Transcription profiling of high and low grade gliomas from human patients to identify new diagnostic and prognostic markers
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Payne CA
PROVIDER: S-ECPF-TABM-167 | biostudies-other | 2008 Oct
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Comparison of high grade to low grade gliomas.
2007-06-01 | E-TABM-167 | biostudies-arrayexpress
Project description:Low-grade gliomas (LGG) are central nervous system Grade I tumors, and as they progress they are becoming one of the deadliest brain tumors. There is still great need for timely and accurate diagnosis and prognosis of LGG. Herein, we aimed to identify diagnostic and prognostic biomarkers associated with LGG, by employing diverse computational approaches. For this purpose, differential gene expression analysis on high-throughput transcriptomics data of LGG versus corresponding healthy brain tissue, derived from TCGA and GTEx, respectively, was performed. Weighted gene co-expression network analysis of the detected differentially expressed genes was carried out in order to identify modules of co-expressed genes significantly correlated with LGG clinical traits. The genes comprising these modules were further used to construct gene co-expression and protein-protein interaction networks. Based on the network analyses, we derived a consensus of eighteen hub genes, namely, CD74, CD86, CDC25A, CYBB, HLA-DMA, ITGB2, KIF11, KIFC1, LAPTM5, LMNB1, MKI67, NCKAP1L, NUSAP1, SLC7A7, TBXAS1, TOP2A, TYROBP, and WDFY4. All detected hub genes were up-regulated in LGG, and were also associated with unfavorable prognosis in LGG patients. The findings of this study could be applicable in the clinical setting for diagnosing and monitoring LGG.
| S-EPMC10024901 | biostudies-literature
Project description:Background Pediatric low-grade gliomas (pLGGs), particularly incompletely resected supratentorial tumours, can undergo progression after surgery. However to date, there are no predictive biomarkers for progression. Here, we aimed to identify pLGG-specific microRNA signatures and evaluate their value as a prognostic tool. Methods We identified and validated supratentorial incompletey resected pLGG-specific microRNAs in independent cohorts from four European Pediatric Neuro-Oncology Centres. Results These microRNAs demonstrated high accuracy in differentiating patients with or without progression. Specifically, incompletely resected supratentorial pLGGs with disease progression showed significantly higher miR-1248 combined with lower miR-376a-3p and miR-888-5p levels than tumours without progression. A significant (p < 0.001) prognostic performance for miR-1248 was reported with an area under the curve (AUC) of 1.00. We also highlighted a critical oncogenic role for miR-1248 in gliomas tumours. Indeed, high miR-1248 levels maintain low its validated target genes (CDKN1A (p21)/FRK/SPOP/VHL/MTAP) and consequently sustain the activation of oncogenic pathways. Conclusions Altogether, we provide a novel molecular biomarker able to successfully identify pLGG patients associated with disease progression that could support the clinicians in the decision-making strategy, advancing personalized medicine. Supplementary Information The online version contains supplementary material available at 10.1186/s40364-022-00389-x.
