Limits...
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

Validation of two lncRNAs regulated by SOX2 in GSC11 cells.(A) The expression of the transcripts located in chr11:121899032–121899389 (TCONS_00020142) and chr19:28,281,401–28,284,848 (TCONS_00027256) were assessed. In both cases GSC11 cells were transfected with siRNA control or siRNA against SOX2 and three days later RNA was extracted and subject to RT-PCR. Values are normalized to GAPDH and are the mean ± SD of three replicates. (B) Comparison between microarray and qRT-PCR results. The height of each column in this graph represents the log-transformed mean fold changes in the expression of lncRNA between Scramble and siSOX2 transfected cell line.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5036841&req=5

pone.0163155.g006: Validation of two lncRNAs regulated by SOX2 in GSC11 cells.(A) The expression of the transcripts located in chr11:121899032–121899389 (TCONS_00020142) and chr19:28,281,401–28,284,848 (TCONS_00027256) were assessed. In both cases GSC11 cells were transfected with siRNA control or siRNA against SOX2 and three days later RNA was extracted and subject to RT-PCR. Values are normalized to GAPDH and are the mean ± SD of three replicates. (B) Comparison between microarray and qRT-PCR results. The height of each column in this graph represents the log-transformed mean fold changes in the expression of lncRNA between Scramble and siSOX2 transfected cell line.

Mentions: The top four differentially expressed lncRNAs (Table 7) that presented chromatin marks and high abundance in brain were selected using GRCh37/hg19 assembly in UCSC Genome Browser, and their expression was validated using qRT-PCR in GSC11 cells, comparing SOX2-siRNA versus scrambled control. Our data indicated that the expression of chr19:28,281,401–28,284,848 (TCONS_00027256) was significantly down-regulated (p value = 0,018), while chr11:121899032–121899389 (TCONS_00020142) was significantly up-regulated (p value = 0.042) after SOX2 inhibition (Fig 6A). The results were consistent with the microarray data (Fig 6B).


Analysis of SOX2-Regulated Transcriptome in Glioma Stem Cells
Validation of two lncRNAs regulated by SOX2 in GSC11 cells.(A) The expression of the transcripts located in chr11:121899032–121899389 (TCONS_00020142) and chr19:28,281,401–28,284,848 (TCONS_00027256) were assessed. In both cases GSC11 cells were transfected with siRNA control or siRNA against SOX2 and three days later RNA was extracted and subject to RT-PCR. Values are normalized to GAPDH and are the mean ± SD of three replicates. (B) Comparison between microarray and qRT-PCR results. The height of each column in this graph represents the log-transformed mean fold changes in the expression of lncRNA between Scramble and siSOX2 transfected cell line.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5036841&req=5

pone.0163155.g006: Validation of two lncRNAs regulated by SOX2 in GSC11 cells.(A) The expression of the transcripts located in chr11:121899032–121899389 (TCONS_00020142) and chr19:28,281,401–28,284,848 (TCONS_00027256) were assessed. In both cases GSC11 cells were transfected with siRNA control or siRNA against SOX2 and three days later RNA was extracted and subject to RT-PCR. Values are normalized to GAPDH and are the mean ± SD of three replicates. (B) Comparison between microarray and qRT-PCR results. The height of each column in this graph represents the log-transformed mean fold changes in the expression of lncRNA between Scramble and siSOX2 transfected cell line.
Mentions: The top four differentially expressed lncRNAs (Table 7) that presented chromatin marks and high abundance in brain were selected using GRCh37/hg19 assembly in UCSC Genome Browser, and their expression was validated using qRT-PCR in GSC11 cells, comparing SOX2-siRNA versus scrambled control. Our data indicated that the expression of chr19:28,281,401–28,284,848 (TCONS_00027256) was significantly down-regulated (p value = 0,018), while chr11:121899032–121899389 (TCONS_00020142) was significantly up-regulated (p value = 0.042) after SOX2 inhibition (Fig 6A). The results were consistent with the microarray data (Fig 6B).

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