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Genetic heterogeneity versus molecular analysis of prion susceptibility in neuroblasma N2a sublines

ABSTRACT: The neuroblastoma-derived cell line N2a is permissive to certain prion strains but resistant sublines unable to accumulate the pathological proteinase-K resistant form of the prion protein can be isolated. We compared for gene expression and phenotypes different N2a sublines that were susceptible or resistant to the 22L prion strain. Karyotypes and comparative genomic hybridization arrays revealed chromosomal imbalances but did not demonstrate a characteristic profile of genomic alterations linked to prion susceptibility. Likewise, we showed that this phenotype was not dependent on the binding of PrPres, the expression of the prion protein gene, or on its primary sequence. We completed this analysis by looking using real-time quantitative PCR at the expression of a set of genes encoding proteins linked to prion biology. None of the candidates could account by itself for the infection phenotype, nevertheless sublines had distinct transcriptional profiles. Taken together, our results do not support a role for specific genomic abnormalities and possible candidate proteins in N2a prion susceptibility. They also reveal genetic heterogeneity among the sublines and serve as a guidance for further investigation into the molecular mechanisms of prion infection.

ORGANISM(S): Mus musculus

PROVIDER: GSE5374 | GEO | 2008/09/08

SECONDARY ACCESSION(S): PRJNA96275

REPOSITORIES: GEO

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Genetic heterogeneity versus molecular analysis of prion susceptibility in neuroblasma N2a sublines

Project description:The neuroblastoma-derived cell line N2a is permissive to certain prion strains but resistant sublines unable to accumulate the pathological proteinase-K resistant form of the prion protein can be isolated. We compared for gene expression and phenotypes different N2a sublines that were susceptible or resistant to the 22L prion strain. Karyotypes and comparative genomic hybridization arrays revealed chromosomal imbalances but did not demonstrate a characteristic profile of genomic alterations linked to prion susceptibility. Likewise, we showed that this phenotype was not dependent on the binding of PrPres, the expression of the prion protein gene, or on its primary sequence. We completed this analysis by looking using real-time quantitative PCR at the expression of a set of genes encoding proteins linked to prion biology. None of the candidates could account by itself for the infection phenotype, nevertheless sublines had distinct transcriptional profiles. Taken together, our results do not support a role for specific genomic abnormalities and possible candidate proteins in N2a prion susceptibility. They also reveal genetic heterogeneity among the sublines and serve as a guidance for further investigation into the molecular mechanisms of prion infection. In a first approach, CGHa profiles were established for the parental cell line N2apcl, a sensitive (G9) and a resistant (F1) sublines, as compared to A/HeJ mouse strain normal DNA. To allow a more precise description of the differences between N2apcl and six of its derived sub-lines (58, D11, F1, G9, R4, R10), N2apcl DNA was used as reference DNA in a series of CGHa experiments, avoiding the potential copy number polymorphisms between the cell lines and A/HeJ murine DNAs.

2010-06-19 | E-GEOD-5374 | biostudies-arrayexpress

Gene expression imprinting of N2a sublines upon infection with the prion strain 22L

Project description:Cell culture models allow prion propagation studies ex vivo after contact with infectious brain homogenates. To date, among the neural cell lines, the mouse neuroblastoma-derived cell line N2a has been one of the most widely used model and has yet provided interesting insights into cell biology of prion propagation. Remarkably, persistently-infected N2a sublines have been set up and replicate prions without exhibiting any pathological changes. One further interesting feature of N2a is the possibility to establish by subcloning, sublines with a range of susceptibility to prions. Indeed, susceptible sublines propagate prions and accumulate the pathogenic isoform of the prion protein, PrPSc, at the opposite of resistant sublines. The aim of our study was to apply large-scale expression analysis using microarrays combined with quantitative real-time PCR to examine the gene expression profile in a persistently-infected N2a cell line, N2a58, infected with the mouse-adapted prion strain 22L, to seek for prion-specific gene transcription. We also questioned if we could observe identical variations of expression of these genes in three other 22L-infected N2a sublines. Finally, we examined the transcriptional state of a N2a subline considered as resistant when exposed to prions. Common pathways of gene transcription would disclose information on the molecular basis of the cell infection and help to identify potential therapeutic targets. Keywords: other

2009-07-07 | GSE5844 | GEO

Gene expression profile of a murin neuroblastoma cell line infected with the prion strain 22L

Project description:The underlying pathogenic mechanisms of prion infection are not well characterized. To study the effect of prion infection on gene expression in neuronal cell cultures, a neuroblastoma (N2a) cell clone was infected with either the mouse adapted prion strain 22L or exposed to uninfected brain homogenate as a negative control. Large scale expression analysis was performed using a cDNA microarray chip comprising about 21,000 spotted ESTs. Over hundred genes were identified that are differentially expressed in 22L-infected cells when compared to uninfected cells. Several of the identified changes in gene expression have also been reported for other neurodegenerative diseases such as Alzheimer`s disease. Keywords: cDNA arrays, prion, N2a, neuroblastoma cell line, murine A neuroblastoma (N2a) cell clone was infected with either the mouse adapted prion strain 22L or exposed to uninfected brain homogenate as a negative control. Eight replicates including four dye swap experiments have been performed for the comparison of prion infected cells versus control cells.

