The Transcriptomic Landscape of Pediatric Astrocytoma
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ABSTRACT:
PROVIDER: PRJNA806881 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18015779_1.fastq.gz | Fastqsanger.gz | |||
| SRR18015779_2.fastq.gz | Fastqsanger.gz | |||
| SRR18015780_1.fastq.gz | Fastqsanger.gz | |||
| SRR18015780_2.fastq.gz | Fastqsanger.gz | |||
| SRR18015781_1.fastq.gz | Fastqsanger.gz |
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Project description:Tumors of the central nervous system are the most common solid neoplasia during human childhood, representing one of the leading causes of cancer-related mortality. Tumors that originate from astrocyte cells (astrocytoma) in the brain are the most frequently found. According to their histological and pathological features, these tumors are classified into four categories. However, recently an extra layer of molecular classification of the tumorigenesis-associated genes IDH1/2 and H3F3A has been incorporated into the classification guidelines. While mutations in H3F3A are exclusively found in a subtype of pediatric astrocytoma grade IV, mutations in IDH1/2 are very rare in children younger than 14 years old. The transcriptomic profiles of astrocytoma in adults and children have been extensively studied however focusing on the study of the transcriptomic profile of the different grades of astrocytoma (including the additional layer of molecular classification) in pediatric populations are scarce. Therefore, we have profiled the transcriptomic landscape of the four grades of pediatric astrocytoma by RNA sequencing.
2022-10-25 | GSE196694 | GEO
Project description:Central nervous system tumors are the most common solid neoplasia during childhood and represent one of the leading causes of cancer-related mortality. Tumors arising from astrocytic cells (astrocytomas) are the most frequently diagnosed, and according to their histological and pathological characteristics, they are classified into four categories. However, an additional layer of molecular classification considering the DNA sequence of the tumorigenesis-associated genes IDH1/2 and H3F3A has recently been incorporated into the classification guidelines. Although mutations in H3F3A are found exclusively in a subtype of grade IV pediatric astrocytoma, mutations in IDH1/2 genes are very rare in children under 14 years of age. The transcriptomic profiles of astrocytoma in adults and children have been extensively studied. However, there is scarce information on these profiles in pediatric populations considering the status of tumorigenesis-associated genes. Therefore, here we report the transcriptomic landscape of the four grades of pediatric astrocytoma by RNA sequencing. We found several well-documented biological functions associated with the misregulated genes in the four grades of astrocytoma, as well as additional biological pathways. Among the four grades of astrocytoma, we found shared misregulated genes that could have implications in tumorigenesis. Finally, we identified a transcriptional signature for almost all grades of astrocytoma that could be used as a transcription-based identification method.
| S-EPMC9604090 | biostudies-literature
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.
2015-08-25 | GSE72269 | GEO
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
Project description:Y-RNAs are small noncoding RNAs firstly identified in patients suffering the Sjögren’s syndrome and lupus erythematosus, having different predicted cellular functions. Y-RNAs are very abundant ncRNAs present in serum and only a few is known respect their molecular roles. The aim of the study was to determine the circulating Y-RNAs expression from blood serum of pediatric patients with pilocytic or diffuse astrocytoma. Y-RNAs expression was determined by means of the HTA 2.0 arrays. In addition, a bioinformatic approximation of the possible biological functions of Y-RNAs was determined with the “Random Forest” (RF) and “Vector Support Machine” (VSM) algorithms. Results. Data showed a differential expression of RNY-3, RNY-4, and RNY-5 in pediatric patients with astrocytoma, relative to the control. Meanwhile, RNY-1 was shown to be upregulated in the Diffuse condition versus the Pilocytic. The bioinformatic analysis showed that RNY-4 and RNY-5 had the highest scores of interaction with Claudin, Toll-like receptors, and Hyaluronidase-1. In addition, the Y-RNAs loop domain by itself had the highest score of interaction with B cell receptor CD22 (RNY-3) and Toll-like receptor 7 and 3 (RNY-4). Conclusions. Our results showed, for the first time a differential expression of circulating Y-RNAs in pediatric astrocytoma, allowing to distinguish pediatric subjects without cancer from patients with pediatric diffuse or pilocytic astrocytoma and their potential involvement in regulating diverse biological processes, such as immune activation-suppression, cell signaling, selective transcription, and cell proliferation through activation of DNA replication.
