Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling

Biology Direct
Lin LiuZhang Zhang

Abstract

Glioma is one of the most common malignant brain tumors and exhibits low resection rate and high recurrence risk. Although a large number of glioma studies powered by high-throughput sequencing technologies have led to massive multi-omics datasets, there lacks of comprehensive integration of glioma datasets for uncovering candidate biomarker genes. In this study, we collected a large-scale assemble of multi-omics multi-cohort datasets from worldwide public resources, involving a total of 16,939 samples across 19 independent studies. Through comprehensive molecular profiling across different datasets, we revealed that PRKCG (Protein Kinase C Gamma), a brain-specific gene detectable in cerebrospinal fluid, is closely associated with glioma. Specifically, it presents lower expression and higher methylation in glioma samples compared with normal samples. PRKCG expression/methylation change from high to low is indicative of glioma progression from low-grade to high-grade and high RNA expression is suggestive of good survival. Importantly, PRKCG in combination with MGMT is effective to predict survival outcomes in a more precise manner. PRKCG bears the great potential for glioma diagnosis, prognosis and therapy, and PRKCG-like genes ...Continue Reading

References

Jun 8, 2001·Genes & Development·E A MaherR A DePinho
Nov 6, 2002·Journal of Biochemistry·Naoaki Saito, Yasuhito Shirai
Dec 17, 2003·Archives of Neurology·Ichiro YabeKunio Tashiro
Mar 11, 2005·The New England Journal of Medicine·Roger StuppUNKNOWN National Cancer Institute of Canada Clinical Trials Group
Mar 11, 2005·The New England Journal of Medicine·Monika E HegiRoger Stupp
Sep 30, 2005·Annals of Neurology·Stephan KlebeGiovanni Stevanin
Dec 21, 2005·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Markus BredelBranimir I Sikic
Aug 26, 2006·Nature Clinical Practice. Neurology·Judith A SchwartzbaumMargaret Wrensch
Jan 24, 2007·Neuropathology and Applied Neurobiology·J E ReedC Walker
Feb 13, 2007·Cancer Cell·Norman J KennedyRoger J Davis
Mar 7, 2007·Nature Reviews. Genetics·Manel Esteller
Mar 27, 2007·Bioinformatics·George VasmatzisFarhad Kosari
Jul 10, 2007·Acta Neuropathologica·David N LouisPaul Kleihues
Sep 29, 2007·The Journal of Gene Medicine·Maarten ter HorstPeter Sillevis Smitt
Jan 16, 2008·Clinics in Laboratory Medicine·Eric W Klee
Mar 20, 2009·Human Molecular Genetics·Charlotte N HenrichsenAlexandre Reymond
Mar 28, 2009·Journal of Clinical Neuroscience : Official Journal of the Neurosurgical Society of Australasia·Hui K GanRodney B Luwor
Nov 19, 2009·Cancer Research·Lonneke A M GravendeelPim J French
Apr 20, 2010·Cancer Cell·Houtan NoushmehrUNKNOWN Cancer Genome Atlas Research Network
Jul 10, 2010·The Lancet Oncology·Nanne K KloosterhofMartin J van den Bent
Sep 9, 2010·Neoplasia : an International Journal for Oncology Research·Kimmo J HatanpaaAmyn A Habib
Jan 1, 2010·Genetics and Molecular Biology·Patricia Oliveira CarminatiElza Tiemi Sakamoto-Hojo
Apr 21, 2012·BMC Medicine·Ioannis PrassasEleftherios P Diamandis
Oct 17, 2012·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Gregory CairncrossMinesh Mehta
Jan 30, 2013·Cancer Biology & Therapy·Anália do CarmoMaria Celeste Lopes
Mar 28, 2013·Current Neurology and Neuroscience Reports·Adam L CohenHoward Colman
May 28, 2013·Journal of Clinical Neuroscience : Official Journal of the Neurosurgical Society of Australasia·Liang WangYongsheng Zhang
May 30, 2013·Nature Genetics·UNKNOWN GTEx Consortium
Oct 1, 2013·The Journal of Immunology : Official Journal of the American Association of Immunologists·Andrea M GriesingerNicholas K Foreman

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Citations

Dec 11, 2020·Cell Death Discovery·Ivano AmelioGerry Melino
Apr 20, 2021·Frontiers in Immunology·Jessica M ZielinskiCarsten Krieg
Jul 11, 2021·Molecular Oncology·Carlo GaniniGerry Melino
Aug 6, 2021·Biology Direct·Eleonora MammarellaIvano Amelio
Aug 7, 2021·Cell Death & Disease·David Della-MorteNicola Di Daniele
Aug 8, 2021·Biology Direct·Emanuele PanattaIvano Amelio
Oct 23, 2021·Experimental and Therapeutic Medicine·Ani-Simona SevastreAnica Dricu

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Datasets Mentioned

BETA
GSE16011
GSE36278
GSE83710

Software Mentioned

GenTree
R

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