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Characterizing the tumor immune microenvironment of ependymomas using targeted gene expression profiles and RNA sequencing

ABSTRACT: Characterizing the tumor immune microenvironment of ependymomas using targeted gene expression profiles and RNA sequencing

PROVIDER: PRJNA893679 | ENA |

REPOSITORIES: ENA

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Characterizing the tumor immune microenvironment of ependymomas using targeted gene expression profiles and RNA sequencing.

Project description:BackgroundDefining the tumor immune microenvironment (TIME) of patients using transcriptome analysis is gaining more popularity. Here, we examined and discussed the pros and cons of using RNA sequencing for fresh frozen samples and targeted gene expression immune profiles (NanoString) for formalin-fixed, paraffin-embedded (FFPE) samples to characterize the TIME of ependymoma samples.ResultsOur results showed a stable expression of the 40 housekeeping genes throughout all samples. The Pearson correlation of the endogenous genes was high. To define the TIME, we first checked the expression of the PTPRC gene, known as CD45, and found it was above the detection limit in all samples by both techniques. T cells were identified consistently using the two types of data. In addition, both techniques showed that the immune landscape was heterogeneous in the 6 ependymoma samples used for this study.ConclusionsThe low-abundant genes were detected in higher quantities using the NanoString technique, even when FFPE samples were used. RNA sequencing is better suited for biomarker discovery, fusion gene detection, and getting a broader overview of the TIME. The technique that was used to measure the samples had a considerable effect on the type of immune cells that were identified. The limited number of tumor-infiltrating immune cells compared to the high density of tumor cells in ependymoma can limit the sensitivity of RNA expression techniques regarding the identification of the infiltrating immune cells.

| S-EPMC10361846 | biostudies-literature

Characterizing the tumor immune microenvironment of ependymomas using targeted gene expression profiles and RNA sequencing

Project description:Defining the tumor immune microenvironment (TIME) of patients using transcriptome analysis is gaining more popularity. Here, we examined and discussed the pros and cons of using RNA -sequencing for Fresh Frozen (FF) samples and targeted gene expression immune profiles (NanoString) for Formalin-Fixed, Paraffin-Embedded (FFPE) samples to characterize the TIME of ependymoma samples.

2022-10-25 | GSE216478 | GEO

Exploring Immune Microenvironment of Colorectal Cancer Patients after Renal Transplantation

Project description:The present data characterizing the colorectal cancer tumor microenvironment influenced by immunosuppressants.

2024-10-22 | GSE277905 | GEO

Characterizing the tumor immune microenvironment of ependymomas using targeted gene expression profiles and RNA-sequencing the pros and cons

Project description:RNA sequencing data of a collection of 6 pediatric ependymoma cases

| EGAS00001006535 | EGA

Epigenomic Alterations Define Lethal CIMP positive Ependymomas of Infancy

Project description:Ependymomas are common childhood brain tumors that occur throughout the nervous system, but are most common in the pediatric hindbrain. Current standard therapy comprises surgery and radiation, but not cytotoxic chemotherapy as it does not further increase survival. Whole-genome and whole-exome sequencing of 47 hindbrain ependymomas reveals an extremely low mutation rate, and zero significant recurrent somatic SNVs. While devoid of recurrent SNVs and focal copy number aberrations, poor prognosis hindbrain ependymomas exhibit a CpG island methylator phenotype (CIMP). Transcriptional silencing driven by CpG methylation converges exclusively on targets of the polycomb repressor complex 2 (PRC2) that represses expression of differentiation genes through tri-methylation of H3K27. CIMP-positive (CIMP+) hindbrain ependymomas are responsive to clinical drugs that target either DNA or H3K27 methylation both in vitro and in vivo. We conclude that epigenetic modifiers are the first rational therapeutic candidates for this deadly malignancy, which is epigenetically de-regulated but genetically bland. 10 primary posterior fossa ependymomas have been analyzed

2014-03-15 | E-GEOD-55920 | biostudies-arrayexpress

Epigenomic Alterations Define Lethal CIMP-positive Ependymomas of Infancy

Project description:1) Illumina 450K methylation profiles-48 posterior fossa ependymomas

2014-03-25 | GSE45353 | GEO

Epigenomic Alterations Define Lethal CIMP positive Ependymomas of Infancy

2014-03-15 | GSE55920 | GEO

Epigenomic Alterations Define Lethal CIMP-positive Ependymomas of Infancy

Project description:1) Illumina 450K methylation profiles-48 posterior fossa ependymomas NA

2014-03-25 | E-GEOD-45353 | biostudies-arrayexpress

Characterizing the tumor microenvironment of metastatic ovarian cancer by single cell transcriptomics

Project description:Characterizing the tumor microenvironment of metastatic ovarian cancer by single cell transcriptomics

| PRJNA612966 | ENA

Gene expression of LMPC cells of infratentorial ependymomas when compared to LMPC ependymal cells

Project description:Ependymomas are glial tumors that share morphologic similarities with ependymal cells. Here we laser microdissected ependymoma cells of 15 infratentorial tumors and generated gene expression profiles. These profiles were compared to those of 7 laser microdissected ependymal tissues. 10 000 laser microdissected cells of each of the 15 different infratentorial ependymomas and seven ependymal autopsy tissues were lysed and gene expression profiles were generated. Expression profiles of ependymomas were compared to those of ependymal cells.

2010-12-10 | E-GEOD-25604 | biostudies-arrayexpress

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