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ABSTRACT: The molecular characteristics of low-grade and high-grade areas in desmoplastic infantile astrocytoma / ganglioglioma

PROVIDER: PRJNA793884 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17413661_1.fastq.gz	Fastqsanger.gz
	SRR17413661_2.fastq.gz	Fastqsanger.gz
	SRR17413662_1.fastq.gz	Fastqsanger.gz
	SRR17413662_2.fastq.gz	Fastqsanger.gz
	SRR17413663_1.fastq.gz	Fastqsanger.gz

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The molecular characteristics of low-grade and high-grade areas in desmoplastic infantile astrocytoma / ganglioglioma [RNA-seq]

Project description:The molecular characteristics of low-grade and high-grade areas in desmoplastic infantile astrocytoma / ganglioglioma [RNA-seq]

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The molecular characteristics of low-grade and high-grade areas in desmoplastic infantile astrocytoma / ganglioglioma [methylation array]

Project description:The molecular characteristics of low-grade and high-grade areas in desmoplastic infantile astrocytoma / ganglioglioma [methylation array]

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The molecular characteristics of low-grade and high-grade areas in desmoplastic infantile astrocytoma / ganglioglioma [methylation array]

Project description:A distinctive feature of the histopathology of desmoplastic infantile astrocytomas and gangliogliomas (DIA/DIGs) is a combination of low-grade and high-grade areas. In this study, we test the hypothesis that low-grade and high-grade areas in DIA/DIGs have distinct molecular characteristics. Tissue samples from microdissected low-grade and high-grade areas in 12 DIA/DIGs were analyzed by DNA methylome profiling, whole exome sequencing, RNA sequencing, and immunohistochemistry. Copy number variants among the tumours and between the two morphologically distinct areas were infrequent. No recurrent genetic alterations were identified across the tumor series, and high-grade areas did not have additional genetic alterations to explain their distinct morphology or biological behaviour. However, high-grade areas showed relative hypomethylation in genes downstream of the transcription factors SOX9 and LEF1 and evidence of a core SOX9 transcription network alongside activation of the BMP, WNT, and MAPK signalling pathways. This study contributes to our knowledge of molecular genetic alterations in DIA/DIGs, uncovers molecular differences between the two distinct cell populations in these tumours, and suggests potential therapeutic targets among the more proliferative cell population in DIA/DIGs.

2022-05-24 | GSE193196 | GEO

The molecular characteristics of low-grade and high-grade areas in desmoplastic infantile astrocytoma / ganglioglioma [RNA-seq]

2022-05-24 | GSE193129 | GEO

iTRAQ-based quantitative proteomic analysis of nuclear fractions of glioma (WHO grade II, III and IV) tissues to identify altered transcriptional regulatory proteins

Project description:Glioma tumors arise from normal glial cells (astrocytes). Gliomas are morphologically and clinically classified into four malignancy grades as Grade I, II, III and IV. Grade I and II comprise low grade gliomas that grow slowly, are well differentiated and have a better prognosis and survival compared to grades III and IV. In contrast, grade III-IV lack endothelial proliferation and are highly vascular with a tendency to infiltrate and have areas of extensive necrosis and hypoxia. In the present study, we used iTRAQ (isobaric tags for relative and absolute quantitation) - based quantitative proteomic approach followed by online liquid chromatography and high resolution tandem mass spectrometry (LC-MS/MS) to identify differential nuclear proteins enriched with transcriptional regulatory function from three different grades of astrocytoma tumors (WHO Grade II, III and IV) compared to control.

2019-08-06 | PXD014111 | Pride

iTRAQ-based quantitative proteomic analysis of membrane and nuclear fractions of glioma (WHO grade II, III and IV) tissues to map on Chromosome 12 and identification of mass spectrometry evidence for 'missing proteins'

Project description:Glioma tumors arise from normal glial cells (astrocytes). Gliomas are morphologically and clinically classified into four malignancy grades as Grade I, II, III and IV. Grade I and II comprise low grade gliomas that grow slowly, are well differentiated and have a better prognosis and survival compared to grades III and IV. In contrast, grade III-IV lack endothelial proliferation and are highly vascular with a tendency to infiltrate and have areas of extensive necrosis and hypoxia. In the present study, we used iTRAQ (isobaric tags for relative and absolute quantitation) - based quantitative proteomic approach followed by liquid chromatography and high resolution tandem mass spectrometry (LC-MS/MS) to identify differential membrane and nuclear proteins mapping to Chromosome 12 from three different grades of astrocytoma tumors (WHO Grade II, III and IV) compared to control.

