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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]

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

PROVIDER: PRJNA1015698 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26045700_1.fastq.gz	Fastqsanger.gz
	SRR26045700_2.fastq.gz	Fastqsanger.gz
	SRR26045701_1.fastq.gz	Fastqsanger.gz
	SRR26045701_2.fastq.gz	Fastqsanger.gz
	SRR26045702_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 [RNA-seq]

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

| PRJNA1015697 | 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

Illumina Infinium HumanMethylation EPIC beadchip profiling of supratentorial ependymomas: TEAD1::NCOA2 Fusion

Project description:This study investigates the epigenetic and genetic landscape of a rare case of supratentorial ependymoma (ST-EPN), characterised by a novel TEAD1::NCOA2 fusion, expanding the molecular understanding of YAP1 fusion-positive ependymomas. Using Illumina methylation arrays, we performed DNA methylation profiling to classify the tumour subtype. (Additionally, RNA sequencing identified the TEAD1::NCOA2 fusion, implicating the activation of the HIPPO-YAP/TAZ pathway. These findings highlight the complexity of central nervous system tumour classifications and demonstrate the utility of advanced molecular diagnostics in cases where conventional methods, such as fluorescence in situ hybridisation (FISH), yield inconclusive results.)

2025-02-22 | E-MTAB-14789 | biostudies-arrayexpress

The Immunopeptidomic Landscape of Ependymomas provide actionable antigens for T cell-based immunotherapy

Project description:Ependymoma (EPN) are primary tumors of the nervous system. Due to their growth pattern, most ependymoma can be managed with neurosurgical resection alone. A substantial proportion of these tumors recurs or display infiltrative growth pattern, however. Therapeutic options after neurosurgical resection are limited. Based on tumor board recommendations, radiation therapy will be recommended for some patients. Systemic treatment options for progressive ependymoma include platin-based therapeutic regimes or a combination of lapatinib and temozolomide. Peptide-based immunotherapy represents a promising low-side effect therapeutic option relying on the induction of tumor-specific T cells targeting human leukocyte antigens (HLA)-presented peptides. We here analyzed the landscape of naturally presented HLA class I and II ligands of primary ependymomas using a comparative mass-spectrometry-based immunopeptidomic approach to delineate naturally presented ependymoma-associated antigens. We discovered a subset of EPN-exclusive peptides including HLA-A*02 and HLA-A*25/HLA-A*26–restricted HLA ligands and identified a small panel of cancer/testis antigens (CTAs)-derived HLA ligands. Furthermore, we outlined immunopeptidomic alterations in different EPN-subgroups and progressive EPNs and performed subsequent functional characterization for demonstrating immunogenicity in vitro. Taken together, we provide actionable targets that could further be explored as a T-cell based immunotherapeutic strategy in this tumor entity.

2025-05-26 | PXD052448 | Pride

Systems Pharmacology Screening Reveals Targetable Kinases in Supratentorial Ependymoma Kinases in Supratentorial Ependymomas

Project description:Ependymomas (EPN) are central nervous system tumors arising from ependymal cells, primarily affecting young children and accounting for 10% of intracranial tumors in children and 4% in adults. Current treatments are limited to surgery and radiotherapy, with chemotherapy providing minimal benefit. Over 70% of supratentorial ependymomas (ST-EPNs) are driven by ZFTARELA fusions (ZFTA-RELAfus), which are associated with poor prognosis. Recent molecular classifications have identified two distinct ST-EPN clusters, E1 and E2, with the E1 cluster predominantly composed of ZFTA-RELAfus tumors. However, effective targeted therapies for these tumors remain lacking. Here, we show that the ZFTA-RELAfus mouse model closely mirrors the human E1 cluster, validating its use for therapeutic discovery. Using this model and a systems polypharmacology approach called Kinome Regularization, we identified mer tyrosine kinase (Mertk) as a key regulator of ZFTA-RELAfus cell viability and proliferation. Genetic depletion or pharmacological inhibition of Mertk reduced cell growth ex vivo and treatment with the clinical-grade Mertk inhibitor significantly suppressed tumor proliferation in vivo. Mechanistically, both human E1 tumors and mouse ZFTA-RELAfus tumors showed elevated Mertk expression, with Mertk inhibition leading to decreased activity of pro-survival pathways. Further, substantial overlap (>80%) between genes upregulated in ZFTA-RELAfus tumors and those downregulated following Mertk inhibition treatment suggest a dependency on Mertkmediated signaling for tumor growth. These findings highlight Mertk as a promising therapeutic target and support the clinical development of Mertk inhibitors for treating human E1 subtype and ZFTA-RELAfus -driven ependymomas.

2025-12-30 | GSE291213 | GEO

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

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