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Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies [RNA-Seq]

ABSTRACT: Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies [RNA-Seq]

PROVIDER: PRJNA784116 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17053100_1.fastq.gz	Fastqsanger.gz
	SRR17053100_2.fastq.gz	Fastqsanger.gz
	SRR17053101_1.fastq.gz	Fastqsanger.gz
	SRR17053101_2.fastq.gz	Fastqsanger.gz
	SRR17053102_1.fastq.gz	Fastqsanger.gz

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Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies

Project description:Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies

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Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies [Methylation array]

Project description:Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies [Methylation array]

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Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies [RNA-Seq]

Project description:Purpose: Clustering of meningiomas using DNA methylation and RNA-sequencing data yields groups which predict clinical behavior than the current clinical standard of histopathologic grading. Both techniques segregate many common genomic features seen in meningiomas similarly, raising the question of whether they were identifying the same underyling groups. Methods: DNA methylation profiling (EPIC 850K array) and RNA-sequencing of 110 primary meningiomas was performed. Unsupervised clustering was performed using each type of data, followed by computational modeling which explored correlations of promoter methylation and copy number variation (CNV) with gene expression. Results: We performed unsupervised clustering of the DNA methylation data and gound three clusters to be optimal. These clusters aligned closely with our prior transcriptional classification (Patel et al. PNAS 2019). These groups also closely aligned with groups defined by large-scale cytogenetic changes and merlin expression/genomic instability, suggesting the presence of three biologic groups of meningioma that can be identified by multiple methods. Computational modeling demonstrated that both promoter methylation and CNV correlated closely with gene expression differences seen in meningioma and our biologic groups, although cytogenetic changes (particularly chr 1p loss) was predominant in the clinically aggressive tumors. Conclusions: Our anaylsis suggests the presence of three biologic groups of meningioma (MenG A, B, and C) which can be accurately identified through DNA methylation, RNA-seq, and cytogenetic profiling.

2021-11-30 | GSE189672 | GEO

Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies [Methylation array]

Project description:Purpose: Clustering of meningiomas using DNA methylation and RNA-sequencing data yields groups which predict clinical behavior than the current clinical standard of histopathologic grading. Both techniques segregate many common genomic features seen in meningiomas similarly, raising the question of whether they were identifying the same underyling groups. Methods: DNA methylation profiling (EPIC 850K array) and RNA-sequencing of 110 primary meningiomas was performed. Unsupervised clustering was performed using each type of data, followed by computational modeling which explored correlations of promoter methylation and copy number variation (CNV) with gene expression. Results: We performed unsupervised clustering of the DNA methylation data and gound three clusters to be optimal. These clusters aligned closely with our prior transcriptional classification (Patel et al. PNAS 2019). These groups also closely aligned with groups defined by large-scale cytogenetic changes and merlin expression/genomic instability, suggesting the presence of three biologic groups of meningioma that can be identified by multiple methods. Computational modeling demonstrated that both promoter methylation and CNV correlated closely with gene expression differences seen in meningioma and our biologic groups, although cytogenetic changes (particularly chr 1p loss) was predominant in the clinically aggressive tumors. Conclusions: Our analysis suggests the presence of three biologic groups of meningioma (MenG A, B, and C) which can be accurately identified through DNA methylation, RNA-seq, and cytogenetic profiling.

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Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies.

Project description:One-fifth of meningiomas classified as benign by World Health Organization (WHO) histopathological grading will behave malignantly. To better diagnose these tumors, several groups turned to DNA methylation, whereas we combined RNA-sequencing (RNA-seq) and cytogenetics. Both approaches were more accurate than histopathology in identifying aggressive tumors, but whether they revealed similar tumor types was unclear. We therefore performed unbiased DNA methylation, RNA-seq, and cytogenetic profiling on 110 primary meningiomas WHO grade I and II). Each technique distinguished the same three groups (two benign and one malignant) as our previous molecular classification; integrating these methods into one classifier further improved accuracy. Computational modeling revealed strong correlations between transcription and cytogenetic changes, particularly loss of chromosome 1p, in malignant tumors. Applying our classifier to data from previous studies also resolved certain anomalies entailed by grouping tumors by WHO grade. Accurate classification will therefore elucidate meningioma biology as well as improve diagnosis and prognosis.

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Multiple approaches converge on three biological subtypes of meningioma and extract new insights from published studies

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Project description:Comparison of the gene expression profiles with meningiomas of different grading. 24 primary meningioma cultures from surgical specimen were maintained to primary meningioma cultures.

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Project description:We performed expression profiling of 24 meningioma and two dura controls analyzing 55000 transcripts including 18300 known genes. We compared expression in meningioma vs. dura, expression of low grade (WHO I) vs. higher-grade (WHO II and WHO IIII) tumors and expression of meningothelial and syncytial meningioma vs. fibroblastic meningioma. Gene expression was analysed in 24 meningioma including eight of each WHO grade and two dura controls analyzing 55000 transcripts including 18300 known genes.

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Project description:Methylation analysis of meningioma cases Genomic DNA isolated directly from human meningioma samples

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