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Transcriptomic and epigenetic dissection of spinal ependymomas (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation [RNA-seq]

ABSTRACT: Transcriptomic and epigenetic dissection of spinal ependymomas (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation [RNA-seq]

PROVIDER: PRJNA1015697 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26045000_1.fastq.gz	Fastqsanger.gz
	SRR26045000_2.fastq.gz	Fastqsanger.gz
	SRR26045001_1.fastq.gz	Fastqsanger.gz
	SRR26045001_2.fastq.gz	Fastqsanger.gz
	SRR26045002_1.fastq.gz	Fastqsanger.gz

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Transcriptomic and epigenetic dissection of spinal ependymomas (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation [WES]

Project description:Background: Ependymomas encompass multiple, clinically relevant tumor types based on localization and molecular profiles. Although tumors of the methylation class “spinal ependymoma” (SP-EPN) represent the most common intramedullary neoplasms in children and adults, their developmental origin is ill-defined, molecular data are scarce, and the potential heterogeneity within SP-EPN remains unexplored. The only known recurrent genetic events in SP-EPN are loss of chromosome 22q and NF2 mutations, but neither types and frequency of these alterations nor their clinical meaning have been described in a large, epigenetically defined series. Methods: We mapped SP-EPN transcriptomes (n=76) to developmental atlases of the developing and adult spinal cord to uncover potential developmental origins of these tumors. In addition, transcriptomic, epigenetic (n=234), genetic (n=140), and clinical analyses (n=115) were integrated for a detailed overview on this entity. Results: Integration of transcriptomic ependymoma data with single-cell atlases of the spinal cord identified mature adult ependymal cells to display highest similarities to SP-EPN. Unsupervised hierarchical clustering of tumor data together with integrated analysis of methylation profiles identified two molecular SP-EPN subtypes. Subtype 1 predominantly contained NF2 wild type sequences with regular NF2 expression but revealed more extensive copy number alterations. Subtype 2 harbored previously known germline or sporadic NF2 mutations and was NF2-deficient in most cases, more often showed multilocular disease, and demonstrated a significantly reduced progression-free survival. Conclusion: Based on integrated molecular profiling of a large tumor series we identify two distinct SP-EPN subtypes with important implications for genetic counseling, patient surveillance, and drug development priorities.

2024-01-26 | GSE242993 | GEO

Transcriptomic and epigenetic dissection of spinal ependymomas (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation [RNA-seq]

2024-01-26 | GSE242992 | GEO

Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutations [Methylation]

2024-01-26 | GSE242991 | GEO

Transcriptomic and epigenetic dissection of spinal ependymomas (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation [WES]

Project description:Transcriptomic and epigenetic dissection of spinal ependymomas (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation [WES]

| PRJNA1015698 | ENA

Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutations

Project description:Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutations

| PRJNA1015696 | ENA

Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutations [Methylation]

Project description:Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutations [Methylation]

| PRJNA1015699 | ENA

Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation.

Project description: Not available

| S-EPMC10808175 | biostudies-literature

Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology

Project description:Posterior fossa type A (PF-EPN-A, PFA) ependymoma are aggressive tumors that mainly affect children and have a poor prognosis. Histopathology shows significant intratumoral heterogeneity, ranging from loose tissue to often sharply demarcated, extremely cell dense tumor areas. To determine molecular differences between these morphologically different areas and to understand their clinical significance, we analyzed 113 PF-EPN-A samples, including 40 corresponding relapse samples. Inter alia, DNA methylation profiles were analysed for high and low cell density regions seperately in 21 cases. Tumor areas with low and high cell density showed diverging DNA methylation profiles regarding their similarity to distinct previously discovered PF-EPN-A subtypes in 9/21 cases. Prognostically relevant chromosomal changes at 1q and 6q showed spatial heterogeneity within single tumors.

2024-01-31 | GSE248618 | GEO

Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology.

Project description:Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology.

| PRJNA1046044 | ENA

Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology

Project description:Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology

| PRJNA1045254 | ENA

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