Gene expression based profiling of pleomorphic xanthoastrocytoma highlights two prognostic subgroups
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE168904 | GEO | 2021/12/14
REPOSITORIES: GEO
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Project description:Gene expression based profiling of pleomorphic xanthoastrocytoma highlights two prognostic subgroups
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Project description:Gene expression (mRNA) profiling of human ependymomas Despite the histological similarity of ependymomas from throughout the neuraxis, the disease likely comprises multiple independent entities, each with a distinct molecular pathogenesis. Transcriptional profiling of two large independent cohorts of ependymoma reveals the existence of two demographically, transcriptionally, genetically, and clinically distinct groups of posterior fossa (PF) ependymoma. Group-A patients are younger, have laterally located tumors with a balanced genome, and are much more likely to exhibit recurrence, secondary metastasis, and death as compared to Group-B patients. Identification and optimization of immunohistochemical markers for PF ependymoma subgroups allowed validation of our findings on a third independent group of tumors using a human ependymoma tissue microarray, and provides a tool for prospective prognostication and stratification of PF ependymoma patients. We analyzed 102 primary ependymomas on the Affymetrix Exon 1.0ST platform (Gene Level).
2011-08-14 | E-GEOD-27279 | biostudies-arrayexpress
Project description:Despite histological similarity of ependymomas from throughout the neuraxis, the disease likely comprises multiple independent entities, each with a distinct molecular pathogenesis. Transcriptional profiling of two large independent cohorts of ependymomas reveals the existence of two demographically, transcriptionally, genetically and clinically distinct groups of posterior fossa (PF) ependymoma. Group A patients are younger, have laterally located tumors with a balanced genome, and are much more likely to exhibit recurrence, metastasis, and death as compared to Group B patients. Identification and optimization of immunohistochemical markers for PF ependymoma subgroups allowed validation of our findings on a third group of independent ependymomas using a human ependymoma tissue microarray, and provides a tool for prospective prognostication and stratification of PF ependymoma patients. This SuperSeries is composed of the SubSeries listed below.
2011-08-15 | GSE27287 | GEO
Project description:Gene expression (mRNA) profiling of human ependymomas Despite the histological similarity of ependymomas from throughout the neuraxis, the disease likely comprises multiple independent entities, each with a distinct molecular pathogenesis. Transcriptional profiling of two large independent cohorts of ependymoma reveals the existence of two demographically, transcriptionally, genetically, and clinically distinct groups of posterior fossa (PF) ependymoma. Group-A patients are younger, have laterally located tumors with a balanced genome, and are much more likely to exhibit recurrence, secondary metastasis, and death as compared to Group-B patients. Identification and optimization of immunohistochemical markers for PF ependymoma subgroups allowed validation of our findings on a third independent group of tumors using a human ependymoma tissue microarray, and provides a tool for prospective prognostication and stratification of PF ependymoma patients.
2011-08-15 | GSE27279 | GEO
Project description:Despite histological similarity of ependymomas from throughout the neuraxis, the disease likely comprises multiple independent entities, each with a distinct molecular pathogenesis. Transcriptional profiling of two large independent cohorts of ependymomas reveals the existence of two demographically, transcriptionally, genetically and clinically distinct groups of posterior fossa (PF) ependymoma. Group A patients are younger, have laterally located tumors with a balanced genome, and are much more likely to exhibit recurrence, metastasis, and death as compared to Group B patients. Identification and optimization of immunohistochemical markers for PF ependymoma subgroups allowed validation of our findings on a third group of independent ependymomas using a human ependymoma tissue microarray, and provides a tool for prospective prognostication and stratification of PF ependymoma patients. This SuperSeries is composed of the following subset Series: GSE27283: Human ependymoma samples [expression] GSE27286: Human ependymoma samples, Subgrouping [aCGH - German Cancer Research Center human 33K BAC array] Refer to individual Series
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Project description:Advances in transcriptomics have impacted the way of looking atimproved our understanding of leukemic development and helped enhancing the stratification of patients. Analyses of individual cohortsTranscriptomics studies often combined AML samples regardless of cytogenetic abnormalities. , which would lead to bias in Hence, deregulated genesdifferential gene expression analysis that may result from the differential representation of in less frequent AML subgroups have low weight, contrarily to those in abundant subgroups. We, thusHence, we performed a horizontal meta-analysis that integrated transcriptomic data of AML from multicentric multiple studies to enrich the less frequent cytogenetic subgroups and to uncover common genes involved in AML development and response to therapy. A total of 28 Affymetrix microarray datasets harboring 3940 AML samples were downloaded from the GEO database. After stringent quality control, transcriptomics data of 1523 samples from 11 datasets, covering 10 AML cytogenetic subgroups, were retained and merged with the transcriptomic data of 198 healthy bone marrow samples. Differentially expressed genes between each cytogenetic subgroup and normal samples were extracted, allowing the unbiased identification of 330 commonly deregulated genes (CODEGs)., which CODEGs showed enriched expression profiles in myeloid differentiation, leukemic stem cell status and relapse. Most of these genes were downregulated, in accordance with DNA hypermethylation. CODEGS were then used to create a prognostic score based on the weighted sum of expression of 22 core genes (CODEG22). The score was validated in on microarray data of five independent cohorts, and by qRT-PCR in a cohort of 142 samples, by qRT-PCR. CODEG22 stratified patients globally, as well as in subpopulations of cytologically normal and elderly patients. , and hence, couldSo, it may complement the European LeukemiaNet classification for a more accurate prediction of AML outcomes.
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Project description:Pilocytic astrocytoma (PA) is the most common pediatric brain tumor and driven by aberrant MAPK signaling, typically mediated by BRAF alterations. While five-year overall survival rates exceed 95%, tumor recurrence constitutes a major clinical challenge in incompletely resected tumors despite chemotherapeutic or radiation based therapies. Therefore, we used proteogenomics to discern the biological heterogeneity of PA to improve classification of this tumor entity and identify novel therapeutic targets. Our proteogenomics approach integrates RNA sequencing and LC/MS-based proteomic profiling data from a cohort of 58 confirmed, primary PA samples. An integrative genomics approach was conducted to discern the biological heterogeneity of PA and to identify aberrant pathway activation in these biological subgroups. In summary, Pilocytic astrocytomas segregate into two groups where younger patients are significantly associated with Group 1. Importantly, we validate the two distinct biological subgroups in two non-overlapping cohorts. The biological heterogeneity seen here may improve biological classification and reveal novel therapeutic targets specifically useful for non-resectable tumors with high risk of recurrent or progressive disease.
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