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Analysis of SOX2-Regulated Transcriptome in Glioma Stem Cells

View Article: PubMed Central - PubMed

ABSTRACT

Introduction: Glioblastoma is the most malignant brain tumor in adults and is associated with poor survival despite multimodal treatments. Glioma stem-like cells (GSCs) are cells functionally defined by their self-renewal potential and the ability to reconstitute the original tumor upon orthotopic implantation. They have been postulated to be the culprit of glioma chemo- and radio-resistance ultimately leading to relapse. Understanding the molecular circuits governing the GSC compartment is essential. SOX2, a critical transcription regulator of embryonic and neural stem cell function, is deregulated in GSCs however; the precise molecular pathways regulated by this gene in GSCs remain poorly understood.

Results: We performed a genome-wide analysis of SOX2-regulated transcripts in GSCs, using a microarray. We identified a total of 2048 differentially expressed coding transcripts and 261 non-coding transcripts. Cell adhesion and cell-cell signaling are among the most enriched terms using Gene Ontology (GO) classification. The pathways altered after SOX2 down-modulation includes multiple cellular processes such as amino-acid metabolism and intercellular signaling cascades. We also defined and classified the set of non-coding transcripts differentially expressed regulated by SOX2 in GSCs, and validated two of them.

Conclusions: We present a comprehensive analysis of the transcriptome controlled by SOX2 in GSCs, gaining insights in the understanding of the potential roles of SOX2 in glioblastoma.

No MeSH data available.


Related in: MedlinePlus

Analysis by qRT-PCR of the top 5 (A) up- and (B) down-regulated coding transcripts in SOX2 downmodulated GSC11 and GSC23 cells. Total RNA was extracted after 72h of si-Sc or si-SOX2 transfection in GSC11 and GSC23 cells. In GSC23 cells we used two different siRNAs against human SOX2, si-SOX2 (1) is referred to s13295 and si-SOX2 (2) is referred to s13294 from Ambion. Values are normalized to GAPDH and each bar represents the mean ± SD.
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pone.0163155.g002: Analysis by qRT-PCR of the top 5 (A) up- and (B) down-regulated coding transcripts in SOX2 downmodulated GSC11 and GSC23 cells. Total RNA was extracted after 72h of si-Sc or si-SOX2 transfection in GSC11 and GSC23 cells. In GSC23 cells we used two different siRNAs against human SOX2, si-SOX2 (1) is referred to s13295 and si-SOX2 (2) is referred to s13294 from Ambion. Values are normalized to GAPDH and each bar represents the mean ± SD.

Mentions: To further narrow the coding transcripts data a cut-off 1 logarithmic fold difference between SOX2 knockdown and scrambled GSC11 cells was set, identifying 35 up-regulated and 100 down-regulated genes, which suggest that SOX2 act primarily as a transcriptional activator. In Table 3 we showed the top-10 up or down-regulated protein coding-genes, and select the top 5 candidates of each group for further validation by qRT-PCR using the GSC11 and GSC23 cell lines. We confirmed the observed microarray expression changes in 5 out of 5 down-regulated coding-genes (Fig 2B) and in one out of 5 up-regulated coding genes in GSC11 cells (Fig 2A). Regarding GSC-23 cells, we down-modulate SOX2 expression using two different siRNAs against human SOX2, and we validate the expression of 5 out of 5 up-regulated coding-genes (Fig 2A) and of 4 out of 5 down-regulated coding genes (Fig 2B), partially validating the microarray results.


Analysis of SOX2-Regulated Transcriptome in Glioma Stem Cells
Analysis by qRT-PCR of the top 5 (A) up- and (B) down-regulated coding transcripts in SOX2 downmodulated GSC11 and GSC23 cells. Total RNA was extracted after 72h of si-Sc or si-SOX2 transfection in GSC11 and GSC23 cells. In GSC23 cells we used two different siRNAs against human SOX2, si-SOX2 (1) is referred to s13295 and si-SOX2 (2) is referred to s13294 from Ambion. Values are normalized to GAPDH and each bar represents the mean ± SD.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5036841&req=5

pone.0163155.g002: Analysis by qRT-PCR of the top 5 (A) up- and (B) down-regulated coding transcripts in SOX2 downmodulated GSC11 and GSC23 cells. Total RNA was extracted after 72h of si-Sc or si-SOX2 transfection in GSC11 and GSC23 cells. In GSC23 cells we used two different siRNAs against human SOX2, si-SOX2 (1) is referred to s13295 and si-SOX2 (2) is referred to s13294 from Ambion. Values are normalized to GAPDH and each bar represents the mean ± SD.
Mentions: To further narrow the coding transcripts data a cut-off 1 logarithmic fold difference between SOX2 knockdown and scrambled GSC11 cells was set, identifying 35 up-regulated and 100 down-regulated genes, which suggest that SOX2 act primarily as a transcriptional activator. In Table 3 we showed the top-10 up or down-regulated protein coding-genes, and select the top 5 candidates of each group for further validation by qRT-PCR using the GSC11 and GSC23 cell lines. We confirmed the observed microarray expression changes in 5 out of 5 down-regulated coding-genes (Fig 2B) and in one out of 5 up-regulated coding genes in GSC11 cells (Fig 2A). Regarding GSC-23 cells, we down-modulate SOX2 expression using two different siRNAs against human SOX2, and we validate the expression of 5 out of 5 up-regulated coding-genes (Fig 2A) and of 4 out of 5 down-regulated coding genes (Fig 2B), partially validating the microarray results.

View Article: PubMed Central - PubMed

ABSTRACT

Introduction: Glioblastoma is the most malignant brain tumor in adults and is associated with poor survival despite multimodal treatments. Glioma stem-like cells (GSCs) are cells functionally defined by their self-renewal potential and the ability to reconstitute the original tumor upon orthotopic implantation. They have been postulated to be the culprit of glioma chemo- and radio-resistance ultimately leading to relapse. Understanding the molecular circuits governing the GSC compartment is essential. SOX2, a critical transcription regulator of embryonic and neural stem cell function, is deregulated in GSCs however; the precise molecular pathways regulated by this gene in GSCs remain poorly understood.

Results: We performed a genome-wide analysis of SOX2-regulated transcripts in GSCs, using a microarray. We identified a total of 2048 differentially expressed coding transcripts and 261 non-coding transcripts. Cell adhesion and cell-cell signaling are among the most enriched terms using Gene Ontology (GO) classification. The pathways altered after SOX2 down-modulation includes multiple cellular processes such as amino-acid metabolism and intercellular signaling cascades. We also defined and classified the set of non-coding transcripts differentially expressed regulated by SOX2 in GSCs, and validated two of them.

Conclusions: We present a comprehensive analysis of the transcriptome controlled by SOX2 in GSCs, gaining insights in the understanding of the potential roles of SOX2 in glioblastoma.

No MeSH data available.


Related in: MedlinePlus