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Early embryonic gene expression profiling of zebrafish prion protein (Prp2) morphants.

Nourizadeh-Lillabadi R, Seilø Torgersen J, Vestrheim O, König M, Aleström P, Syed M - PLoS ONE (2010)

Bottom Line: The resulting changes in gene expression profiles revealed 249 differently expressed genes linked to biological processes like cell death, neurogenesis and embryonic development.The current study contributes to the understanding of basic Prp functions and demonstrates that the zebrafish is an excellent model to address the role of Prp in vertebrates.The gene knockdown of prp2 indicates an essential biological function for the zebrafish ortholog with a morphant phenotype that suggests a neurodegenerative action and gene expression effects which are apoptosis related and effects gene networks controlling neurogenesis and embryo development.

View Article: PubMed Central - PubMed

Affiliation: Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, Oslo, Norway.

ABSTRACT

Background: The Prion protein (PRNP/Prp) plays a crucial role in transmissible spongiform encephalopathies (TSEs) like Creutzfeldt-Jakob disease (CJD), scrapie and mad cow disease. Notwithstanding the importance in human and animal disease, fundamental aspects of PRNP/Prp function and transmission remains unaccounted for.

Methodology/principal findings: The zebrafish (Danio rerio) genome contains three Prp encoding genes assigned prp1, prp2 and prp3. Currently, the second paralogue is believed to be the most similar to the mammalian PRNP gene in structure and function. Functional studies of the PRNP gene ortholog was addressed by prp2 morpholino (MO) knockdown experiments. Investigation of Prp2 depleted embryos revealed high mortality and apoptosis at 24 hours post fertilization (hpf) as well as impaired brain and neuronal development. In order to elucidate the underlying mechanisms, a genome-wide transcriptome analysis was carried out in viable 24 hpf morphants. The resulting changes in gene expression profiles revealed 249 differently expressed genes linked to biological processes like cell death, neurogenesis and embryonic development.

Conclusions/significance: The current study contributes to the understanding of basic Prp functions and demonstrates that the zebrafish is an excellent model to address the role of Prp in vertebrates. The gene knockdown of prp2 indicates an essential biological function for the zebrafish ortholog with a morphant phenotype that suggests a neurodegenerative action and gene expression effects which are apoptosis related and effects gene networks controlling neurogenesis and embryo development.

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IPA cluster analysis of significantly differentially expressed genes.IPA cluster analysis of significantly differentially expressed genes for 24 hpf zebrafish prp2-MO2 morphant embryos. The clusters reveal genes involved in (A) cell death and apoptosis with functions focused on apoptosis in neural cells and (B) genes involved in nervous system development. Red color indicates up- and green downregulation.
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pone-0013573-g004: IPA cluster analysis of significantly differentially expressed genes.IPA cluster analysis of significantly differentially expressed genes for 24 hpf zebrafish prp2-MO2 morphant embryos. The clusters reveal genes involved in (A) cell death and apoptosis with functions focused on apoptosis in neural cells and (B) genes involved in nervous system development. Red color indicates up- and green downregulation.

Mentions: Microarray analysis using a 16k oligonucleotide library revealed that 249 genes were significantly differentially expressed in the prp2-MO2 samples (Table 1). IPA analysis identified and mapped 120 of the 249 genes as being genes with mammalian ortholog identifiers (Table S2). The remaining 129 genes were either zebrafish specific or yet non-annotated genes with hypothetical or unknown function (Table S3). The most upregulated gene was cyclin G1 (CCNG1) with a 4.2 fold change. Leucine rich repeat neuronal 1 gene (LPRN1) was the most downregulated gene with a minus 2.46 fold change. The majority of the differentially expressed genes were encoding enzymes or transcription regulators with their location in the cytoplasm or nucleus, respectively. The IPA organization of differentially expressed genes into biological function and disease clusters included “cell death”, “embryonic development” and “nervous system development and function” (Fig. S1, Table 2). The “cell death/apoptosis” related gene cluster was the largest sub-cluster with a total of 32 genes, of which 5 were related to apoptosis of neural cells: TP53, TP73, and BAX (upregulated) and SNPR1 and SNCB (downregulated, Fig. 4A, Table S2). The cluster of “embryonic development” (Fig. S1, Table 2) contained 11 genes, of which IPA could join 9 to each other in a network of sub-clusters in which SHH was the only downregulated gene and BMP4 had the highest score of the upregulated (Fig. S2). Both SHH and TP53 were included in one of the sub-clusters directly involved in the developmental process of embryonic cell lines. Analysis of genes related to “nervous system development and function” (Fig. S1, Table 2) revealed 5 sub-functional clusters involved in the developmental processes. Among these clusters, development of brain, forebrain, neuroepithelial cells, neurons and the central nervous system (CNS) were present (Fig. 4B). Here TP73, AKTIP and BMP4 (upregulated) with SHH (downregulated) play a central role with TP53 acting on CNS and BAX on neuron development (Fig. 4B). In the cluster “nervous system development and function”, IPA connected 13 of the differentially expressed genes to each other in a network of different sub-function clusters. The most prominent network was the sub-function cluster “neurogenesis”, which contained TP53, BMP4, MEF2C and BAX (upregulated) together with SOX11, GFAP, ACHE and SHH (downregulated) (Fig. S2). Also, the “differentiation of neuroglia” and “migration of neurons” harbored 5 genes each.