2022-10-31 | GSE216815 | GEO
Project description:Immuno-Transcriptomic Profiling Identifies Actionable Alterations in Pediatric Solid Malignancies
2021-12-07 | PXD017130 | Pride
Project description:Pediatric pilocytic astrocytoma (PA) is the most common brain tumor in children. Complete resection provides a good prognosis, except for unresectable PA forms. There is an incomplete understanding of the molecular and cellular pathogenesis of PA. Potential biomarkers for PA patients, especially the non-BRAF-mutated ones are needed. Cerebrospinal fluid (CSF) is a valuable source of brain tumor biomarkers. Extracellular vesicles express valuable disease targets. These can be isolated from CSF from waste extraventricular drainage (EVD). We analyzed the proteome of EVD CSF from 24 PA, cerebral hemorrhage (CH, non-tumor controls), or medulloblastoma (MB, unrelated tumoral controls) patients. 3072 proteins were identified, 47.1%, 65.6%, and 86.2% of which expressed in the unprocessed total, and its microvesicle (Mv), and exosome (Ex) fractions. Bioinformatics identified 50 statistically significant proteins in the comparison between PA and HC, and PA and MB patients, in the same fractions. Kinase enrichment analysis predicted five enriched kinases involved in signaling. Among these, only Cyclin-dependent kinase 2 (CDK2) kinase was overexpressed in PA samples. PLS-DA highlighted inactive carboxypeptidase-like protein X2 (CPXM2) and aquaporin-4 (AQP4) as statistically significant in all the comparisons, with CPXM2 being overexpressed (validated by ELISA and Western Blot) and AQP4 downregulated in PA. These proteins were considered the most promising potential biomarkers to discriminate among pilocytic astrocytoma, and unrelated tumoral (MB) or non-tumoral conditions, in all the fractions examined, proposed to be prospectively validated in the plasma for translational medicine applications.
2024-05-23 | PXD050589 | Pride
Project description:Epigenetic Landscape of Pediatric Ependymoma Recurrence
| PRJNA658524 | ENA
Project description:Pilocytic astrocytoma is the most common type of brain tumor in pediatric population, generally connected with favorable prognosis, although recurrences or dissemination sometimes are also observed. For tumors originating in supra- or infratentorial location different molecular background was suggested but plausible correlations between transcriptional profile and radiological features and/or clinical course are still undefined. The purpose of this study was to identify gene expression profiles related to the most frequent locations of this tumor, subtypes based on various radiological features and clinical pattern of the disease. According to the radiological features presented on MRI, all cases were divided into four subtypes: solid or mainly solid, cystic with an enhancing cyst wall, cystic with a non-enhancing cyst wall and solid with central necrosis. Bioinformatic analyses showed that gene expression profile of pilocytic astrocytoma highly depends on the tumor location. Most prominent differences were noted for IRX2, PAX3, CXCL14, LHX2, SIX6, CNTN1 and SIX1 genes expression which could distinguish pilocytic astrocytomas of different location even within supratentorial region. Analysis of the genes potentially associated between radiological features showed much weaker transcriptome differences. Single genes showed association with the tendency to progression. Here we showed that pilocytic astrocytomas of three different locations could be precisely differentiated on the basis of gene expression level but their transcriptional profiles did not strongly reflect the radiological appearance of the tumor or the course of the disease. Gene expression profiling was performed in 47 pilocytic astrocytoma tumours characterized by different localization, radiology and progression.
2015-10-30 | E-GEOD-73066 | biostudies-arrayexpress
Project description:Genomic landscape of pediatric germ cell tumors
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