| S-EPMC9205050 | biostudies-literature
Project description:We performed gene expression profiling on 151 paraffin-embedded PLGGs from different locations, ages, histological subtypes as well as BRAF genetic status We also compared molecular differences to normal pediatric brain expression profiles to observe whether those patterns were mirrored in normal brain expression. We analyzed the expression of 6,100 genes among 151 FFPE pediatric and 15 FFPE adult low-grade gliomas and analyzed how the expression patterns changes with location, age, histology and BRAF genomic status and how those differences were mirrored in normal brain expression. The values in the sample 'characteristics' columns represent; Location; SUP= Supratentorial, INF= Infratentorial Histology; PA= pilocytic astrocytoma, GG= ganglioglioma, DNT= dysembryoplastic neuroepithelial tumor, OD= oligodendroglial tumors, NOS= not otherwise specified tumors BRAF status; DUP= BRAF duplication, MUT= BRAF V600E mutation, WT= wild type, ND= not determined Primary or recurrent tumor; P=primary, R=recurrent Primary tumor that further progressed; 1=yes, 0=no, _=recurrent tumors only
| S-ECPF-GEOD-60898 | biostudies-other
Project description:Low-grade gliomas (LGGs) are a diverse group of primary brain tumors that often arise in young, otherwise healthy patients and generally have an indolent course with longer-term survival in comparison with high-grade gliomas. Treatment options include observation, surgery, radiation, chemotherapy, or a combined approach, and management is individualized based on tumor location, histology, molecular profile, and patient characteristics. Moreover, in this type of brain tumor with a relatively good prognosis and prolonged survival, the potential benefits of treatment must be carefully weighed against potential treatment-related risks. We review in this article current management strategies for LGG, including surgery, radiotherapy, and chemotherapy. In addition, the importance of profiling the genetic and molecular properties of LGGs in the development of targeted anticancer therapies is also reviewed. Finally, given the prevalence of these tumors in otherwise healthy young patients, the impact of treatment on neurocognitive function and quality of life is also evaluated.
| S-EPMC3983820 | biostudies-literature
Project description:Categorisation of LGGs related to their lesion site (infratentorial vs. supratentorial) 40 Low grade gliomas samples
2013-09-21 | E-GEOD-28238 | biostudies-arrayexpress
Project description:Categorisation of LGGs related to their lesion site (infratentorial vs. supratentorial)
2013-09-21 | GSE28238 | GEO
Project description:BackgroundRecent studies have highlighted the heterogeneity of gliomas and demonstrated that molecular and genetic analysis could help in their classification and in the design of treatment protocols. In a previous study we have identified a 4-gene signature highly correlated with survival of glioma patients. The aim of this study is to confirm and extend these findings by investigating the expression of these genes at the protein level and their association with outcome of patients with high grade gliomas.Methodology/principal findingsImmunohistochemical staining for EDN/RB, HJURP, p60/CAF-1 and PDLI4 was studied on archive materials from 96 patients (64 glioblastomas and 32 grade III gliomas). The levels of all four proteins differed significantly between grade III and grade IV tumours. The levels of the EDN/RB, HJURP and p60/CAF-1 proteins were strongly associated with overall survival (p<0.001, p<0.001 and p=0.002, respectively), whereas the one of PDLI4 was not (P=0.11). A risk criterion defined as high levels of at least two of the EDN/RB, HJURP and p60/CAF-1 proteins accurately predicted the prognosis of patients. Multivariate analysis confirmed that this criterion was an independent negative prognostic marker (hazard ratio = 2.225; 95% CI, 1.248 to 3.966, p=0.007).ConclusionsThe expression of the EDN/RB, HJURP, p60/CAF-1 and PDLI4 proteins is disrupted in high grade gliomas and increases in the levels of these proteins are closely linked to tumour aggressiveness and poor outcome.
| S-EPMC3770632 | biostudies-literature
Project description:Gene expression profiling of 23 grade II gliomas of different histological subtype. Analyses was done on 9 astrocytomas, 8 oligoastrocytomas and 6 oligodendrogliomas.
| S-ECPF-MEXP-938 | biostudies-other
Project description:Brain tumors constitute the largest source of oncologic mortality in children and low-grade gliomas are among most common pediatric central nervous system tumors. Pediatric low-grade gliomas differ from their counterparts in the adult population in their histopathology, genetics, and standard of care. Over the past decade, an increasingly detailed understanding of the molecular and genetic characteristics of pediatric brain tumors led to tailored therapy directed by integrated phenotypic and genotypic parameters and the availability of an increasing array of molecular-directed therapies. Advances in neuroimaging, conformal radiation therapy, and conventional chemotherapy further improved treatment outcomes. This article reviews the current classification of pediatric low-grade gliomas, their histopathologic and radiographic features, state-of-the-art surgical and adjuvant therapies, and emerging therapies currently under study in clinical trials.
| S-EPMC7281318 | biostudies-literature