Early embryonic gene expression profiling of zebrafish prion protein (Prp2) morphants.

Nourizadeh-Lillabadi R, Seilø Torgersen J, Vestrheim O, König M, Aleström P, Syed M - PLoS ONE (2010)

IPA cluster analysis of significantly differentially expressed genes.IPA cluster analysis of significantly differentially expressed genes for 24 hpf zebrafish prp2-MO2 morphant embryos. The clusters reveal genes involved in (A) cell death and apoptosis with functions focused on apoptosis in neural cells and (B) genes involved in nervous system development. Red color indicates up- and green downregulation.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2962645&req=5

pone-0013573-g004: IPA cluster analysis of significantly differentially expressed genes.IPA cluster analysis of significantly differentially expressed genes for 24 hpf zebrafish prp2-MO2 morphant embryos. The clusters reveal genes involved in (A) cell death and apoptosis with functions focused on apoptosis in neural cells and (B) genes involved in nervous system development. Red color indicates up- and green downregulation.
Mentions: Microarray analysis using a 16k oligonucleotide library revealed that 249 genes were significantly differentially expressed in the prp2-MO2 samples (Table 1). IPA analysis identified and mapped 120 of the 249 genes as being genes with mammalian ortholog identifiers (Table S2). The remaining 129 genes were either zebrafish specific or yet non-annotated genes with hypothetical or unknown function (Table S3). The most upregulated gene was cyclin G1 (CCNG1) with a 4.2 fold change. Leucine rich repeat neuronal 1 gene (LPRN1) was the most downregulated gene with a minus 2.46 fold change. The majority of the differentially expressed genes were encoding enzymes or transcription regulators with their location in the cytoplasm or nucleus, respectively. The IPA organization of differentially expressed genes into biological function and disease clusters included “cell death”, “embryonic development” and “nervous system development and function” (Fig. S1, Table 2). The “cell death/apoptosis” related gene cluster was the largest sub-cluster with a total of 32 genes, of which 5 were related to apoptosis of neural cells: TP53, TP73, and BAX (upregulated) and SNPR1 and SNCB (downregulated, Fig. 4A, Table S2). The cluster of “embryonic development” (Fig. S1, Table 2) contained 11 genes, of which IPA could join 9 to each other in a network of sub-clusters in which SHH was the only downregulated gene and BMP4 had the highest score of the upregulated (Fig. S2). Both SHH and TP53 were included in one of the sub-clusters directly involved in the developmental process of embryonic cell lines. Analysis of genes related to “nervous system development and function” (Fig. S1, Table 2) revealed 5 sub-functional clusters involved in the developmental processes. Among these clusters, development of brain, forebrain, neuroepithelial cells, neurons and the central nervous system (CNS) were present (Fig. 4B). Here TP73, AKTIP and BMP4 (upregulated) with SHH (downregulated) play a central role with TP53 acting on CNS and BAX on neuron development (Fig. 4B). In the cluster “nervous system development and function”, IPA connected 13 of the differentially expressed genes to each other in a network of different sub-function clusters. The most prominent network was the sub-function cluster “neurogenesis”, which contained TP53, BMP4, MEF2C and BAX (upregulated) together with SOX11, GFAP, ACHE and SHH (downregulated) (Fig. S2). Also, the “differentiation of neuroglia” and “migration of neurons” harbored 5 genes each.

Bottom Line: The resulting changes in gene expression profiles revealed 249 differently expressed genes linked to biological processes like cell death, neurogenesis and embryonic development.The current study contributes to the understanding of basic Prp functions and demonstrates that the zebrafish is an excellent model to address the role of Prp in vertebrates.The gene knockdown of prp2 indicates an essential biological function for the zebrafish ortholog with a morphant phenotype that suggests a neurodegenerative action and gene expression effects which are apoptosis related and effects gene networks controlling neurogenesis and embryo development.

View Article: PubMed Central - PubMed

Affiliation: Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, Oslo, Norway.

ABSTRACT

Background: The Prion protein (PRNP/Prp) plays a crucial role in transmissible spongiform encephalopathies (TSEs) like Creutzfeldt-Jakob disease (CJD), scrapie and mad cow disease. Notwithstanding the importance in human and animal disease, fundamental aspects of PRNP/Prp function and transmission remains unaccounted for.

Methodology/principal findings: The zebrafish (Danio rerio) genome contains three Prp encoding genes assigned prp1, prp2 and prp3. Currently, the second paralogue is believed to be the most similar to the mammalian PRNP gene in structure and function. Functional studies of the PRNP gene ortholog was addressed by prp2 morpholino (MO) knockdown experiments. Investigation of Prp2 depleted embryos revealed high mortality and apoptosis at 24 hours post fertilization (hpf) as well as impaired brain and neuronal development. In order to elucidate the underlying mechanisms, a genome-wide transcriptome analysis was carried out in viable 24 hpf morphants. The resulting changes in gene expression profiles revealed 249 differently expressed genes linked to biological processes like cell death, neurogenesis and embryonic development.

Conclusions/significance: The current study contributes to the understanding of basic Prp functions and demonstrates that the zebrafish is an excellent model to address the role of Prp in vertebrates. The gene knockdown of prp2 indicates an essential biological function for the zebrafish ortholog with a morphant phenotype that suggests a neurodegenerative action and gene expression effects which are apoptosis related and effects gene networks controlling neurogenesis and embryo development.

Show MeSH
Related in: MedlinePlus