Journal ArticleDOI
Seven genes for the prognostic prediction in patients with glioma.
TLDR
A novel seven-gene signature in patients with glioma is identified, which could be used as a predictor for the prognosis of patients withglioma in the future.Abstract:
Glioma is a common malignant tumor of the central nervous system, which is characterized by a low cure rate, high morbidity, and high recurrence rate. Consequently, it is imperative to explore some indicators for prognostic prediction in glioma. We obtained glioma data from The Cancer Genome Atlas (TCGA). Differentially expressed genes (DEGs) were obtained by R software from TCGA data sets. Through Cox regression analysis, risk scores were obtained to assess the weighted gene-expression levels, which could predict the prognosis of patients with glioma. The validity and the prognostic value of this model in glioma were confirmed by the manifestation of receiver-operating characteristic (ROC) curves, area under the curve (AUC), and 5-year overall survival (OS). In total, 920 DEGs of transcriptome genes in glioma were extracted from the TCGA database. We identified a novel seven-gene signature associated with glioma. Among them, AL118505.1 and SMOC1 were positively related to the 5-year OS of patients with glioma, showing a better prognosis for glioma; however, RAB42, SHOX2, IGFBP2, HIST1H3G, and IGF2BP3 were negatively related to 5-year OS, displaying a worse prognosis. In addition, according to risk scores, AL118505.1 was also a protective factor, while others were risk factors. Furthermore, the expression levels of SHOX2, IGFBP2, and IGF2BP3 were significantly positively correlated with glioma grades. Receiver-operating characteristic (ROC) curve assessed the accuracy and sensitivity of the gene signature. Each of the seven genes for patients with the distribution of the risk score was presented in the heat map. We identified a novel seven-gene signature in patients with glioma, which could be used as a predictor for the prognosis of patients with glioma in the future.read more
Citations
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The molecular feature of macrophages in tumor immune microenvironment of glioma patients.
Hao Zhang,Yue-Bei Luo,Wantao Wu,Liyang Zhang,Zeyu Wang,Ziyu Dai,Songshan Feng,Hui Cao,Quan Cheng,Zhixiong Liu +9 more
TL;DR: Wang et al. as discussed by the authors used weighted gene co-expression network analysis to identify meaningful macrophage-related gene genes for clustering and applied Pamr, SVM, and neural network for validating clustering results.
Journal ArticleDOI
Identification of Crucial Genes Associated With Immune Cell Infiltration in Hepatocellular Carcinoma by Weighted Gene Co-expression Network Analysis
TL;DR: The results of multivariate Cox regression analysis indicated that the abovementioned hub genes are all independent predictors of HCC and are likely to be a therapeutic target for HCC.
Journal ArticleDOI
Identification and validation of a three-gene signature as a candidate prognostic biomarker for lower grade glioma.
TL;DR: This study identified a three-gene model that showed satisfactory performance in predicting the 1, 3- and 5-year survival of LGG patients compared to other models and may be a promising independent biomarker of L GG.
Journal ArticleDOI
Development of a gene expression–based prognostic signature for IDH wild-type glioblastoma
Radia M. Johnson,Heidi S. Phillips,Carlos Bais,Cameron Brennan,Timothy F. Cloughesy,Anneleen Daemen,Ulrich Herrlinger,Robert B. Jenkins,Albert Lai,Christoph Mancao,Michael Weller,Wolfgang Wick,Richard Bourgon,Josep Garcia +13 more
TL;DR: The ATE score showed prognostic value and may enable clinical trial stratification for IDH wild-type glioblastoma and may be able to be used to enable clinical trials stratification in patients with MGMT non-methylated promoter status.
Journal ArticleDOI
Identification of IGF2BP3 as an Adverse Prognostic Biomarker of Gliomas.
TL;DR: Wang et al. as mentioned in this paper determined the prognostic value of the m6A RNA methylation regulator in gliomas and investigated the underlying mechanisms of the aberrant expression of m6a-related genes.
References
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The 2007 WHO Classification of Tumours of the Central Nervous System
David N. Louis,Hiroko Ohgaki,Otmar D. Wiestler,Webster K. Cavenee,Peter C. Burger,Anne Jouvet,Bernd W. Scheithauer,Paul Kleihues +7 more
TL;DR: The fourth edition of the World Health Organization (WHO) classification of tumours of the central nervous system, published in 2007, lists several new entities, including angiocentric glioma, papillary glioneuronal tumour, rosette-forming glioneurs tumour of the fourth ventricle, Papillary tumourof the pineal region, pituicytoma and spindle cell oncocytoma of the adenohypophysis.
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The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary.
David N. Louis,Arie Perry,Guido Reifenberger,Andreas von Deimling,Dominique Figarella-Branger,Webster K. Cavenee,Hiroko Ohgaki,Otmar D. Wiestler,Paul Kleihues,David W. Ellison +9 more
TL;DR: The 2016 World Health Organization Classification of Tumors of the Central Nervous System is both a conceptual and practical advance over its 2007 predecessor and is hoped that it will facilitate clinical, experimental and epidemiological studies that will lead to improvements in the lives of patients with brain tumors.
Journal ArticleDOI
Histone H3F3A and HIST1H3B K27M mutations define two subgroups of diffuse intrinsic pontine gliomas with different prognosis and phenotypes.
David Castel,Cathy Philippe,Raphael Calmon,Ludivine Le Dret,Nathalene Truffaux,Nathalie Boddaert,Mélanie Pagès,Kathryn R. Taylor,Patrick Saulnier,Ludovic Lacroix,Alan Mackay,Chris Jones,Christian Sainte-Rose,Thomas Blauwblomme,Felipe Andreiuolo,Stéphanie Puget,Jacques Grill,Pascale Varlet,Marie-Anne Debily,Marie-Anne Debily +19 more
TL;DR: H3K27 alterations appear as the founding event in DIPG and the mutations in the two main histone H3 variants drive two distinct oncogenic programmes with potential specific therapeutic targets.
Journal ArticleDOI
The short stature homeobox gene SHOX is involved in skeletal abnormalities in Turner syndrome
M Clement-Jones,Simone Schiller,Ercole Rao,Rüdiger J. Blaschke,Aimée Zuniga,Rolf Zeller,Stephen C. Robson,Gerhard Binder,Ian A. Glass,Tom Strachan,Susan Lindsay,Gudrun A. Rappold +11 more
TL;DR: The SHOX expression pattern in the limb and first and second pharyngeal arches not only explains SHOX -related short stature phenotypes, but also for the first time provides evidence for the involvement of this gene in the development of additional Turner stigmata.
Journal ArticleDOI
SHOX2 DNA Methylation is a Biomarker for the diagnosis of lung cancer based on bronchial aspirates
Bernd Schmidt,Volker Liebenberg,Dimo Dietrich,Thomas Schlegel,Christoph Kneip,Anke Seegebarth,Nadja Flemming,Stefanie Seemann,Jürgen Distler,Jörn Lewin,Reimo Tetzner,Sabine Weickmann,Ulrike Wille,Triantafillos Liloglou,Olaide Y. Raji,Martin Walshaw,Michael Fleischhacker,Christian Witt,John K. Field +18 more
TL;DR: Hypermethylation of SHOX2 in bronchial aspirates appears to be a clinically useful tumor marker for identifying subjects with lung carcinoma, especially if histological and cytological findings after bronchoscopy are ambiguous.