2019-06-04 | PXD000848 | Pride

PROTEOMICS REVEALS DIFFERENTIALLY REGULATED PATHWAYS WHEN COMPARING LOW-VERSUS HIGH-GRADE ASTROCYTOMAS

Project description:Astrocytic tumors are known for their high progression capacity and for high mortality rates; in this regard, proteins correlated to prognosis can aid medical conduct. Although several genetic changes related to progression from low to high-grade astrocytoma are already known, mRNA copies do not necessarily correlate with protein abundance and, therefore could shadow further comprehension about this tumor’s biology. This motivates us to seek for complementary strategies to study tumor progression at the protein level. Here we compare the proteomic profile of biopsies from patients with low-grade (diffuse, n=6) versus high-grade astrocytoma (anaplastic and glioblastomas, n =10), using shotgun proteomics. Data analysis performed with PatternLab for proteomics identified 5,206 and 6,004 proteins in the low- and high-grade groups, respectively. Our results revealed seventy-four differentially abundant proteins (p < 0.01); we then shortlist those related to greater malignancy. We also describe molecular pathways distinctly activated in the two groups, such as differences in the organization of the extracellular matrix, decisive both in tumor invasiveness and in signaling for cell division, which, together with marked contrasts in energy metabolism, are determining factors in the speed of growth and dissemination of these neoplasms. The degradation pathways of GABA, enriched in the low-grade group, is consistent with a favorable prognosis. Other functions such as platelet degranulation, apoptosis, and activation of the MAPK pathway were correlated to high-grade tumors and, consequently, unfavorable prognoses. Our results provide an important survey of molecular pathways involved in glioma pathogenesis for these histopathological groups.

2023-08-04 | PXD033782 | Pride

Astrocytoma cell lines transduced to either express GFAP isoforms or to knockdown GFAP isoforms

Project description:Modulation of the GFAP cytoskeleton in astrocytoma cells alters processes involved in extracellular matrix remodelling and cell-cell signalling – a transcriptome analysis Astrocytomas grade IV are malignant brain tumours with no effective treatment and a five year survival rate of only 5%. Expression of Glial Fibrillary Acidic Protein (GFAP) is lower in high astrocytoma grade, but the expression of the splice isoform GFAPδ is similar in low and high-grade astrocytomas. Thus the ratio of GFAPδ/α is increased in high-grade astrocytomas. We studied transcriptome changes in astrocytoma cell lines resulting from an induced alteration of GFAP isoform expression. GFAPα or GFAPδ were increased or decreased by recombinant expression or shRNA mediated knockdown of GFAPpan or GFAPα. We find that the most prominent effects are induced by the modulations where the GFAPδ/GFAPα ratio is increased. Gene ontology analysis revealed that the main effects of GFAP modulation take place in the extracellular matrix remodelling and cellular signalling clusters, with possible implications in astrocytoma invasive behaviour and angiogenesis.

2017-07-03 | GSE74567 | GEO

Dysregulation of p53-RBM25-mediated circAMOTL1L biogenesis contributes to prostate cancer progression (Agilent circRNA data set)

Project description:To explore the molecular mechanisms underlying circRNA role in prostate carcinogenesis and progression of PCa, we first used circular RNA microarrays to acquire circRNA profiles in PCa tissues. Five pairs of samples were taken from the two different areas, i.e., high-grade PCa (Gleason>8) and low-grade PCa (Gleason< 6), within the same PCa sample

2020-08-27 | GSE113153 | GEO

Differentially Expressed LncRNAs Might be Controlling Signaling Pathways by Establishing Interactions with mRNAs and MicroRNAs in Pediatric Astrocytoma

Project description:In this study was determined the global expression pattern of long non-coding RNAs, mRNAs, and miRNAs in pediatric astrocytoma of different histological grades. The Affymetrix HTA 2.0 array showed expression changes on one hundred-sixty two and two hundred-fifteen long non-coding RNAs in tumors (versus the control) and in GBM (versus low-grade astrocytoma), respectively. A total of seven astrocytic tumors and two control tissues were collected during the period of 2012–2014: four low-grade Ast (three pilocytic Ast (PAst) and one diffuse Ast (DAst)) and four high-grade Ast (four glioblastoma multiforme (GBM)).RNA was extracted from tissue samples using TRIzol (Ambion life technologies, Thermo Scientific Inc.) following the methodology described by Hongbao et al. 2008 and with certain modifications described by Vujovic et al. 2013. For expression analysis, Human Transcriptome Array 2.0 (HTA) (Santa Clara, CA, USA) was employed. in this study was determined the global expression pattern of long non-coding RNAs, mRNAs, and miRNAs in pediatric astrocytoma of different histological grades. The HTA 2.0 array showed expression changes on one hundred-sixty two and two hundred-fifteen long non-coding RNAs in tumors (versus the control) and in GBM (versus low-grade astrocytoma), respectively.

2015-08-25 | E-GEOD-72269 | biostudies-arrayexpress

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