Construction and Validation of a 13-Gene Signature for Prognosis Prediction in Medulloblastoma

Frontiers in Genetics
Chang LiXuejun Li

Abstract

Background: Recent studies have identified several molecular subgroups of medulloblastoma associated with distinct clinical outcomes; however, no robust gene signature has been established for prognosis prediction. Our objective was to construct a robust gene signature-based model to predict the prognosis of patients with medulloblastoma. Methods: Expression data of medulloblastomas were acquired from the Gene Expression Omnibus (GSE85217, n = 763; GSE37418, n = 76). To identify genes associated with overall survival (OS), we performed univariate survival analysis and least absolute shrinkage and selection operator (LASSO) Cox regression. A risk score model was constructed based on selected genes and was validated using multiple datasets. Differentially expressed genes (DEGs) between the risk groups were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and protein-protein interaction (PPI) analyses were performed. Network modules and hub genes were identified using Cytoscape. Furthermore, tumor microenvironment (TME) was evaluated using ESTIMATE algorithm. Tumor-infiltrating immune cells (TIICs) were inferred using CIBERSORTx. Results: A 13-gene model was constructed and validated. Patients classi...Continue Reading

References

Feb 28, 1997·Statistics in Medicine·R Tibshirani
Apr 20, 2000·The Journal of Biological Chemistry·C S MayanilE G Bremer
Jan 15, 2003·BMC Bioinformatics·Gary D Bader, Christopher W V Hogue
Jul 8, 2003·Pediatric Neurosurgery·Roger J PackerTobey J MacDonald
May 6, 2004·Cancer Research·Mitsutoshi NakadaMichael E Berens
Jan 4, 2007·The American Journal of Pathology·Eli E BarCharles G Eberhart
Dec 29, 2007·Proceedings of the National Academy of Sciences of the United States of America·Benfang RuanEdmund I Graziani
Mar 19, 2008·Genes & Development·Matthew R Grimmer, William A Weiss
May 10, 2008·Seminars in Cancer Biology·Antonio SicaAlberto Mantovani
Jul 17, 2008·Journal of Cellular and Molecular Medicine·Qiuyu WangPatricia Kumar
Feb 10, 2009·Journal of Neuroimmune Pharmacology : the Official Journal of the Society on NeuroImmune Pharmacology·Erick T TatroUNKNOWN HIV Neurobehavioral Research Center
Feb 21, 2009·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Kimberly Laskie OstrowDavid Sidransky
Jun 9, 2009·Current Opinion in Immunology·Louise J McHeyzer-WilliamsMichael G McHeyzer-Williams
Dec 9, 2009·Journal of Neurochemistry·Ikuo KimuraMasafumi Fujimoto
Nov 26, 2010·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Yoon-Jae ChoScott L Pomeroy
Feb 8, 2011·Current Topics in Developmental Biology·Martine F Roussel, Mary E Hatten
Mar 2, 2011·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Pablo TamayoJill P Mesirov
Jun 7, 2011·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·Yanyun XieDamu Tang
Oct 28, 2011·Nature·Hyo Jung KangNenad Sestan
Nov 8, 2011·Acta Neuropathologica·Paul A NorthcottMichael D Taylor
Dec 3, 2011·Acta Neuropathologica·Michael D TaylorStefan M Pfister
Dec 17, 2011·BMC Bioinformatics·Qiyuan LiAron C Eklund
Dec 17, 2011·Journal of Neuro-oncology·Adam M SonabendRichard C E Anderson
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
May 2, 2012·BMC Bioinformatics·Mark R DalmanZhong-Hui Duan
Jun 23, 2012·Nature·Giles RobinsonRichard J Gilbertson
Jun 23, 2012·Neuro-oncology·Arend H SikkemaEveline S J M de Bont
Feb 23, 2013·Critical Reviews in Immunology·Charles D Mills
Apr 5, 2013·Neoplasia : an International Journal for Oncology Research·Ludivine Coudière MorrisonTamra E Werbowetski-Ogilvie
Apr 25, 2013·PloS One·Peter LangfelderSteve Horvath
Oct 12, 2013·Nature Communications·Kosuke YoshiharaRoel G W Verhaak
Jan 28, 2014·Acta Neuropathologica Communications·Ashirwad MerveSilvia Marino

❮ Previous
Next ❯

Citations

Jun 19, 2021·Expert Review of Hematology·Ganggang WangQiaohua Zhang

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE85217
GPL570
GSE37418
GPL22286

Methods Mentioned

BETA
Gene

Software Mentioned

MCOD
R package “ limma
MCODE
Bioconductor annotation package
CIBERSORTx
clusterProfiler
Molecular Complex Detection ( MCODE
Gene SeT AnaLysis Toolkit
SELENOV
survival ”

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.