. 6, 7 …”

Section: Introductionmentioning

confidence: 99%

“…12, 13 We recently reported that inositol metabolism and PI3-kinase (PI3-K) signaling pathways were enriched in the developing liver and inhibition of PI3-K pathway resulted in hepatic abnormalities. 5 …”

Section: Introductionmentioning

confidence: 99%

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Lack of de novo phosphatidylinositol synthesis leads to endoplasmic reticulum stress and hepatic steatosis in cdipt-deficient zebrafish

et al. 2011

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Hepatic steatosis is the initial stage of non-alcoholic fatty liver disease (NAFLD) and may predispose to more severe hepatic disease, including hepatocellular carcinoma. Endoplasmic reticulum (ER) stress has been recently implicated as a novel mechanism that may lead to NAFLD, although the genetic factors invoking ER stress are largely unknown. During a screen for liver defects from a zebrafish insertional mutant library, we isolated the mutant cdipthi559Tg/+ (hi559). CDIPT is known to play an indispensable role in phosphatidylinositol (PtdIns) synthesis. Here we show that cdipt is expressed in the developing liver and its disruption in hi559 mutants abrogates de novo PtdIns synthesis, resulting in hepatomegaly at 5-dpf. The hi559 hepatocytes display features of NAFLD, including macrovesicular steatosis, ballooning, and necroapoptosis. Gene set enrichment of microarray profiling revealed significant enrichment of ER stress response (ERSR) genes in hi559 mutants. ER stress markers, including atf6, hspa5, calr, xbp1, are selectively upregulated in the mutant liver. The hi559 expression profile showed significant overlap with that of mammalian hepatic ER stress and NAFLD. Ultrastructurally, the hi559 hepatocytes display marked disruption of ER architecture with hallmarks of chronic unresolved ER stress. Induction of ER stress by tunicamycin in wild-type larvae results in a fatty liver similar to hi559, suggesting that ER stress could be a fundamental mechanism contributing to hepatic steatosis. Conclusion: Cdipt-deficient zebrafish exhibit hepatic ER stress and NAFLD pathologies, implicating a novel link between PtdIns, ER stress, and steatosis. The tractability of hi559 mutant provides a valuable tool to dissect ERSR components, their contribution to molecular pathogenesis and evaluation of novel therapeutics of NAFLD.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Lack of de novo phosphatidylinositol synthesis leads to endoplasmic reticulum stress and hepatic steatosis in cdipt-deficient zebrafish

et al. 2011

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“…S1). Interestingly, the function of this protein has previously been studied in zebrafish (Chen et al 2005;Stuckenholz et al 2009). In a forward mutation screen, a loss-of-function mutation of the zebrafish homolog (27.6% identical, 52.4% similar to the yeast Utp25) resulted in homozygous mutant fish displaying formed but severely hypoplastic digestive organs, such as a large, unabsorbed yolk sack and under-expanded intestine, liver, exocrine pancreas, and gallbladder at 5.5 d post-fertilization (dpf) (Chen et al 2005).…”

Section: Discussionmentioning

confidence: 99%

The DEAD-box RNA helicase-like Utp25 is an SSU processome component

Charette

Baserga²

2010

RNA

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The SSU processome is a large ribonucleoprotein complex consisting of the U3 snoRNA and at least 43 proteins. A database search, initiated in an effort to discover additional SSU processome components, identified the uncharacterized, conserved and essential yeast nucleolar protein YIL091C/UTP25 as one such candidate. The C-terminal DUF1253 motif, a domain of unknown function, displays limited sequence similarity to DEAD-box RNA helicases. In the absence of the conserved DEAD-box sequence, motif Ia is the only clearly identifiable helicase element. Since the yeast homolog is nucleolar and interacts with components of the SSU processome, we examined its role in pre-rRNA processing. Genetic depletion of Utp25 resulted in slowed growth. Northern analysis of pre-rRNA revealed an 18S rRNA maturation defect at sites A 0 , A 1 , and A 2 . Coimmunoprecipitation confirmed association with U3 snoRNA and with Mpp10, and with components of the t-Utp/UtpA, UtpB, and U3 snoRNP subcomplexes. Mutation of the conserved motif Ia residues resulted in no discernable temperaturesensitive or cold-sensitive growth defects, implying that this motif is dispensable for Utp25 function. A yeast two-hybrid screen of Utp25 against other SSU processome components revealed several interacting proteins, including Mpp10, Utp3, and Utp21, thereby identifying the first interactions among the different subcomplexes of the SSU processome. Furthermore, the DUF1253 domain is required and sufficient for the interaction of Utp25 with Utp3. Thus, Utp25 is a novel SSU processome component that, along with Utp3, forms the first identified interactions among the different SSU processome subcomplexes.

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“…In newly developing zebrafish embryos, cldn-7 has been shown to mark the earliest stages of gut development, 11 and cldn-c ( = cldn-3d ) is also thought to be involved in the development of the zebrafish gastrointestinal (GI) tract 28 . In zebrafish embryos, cldn-c is preferentially expressed in the GI tract at an early stage of development and is involved in the formation and thickening of the endodermal rod between 1–2 d post fertilization (dpf) 28 .…”

Section: Tissue-specific Claudin Expression In Teleost Fishesmentioning

confidence: 99%

Claudins in teleost fishes

Kolosov¹,

Bui

Chasiotis³

et al. 2013

Tissue Barriers

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Teleost fishes are a large and diverse animal group that represent close to 50% of all described vertebrate species. This review consolidates what is known about the claudin (Cldn) family of tight junction (TJ) proteins in teleosts. Cldns are transmembrane proteins of the vertebrate epithelial/endothelial TJ complex that largely determine TJ permeability. Cldns achieve this by expressing barrier or pore forming properties and by exhibiting distinct tissue distribution patterns. So far, ~63 genes encoding for Cldn TJ proteins have been reported in 16 teleost species. Collectively, cldns (or Cldns) are found in a broad array of teleost fish tissues, but select genes exhibit restricted expression patterns. Evidence to date strongly supports the view that Cldns play a vital role in the embryonic development of teleost fishes and in the physiology of tissues and organ systems studied thus far.

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FACS-Assisted Microarray Profiling Implicates Novel Genes and Pathways in Zebrafish Gastrointestinal Tract Development

Abstract: Background and Aims-The zebrafish Danio rerio is an excellent model system for mammalian gastrointestinal development. To identify differentially regulated genes important in gastrointestinal organogenesis, we profiled the transcriptome of the zebrafish developing gastrointestinal tract.

Cited by 50 publications

References 58 publications

Lack of de novo phosphatidylinositol synthesis leads to endoplasmic reticulum stress and hepatic steatosis in cdipt-deficient zebrafish

Lack of de novo phosphatidylinositol synthesis leads to endoplasmic reticulum stress and hepatic steatosis in cdipt-deficient zebrafish

The DEAD-box RNA helicase-like Utp25 is an SSU processome component

Claudins in teleost fishes

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