2010-05-26 | E-GEOD-7119 | biostudies-arrayexpress

Gene expression profile of a murin neuroblastoma cell line infected with the prion strain 22L

2008-02-22 | GSE7119 | GEO

Mus musculus

Project description:Gene expression imprinting of N2a sublines upon infection with the prion strain 22L

| PRJNA97245 | ENA

Mus musculus

Project description:Genetic heterogeneity versus molecular analysis of prion susceptibility in neuroblasma N2a sublines

| PRJNA96275 | ENA

miRNA sequencing of exosomes derived from N2A and APP-N2A cells

Project description:APP misexpression plays a crucial role in triggering a complex pathological cascade, leading to Alzheimer’s disease (AD). The aim of this study is for determine the influence of APP ectopic expression on the miRNA profiles of neuronal exosomes. In study, miRNA sequencing was done using the exosomes derived from N2A (control) and APP-N2A (N2A with APP overexpression).

2022-03-30 | E-MTAB-11106 | biostudies-arrayexpress

Copy number analysis of OVCAR-3 and CDK2 resistant sublines

Project description:Cyclin E1 (CCNE1) is amplified in various tumor types including high-grade serous ovarian cancer where it is associated with poor clinical outcome. We have demonstrate that suppression of the Cyclin E1 partner kinase, CDK2, induces apoptosis in a CCNE1 amplicon-dependent manner. Little is known of mechanisms of resistance to CDK inhibitors. We therefore generated OVCAR-3 sublines with reduced sensitivity to CDK2 inhibitors and profiled by SNP copy number microarrays. Arrayed samples included parental OVCAR-3 cells and five independently derived sublines resistant to PHA-533533 (OVCAR3-533533-R1, -R3, -R5, -R6, -R7). The resistant cell lines were arrayed after drug selection (P5).

2013-09-01 | E-GEOD-48920 | biostudies-arrayexpress

Human Embryonic Stem Cell Sublines

Project description:Human embryonic stem (ES) cell lines acquire recurrent karyotypic abnormalities that may promote growth and survival in long-term culture. Cells with these abnormalities are often present at low levels in human ES cell cultures, requiring subcloning for isolation and analyses. We have developed a rapid method to isolate either abnormal or normal clones from karyotypically mosaic human ES cell cultures that we call Genetic Diagnosis at Passage (G-DAP). We have used this technique to isolate three distinct abnormal sublines from H9 human ES cells in continuous culture. These sublines were characterized by G-banding, fluorescence in situ hybridization (FISH), spectral karyotyping (SKY), and array comparative genomic hybridization (aCGH). One subline (H9.DT) has, as it’s only abnormality, a duplication of 12p capped by a 5q subtelomere. A related subline (H9.TSF) has an additional copy of the derivative chromosome 12, partial trisomy of 17q, and trisomy 14. The third subline (H9.DE) has an interstitial deletion of 18q as the sole anomaly. Despite these karyotypic abnormalities, all three sublines retain markers of the undifferentiated state. The subline H9.TSF demonstrated the ability to form embryoid bodies consisting of all three germ layers. Significantly, H9.DT and H9.TSF sublines show a classic karyotype progression that mirrors that seen in both hematopoietic and solid tumors. This progression was accompanied by an impressive increase in growth potential. The isolation of human ES cell sublines with clonal cytogenetic abnormalities provides a valuable tool for study of factors that promote in vitro genetic changes and for analysis of mechanisms of aneuploidy related to genetic progression found in human cancers.

2008-07-18 | GSE12119 | GEO

Gene expression analysis of OVCAR-3 and CDK2 resistant sublines

Project description:Cyclin E1 (CCNE1) is amplified in various tumor types including high-grade serous ovarian cancer where it is associated with poor clinical outcome. We have demonstrate that suppression of the Cyclin E1 partner kinase, CDK2, induces apoptosis in a CCNE1 amplicon-dependent manner. Little is known of mechanisms of resistance to CDK inhibitors. We therefore generated OVCAR-3 sublines with reduced sensitivity to CDK2 inhibitors and profiled by gene expression microarrays. Arrayed samples included parental OVCAR-3 cells (n = 4 replicates) and five independently derived sublines resistant to PHA-533533 (OVCAR3-533533-R1, -R3, -R5, -R6, -R7). The resistant cell lines were arrayed after drug selection (P5) and after continued passage in the absence of inhibitor (P10+).

2013-09-01 | E-GEOD-48919 | biostudies-arrayexpress

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